liaison user manual

Schrdinger Press

Liaison User Manual

Liaison 6.1 User Manual

Liaison User Manual Copyright 2013 Schrdinger, LLC. All rights reserved.

While care has been taken in the preparation of this publication, Schrdinger

assumes no responsibility for errors or omissions, or for damages resulting from

the use of the information contained herein.

Canvas, CombiGlide, ConfGen, Epik, Glide, Impact, Jaguar, Liaison, LigPrep,

Maestro, Phase, Prime, PrimeX, QikProp, QikFit, QikSim, QSite, SiteMap, Strike, and

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of William L. Jorgensen. DESMOND is a trademark of D. E. Shaw Research, LLC.

Desmond is used with the permission of D. E. Shaw Research. All rights reserved.

This publication may contain the trademarks of other companies.

Schrdinger software includes software and libraries provided by third parties. For

details of the copyrights, and terms and conditions associated with such included

third party software, see the Legal Notices, or use your browser to open

$SCHRODINGER/docs/html/third_party_legal.html (Linux OS) or

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This publication may refer to other third party software not included in or with

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software.

November 2013

ContentsDocument Conventions ...................................................................................................... v

Chapter 1: Introduction ....................................................................................................... 11.1

1.2

1.3

1.4

1.5

1.6

Chapter 2.1

2.2

2.3

Chapter 3.1

3.2Liaison 6.1 User Manual iii

About Liaison ............................................................................................................. 1

Models of Ligand Binding........................................................................................ 1

Liaison Binding Energy Model................................................................................ 3

Running Schrdinger Software .............................................................................. 4

Starting Jobs from the Maestro Interface ............................................................. 6

Citing Liaison in Publications ................................................................................. 7

2: Liaison Tutorial ............................................................................................... 9 Preparing for the Exercises ..................................................................................... 9

Running the Liaison Simulations ......................................................................... 112.2.1 Importing the Structures ................................................................................... 112.2.2 Setting Up the System ...................................................................................... 122.2.3 Starting and Monitoring the Liaison Job ........................................................... 13

Generating and Validating an LIA Model of Binding Affinity........................... 142.3.1 Importing Liaison Results into Strike for Model Creation .................................. 142.3.2 Creating the LIA Model to Predict Binding Affinities ......................................... 152.3.3 Analyzing the LIA Binding Affinity Model .......................................................... 172.3.4 Predicting Binding Affinities with the LIA Model................................................ 182.3.5 Making Predictions for Additional Molecules..................................................... 19

3: Protein and Ligand Preparation........................................................ 21 Protein Preparation ................................................................................................. 21

Checking the Protein Structures .......................................................................... 233.2.1 Checking the Orientation of Water Molecules................................................... 243.2.2 Checking for Steric Clashes.............................................................................. 243.2.3 Resolving H-Bonding Conflicts ......................................................................... 24

Contents

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3.3 Ligand Preparation.................................................................................................. 253.3.1 Using LigPrep for Ligand Preparation ............................................................... 263.3.2 Using Other Programs for Ligand Preparation.................................................. 28

Chapter 4.1

4.2

4.3

4.4

Getting H

Index ......r Software Release 2013-3

4: Running Liaison........................................................................................... 29 Overview of Liaison Tasks..................................................................................... 29

The Liaison Panel .................................................................................................... 314.2.1 Systems Tab ..................................................................................................... 31

4.2.1.1 Defining the Protein ............................................................................... 314.2.1.2 Defining the Ligands .............................................................................. 32

4.2.2 Parameters Tab................................................................................................. 324.2.3 Analysis Tab...................................................................................................... 34

Liaison Files ............................................................................................................. 35

Running Liaison From the Command Line......................................................... 35

elp ............................................................................................................................. 37

........................................................................................................................................ 41

Document Conventions

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File name, tions. To obpath or direat each end.

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References

Font

Sans serif

Monospace

Italic

Sans serif uppercaseLiaison 6.1 User Manual vto the use of italics for names of documents, the font conventions that are used innt are summarized in the table below.

er locations in the current document or to other PDF documents are colored likeent Conventions.

ons of command syntax, the following UNIX conventions are used: braces { }hoice of required items, square brackets [ ] enclose optional items, and the bareparates items in a list from which one item must be chosen. Lines of commandwrap should be interpreted as a single command.

path, and environment variable syntax is generally given with the UNIX conven-tain the Windows conventions, replace the forward slash / with the backslash \ in

ctory names, and replace the $ at the beginning of an environment variable with a % For example, $SCHRODINGER/maestro becomes %SCHRODINGER%\maestro.

ferences are given in the Windows convention by default, with Mac equivalents in, for example CTRL+H (H). Where Mac equivalents are not given, COMMANDad in place of CTRL. The convention CTRL-H is not used.

ment, to type text means to type the required text in the specified location, and toeans to type the required text, then press the ENTER key.

to literature sources are given in square brackets, like this: [10].

Example Use

Project Table Names of GUI features, such as panels, menus, menu items, buttons, and labels

$SCHRODINGER/maestro File names, directory names, commands, envi-ronment variables, command input and output

filename Text that the user must replace with a valueCTRL+H Keyboard keys

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Chapter 1

Liaison User Manual

Chapter 1: Introduction

1.1 ALiaison pre(LIA) modtraining setcomplex at tion data anand . Theswith the sarather than magnitude. highly effic

Liaison is rfrom Maesdescribed in

Protein Prstructures tProtein Predescribed in

The Impaccan be carrminimizatiopendently oCommand R

The Strike Liaison. Fo

1.2 MThe typicalligand is prin this cavitLiaison 6.1 User Manual 1bout Liaisondicts ligand-receptor binding affinities using a linear interaction approximation

el that is fitted to a set of known binding free energies. For each ligand in the, Liaison runs molecular mechanics (MM) simulations of the ligand-receptorboth endpoints of the binding process, bound ligand and free ligand. The simula-d empirical binding affinities are analyzed to generate the Liaison parameters: , ,e parameters are subsequently used to predict binding energies for other ligandsme receptor. The use of the Surface Generalized Born (SGB) continuum modelexplicit solvation in the MD or HMC simulations reduces CPU time by an order ofFor further time reductions, a simple energy minimization protocol coupled with aient Truncated Newton minimizer can be used with little loss of accuracy.

un primarily from the Maestro graphical user interface. A tutorial in using Liaisontro appears in Chapter 2. Liaison can also be run from the command line, as Section 4.4. Utilities and scripts are run from the command line.

eparation is strongly recommended for protein and protein-ligand complex PDBo be used in Liaison. In most cases, this can be performed in Maestro, using theparation Wizard panel on the Workflows menu. Protein and ligand preparation are Chapter 3.

t computational program runs the MM calculations for Liaison simulations, whichied out using molecular dynamics (MD), hybrid Monte Carlo (HMC), or energyn. Impact uses an OPLS-AA force field. Impact calculations can also be run inde-f Liaison. For more information, see the Impact User Manual and the Impacteference Manual.

statistical analysis package is used for the fitting and prediction analysis tasks ofr more information, see the Strike User Manual.

odels of Ligand Binding binding site for a ligand is the active-site cavity of a protein receptor. When noesent, this cavity is filled with water molecules. When a ligand binds to the proteiny, it displaces water molecules in the active site, which return to bulk solvent.


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The principal factors determining the strength and specificity of binding are as follows:

The degree to which hydrophobic groups on the ligand interact with hydrophobic pocketsor patches on the protein surface to release water into the bulk. This release is favorableboth eand elonger

The exregionmenta

The eait costto chahas tohigherbe losconforconfor

Molecular sligand calcapproaches During the and in pharachieved, F

FEP capplic

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nergetically (more hydrogen bonds are formed by the released water molecules)ntropically (the released waters are less constrained orientationally and are no confined to a restricted cavity). tent to which the ligand forms hydrogen bonds or metal ligations in hydrophilic

s with appropriately placed polar or charged groups on the receptor. Such comple-rity is essential for achieving adequate binding affinity and specificity.

se with which the ligand fits into the protein cavity. An important question is whats the ligand (and the protein) in energy and/or entropy to accomplish this fiti.e.,nge from the free to the bound conformation. Energy will be required if the ligand be distorted away from its naturally preferred, low-energy conformation into a-energy conformation when it binds to the receptor. At the same time, entropy willt if the ligand is very flexible in solution and then is confined to a small number ofmations in the receptor cavity. Both effects, as well as similar restrictions on themation of protein side chains, act against binding.

imulation methods have been used to calculate binding free energies of protein-ulations since the pioneering applications of free energy perturbation (FEP)by McCammon, Kollman, Jorgensen, and others approximately 20 years ago.

past two decades, many FEP calculations have been carried out in academic groupsmaceutical and biotechnology companies. But while notable successes have beenEP methods are in limited use in drug-discovery projects, for several reasons: alculations are typically limited to small changes in ligand structure, restricting theability to the very last phase of lead optimization.

alculations are very expensive computationally, and often cannot be completed on acale compatible with the schedule of a given drug-discovery project.racies in force fields and sampling methods can lead to errors in FEP predictions.

ons of FEP motivated the development of linear-response (LR) methods by AqvistT.; Aqvist, J. Protein Eng. 1995, 8, 11371145). Since that time, studies bynd others have shown that LR methods can effectively address the above difficul-parison with the FEP approach, the advantages of LRM are as follows:

trast to FEP, where a large number of intermediate windows must be evaluated,requires simulations only of the ligand in solution and the ligand bound to the pro-he idea is that one views the binding event as replacement of the aqueous environ-f the ligand with a mixed aqueous/protein environment.


Only interactions between the ligand and either the protein or the aqueous environmententer into the quantities that are accumulated during the simulation. The protein-proteinand protein-water interaction are part of the reference Hamiltonian, and hence are usedto generate conformations in the simulation, but are not used as descriptors in the resul-tant mthe cabecaussimula

As loncan be

LRM

The Lset of energyallowsthe corepresabsorbevent,of theously value paramThis eilar bione ca

under ects.

1.3 LiA Liaison sbuild a modgies. The aenergy of ththis type is(LIA), or a Liaison 6.1 User Manual 3

odel for the binding free energy. This eliminates a considerable amount of noise inlculationsfor example, that arising from variations in the total energy that resulte slightly different geometries of the protein are obtained for each ligand moleculeted.

g as the binding modes of the ligand are fundamentally similar, LRM calculations applied to ligands that differ significantly in chemical structure.

calculations are less computationally expensive than FEP calculations.

RM approach allows the binding-energy model to be calibrated by using a trainingcompounds for which experimental binding affinities are known. The use of the terms as descriptors in the fitting equation introduces an empirical element that some of the limitations in the theoretical framework (for example, the neglect ofst in energy and entropy of fitting the ligand into the protein site) and the physicalentation (as reflected by errors in the force field or solvation model) to be partiallyed into the parameterization. Moreover, some of the steps involved in the binding

such as the removal of water from the protein cavity and subsequent introduction ligand, are not inherently linear. If the linear-response approximation was rigor-valid, the coefficients of the terms would each be 0.5, corresponding to the mean-approximation to the charging integral. In practice, optimization of the fittingeters yields coefficients that are significantly different from the ideal value of 0.5.mpirical element sacrifices generality: the method requires the ligands to have sim-nding modes, and new parameters must be developed for each receptor. In return,n obtain a reasonable level of accuracy with a modest expenditure of CPU time,assumptions that are quite reasonable for many structure-based drug-design proj-

aison Binding Energy Modelimulation combines a molecular-mechanics calculation with experimental data toel scoring function used to correlate or to predict ligand-protein binding free ener-

ssumption used is that the binding energy can be approximated by comparing thee bound complex with the energy of the free ligand-receptor system. A method of called a Linear Response Method (LRM), a Linear Interaction ApproximationLinear Interaction Energy (LIE) method.


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Liaison simulations takes place in implicit (continuum) rather than explicit solventhence thename Liaison, for Linear Interaction Approximation in Implicit SOlvatioN. The explicit-solvent version of the methodology was first suggested by Aqvist (Hansson, T.; Aqvist, J.Protein Eng. 1995, 8, 1137-1145), based on approximating the charging integral in the free-energy-pertas half the sThe empiric

G =

Here < > resents the frethe van der(SGB) contsurface area

e surface area lost by contact with the receptor. The net electrostatic interaction-ntinuum solvent is given by:

Ucoul + 2 Urxnf

l is the Coulomb interaction energy and Urxnf is the SGB-solvent reaction-fielde factor of 2 compensates for the division by 2 made in the definition of the reac-ee energy.)lications, the coefficients , , and are determined empirically by fitting to thelly determined free energies of binding for a training set of ligands. In such appli-

isons simulation task is used to calculate the values of Uvdw, U elec, and U cav for theplexed) and unbound (free) states of the training-set ligands, and its analysis task isive values for the , , and fitting coefficients. The fitted equation can then beict the binding affinities of additional ligands. In the current version of Liaison, a

m is added to G in the fitting process, and is adjusted during the fit. This corre- extension of the strict linear response model.

unning Schrdinger Softwarer applications can be run from a graphical interface or from the command line. Theites input and output files to a directory (folder) which is termed the working direc- run applications from the command line, the directory from which you run theis the working directory for the job.


Linux:

To run any Schrdinger program on a Linux platform, or start a Schrdinger job on a remotehost from a Linux platform, you must first set the SCHRODINGER environment variable to theinstallation directory for your Schrdinger software. To set this variable, enter the followingcommand a

Once you hwith the fol

$SCHRODIN$SCHRODINYou can sta

$SCHRODINIt is usuallyinterface. T

Windows:

The primaryical interfacproject, or Maestro. YoThe defaulton Window

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Schr Schr

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csh/tcsh:bash/ksh:Liaison 6.1 User Manual 5

t a shell prompt:

ave set the SCHRODINGER environment variable, you can run programs and utilitieslowing commands:

GER/program &GER/utilities/utility &

rt the Maestro interface with the following command:

GER/maestro &

a good idea to change to the desired working directory before starting the Maestrohis directory then becomes the working directory.

way of running Schrdinger applications on a Windows platform is from a graph-e. To start the Maestro interface, double-click on the Maestro icon, on a Maestroon a structure file; or choose Start All Programs Schrodinger-2013-3 u do not need to make any settings before starting Maestro or running programs.

working directory is the Schrodinger folder in your documents folder (Documentss 7/Vista, My Documents on XP). to run applications from the command line, you can do so in one of the shells thatd with the installation and have the Schrdinger environment set up:

dinger Command PromptDOS shell. dinger Power ShellWindows Power Shell (if available). en these shells from Start All Programs Schrodinger-2013-3. You do not needhe path to a program or utility when you type the command to run it. If you wantnix-style utilities (such as awk, grep, and sed), preface the commands with sh, orither of these shells to start a Unix-style shell.

setenv SCHRODINGER installation-directory export SCHRODINGER=installation-directory


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Mac:

The primary way of running Schrdinger software on a Mac is from a graphical interface. Tostart the Maestro interface, click its icon on the dock. If there is no Maestro icon on the dock,you can put one there by dragging it from the SchrodingerSuite2013-3 folder in your Applica-tions folderdirectory iSchroding

Running sorun the proLinux. The do not needronment on

defaults

and on OS X

launchctl

1.5 STo run a jobmake settinsettings aremaking sett

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You can thsettings by These settinr Software Release 2013-3

. This folder contains icons for all the available interfaces. The default workings the Schrodinger folder in your Documents folder ($HOME/Documents/er).ftware from the command line is similar to Linuxopen a terminal window andgram. You can also start Maestro from the command line in the same way as ondefault working directory is then the directory from which you start Maestro. You to set the SCHRODINGER environment variable, as this is set in your default envi- installation. To set other variables, on OS X 10.6 and 10.7 use the command

write ~/.MacOSX/environment variable "value"

10.8 use the command

setenv variable "value"

tarting Jobs from the Maestro Interface from the Maestro interface, you open a panel from one of the menus (e.g. Tasks),

gs, and then submit the job to a host or a queueing system for execution. The panel described in the help topics and in the user manuals. When you have finishedings, you can use the Job toolbar to start the job.

rt a job immediately by clicking Run. The job is run on the currently selected hostrent job settings and the job name in the Job name text box. If you want to changee, you can edit it in the text box before starting the job. Details of the job settings in the status bar, which is below the Job toolbar.

to change the job settings, such as the host on which to run the job and the numberrs to use, click the Settings button. (You can also click and hold, and choose Jobm the menu that is displayed.)

en make the settings in the Job Settings dialog box, and choose to just save theclicking Save, or save the settings and start the job by clicking Save and Run.gs apply only to jobs that are started from the current panel.


If you want to save the input files for the job but not run it, click the Settings button and chooseWrite. A dialog box opens in which you can provide the job name, which is used to name thefiles. The files are written to the current working directory.

The Settings button also allows you to change the panel settings. You can choose Read, to readsettings froPanel to res

You can alsstages. Thischoosing Pr

Note: Theabo

The icon oncurrent projwhen the lafully.

Clicking thactive jobs the bottom.launched, rurow to openMonitor panopen. If a jstatus. Click

Jobs are runferring filesoperates, as

1.6 CThe use of t

Liaison, verLLC, New YLiaison 6.1 User Manual 7

m an input file for the job and apply them to the panel, or you can choose Resetet all the panel settings to their default values.

o set preferences for all jobs and how the interface interacts with the job at various is done in the Preferences panel, which you can open at the Jobs section byeferences from the Settings button menu.

items present on the Settings menu can vary with the application. The descriptionsve cover all of the items.

the Job Status button shows the status of jobs for the application that belong to theect. It starts spinning when the first job is successfully launched, and stops spinningst job finishes. It changes to an exclamation point if a job is not launched success-

e button shows a small job status window that lists the job name and status for allsubmitted for the application from the current project, and a summary message at The rows are colored according to the status: yellow for submitted, green fornning, or finished, red for incorporated, died, or killed. You can double-click on a the Monitor panel and monitor the job, or click the Monitor button to open the

el and close the job status window. The job status is updated while the window isob finishes while the window is open, the job remains displayed but with the new anywhere outside the window to close it.

under the Job Control facility, which manages the details of starting the job, trans-, checking on status, and so on. For more information about this facility and how it well as details of the Job Settings dialog box, see the Job Control Guide.

iting Liaison in Publicationshis product and its components should be acknowledged in publications as:

sion 6.1, Schrdinger, LLC, New York, NY, 2013; Strike, version 2.2, Schrdinger,ork, NY, 2013.

Schrdinge8 r Software Release 2013-3

Chapter 2

Liaison User Manual

Chapter 2: Liaison Tutorial

This chapteality of Liaaffinities. Itapply the LLiaison-gensimulation tion of bind

The exercis

How t

How tusing

How tfor no

You will uspanels to cr

To do theseand Strike 2

Some exercyou to begiinput files t

2.1 PTo run the eyou need toautomaticalunzip the lworking dirLiaison 6.1 User Manual 9r contains tutorial exercises to help you quickly become familiar with the function-ison using the Maestro interface. Liaison is used to simulate and predict binding does so by generating for each protein-ligand complex the descriptors necessary toIA equation. Models for the binding affinity are then created and applied fromerated descriptors via Strike. Thus, the Liaison process involves two steps, the

of binding in Liaison to generate a set of descriptors and the creation and applica-ing affinity models from the Liaison descriptors with Strike.

es in this chapter demonstrate:

o perform Liaison simulations on multiple ligands

o create a validated model for the , , and coefficients for the LIA equationStrike

o generate and apply the results of Liaison simulations to predict binding affinitiesvel ligands

e the Liaison panel to set up and run Liaison simulations and then use the Strikeeate, validate, and apply binding affinity models from Strike.

exercises you must have access to an installed version of Maestro 9.4, Liaison 6.1.2. For installation instructions, see the Installation Guide.

ises in this tutorial produce files that are needed in subsequent exercises. To allown at any exercise you choose, the tutorial file set contains copies of the relevanthat will be needed as you perform the tutorial.

reparing for the Exercisesxercises, you need a working directory in which to store the input and output, and copy the input files from the installation into your working directory. This is donely in the Tutorials panel, as described below. To copy the input files manually, justiaison zip file from the tutorials directory of your installation into yourectory.


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On Linux, you should first set the SCHRODINGER environment variable to the Schrdinger soft-ware installation directory, if it is not already set:

If Maestro i

Linux

$SCHR Wind

You ca

Mac:

If it isApplic

Now that M

1. Choos

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2. Ensurebelow

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6. Choos

csh/tcsh: setenv SCHRODINGER installation-path sh/bash/kshr Software Release 2013-3

s not running, start it as follows:

: Enter the following command:

ODINGER/maestro -profile Maestro & ows: Double-click the Maestro icon on the desktop.

n also use Start All Programs Schrodinger-2013-3 Maestro.

Click the Maestro icon on the dock.

not on the dock, drag it there from the SchrodingerSuite2013-3 folder in yourations folder, or start Maestro from that folder.

aestro is running, you can start the setup.

e Help Tutorials.

torials panel opens.

that the Show tutorials by option menu is set to Product, and the option menu is labeled Product and set to All.

Liaison Tutorial in the table.

the directory that you want to use for the tutorial in the Copy to text box, or clicke and navigate to the directory.

directory does not exist, it will be created for you, on confirmation. The default isurrent working directory.

Copy.

torial files are copied to the specified directory, and a progress dialog box is dis- briefly.

the default directory, the files are now in your current working directory, and you next two steps. Otherwise, you should set the working directory to the place thatl files were copied to.

e Project Change Directory.

: export SCHRODINGER=installation-path


7. Navigate to the directory you specified for the tutorial files, and click OK.

You can close the Tutorials panel now, and proceed with the exercises.

2.2 RIn this exercjob that calfile, allowinaffinity.

The Liaisonsingle 2.8 Gcan be reduthis exercistions or not

2.2.1 I

Before runnFor receptoand the ligaused as the

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5. Click

The difile, wLiaison 6.1 User Manual 11

unning the Liaison Simulationsise, starting with a receptor and a set of prepared ligands, you will set up and run a

culates Liaison descriptors. The descriptors are saved in a Maestro file and a CSVg you to use them in the creation, validation, and application of models of binding

calculations to be run in this exercise require about 1.5 hours of CPU time on aHz Xeon processor, though by taking advantage of multiple processors this timeced sharply. The output files from the Liaison simulation have been prepared fore so the tutorial may be completed whether you choose to run the Liaison simula-.

mporting the Structuresing Liaison on a series of ligand-receptor complexes, you must import the receptor.r flexibility, you must also import at least one ligand. In this exercise, the receptornds are in the same file, and you will import them all. The imported ligands will beligand input for the simulation.

the Import button on the Project toolbar.

Import dialog box, select the Maestro file 2boh_sar_series.maegz.

import options are not displayed, click Options.

that Import all structures is selected, and that the Include in Workspace optiond is First Imported Structure.

Open.

alog box closes and the structures in the file are imported. The first structure in thehich is the receptor, is displayed in the Workspace.


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2.2.2 Setting Up the SystemBefore running Liaison on a series of ligand-receptor complexes, you must specify the receptorand ligands and set the parameters for the Liaison simulations.

1. Click

The P

2. Includ

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the Table button on the Project toolbar.

roject Table panel opens. e the first ligand in the Workspace.

n do this by control-clicking in the In column for the ligand. Both the receptor andst ligand should be visible in the Workspace.

ct the receptor.

n do this by control-clicking in the Row column for the receptor. The receptor rowes color, but the receptor should still be visible in the Workspace. The Project Table set up for the Liaison simulation.

e Applications Liaison or Tasks Binding Energy Estimation Linear Interac-odel in the main window.

aison panel opens with the Systems tab displayed.

that Pick to identify ligand and Mark ligand are selected.

Figure 2.1. The Systems tab of the Liaison panel.


6. Pick a ligand atom in the Workspace.

The ligand is now marked in yellow.

7. Ensure that Size of flexible protein region is selected, and from its option menu select Allatoms

8. In the

The liulation

9. In the Simula

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The progresStatus coluthe status chLiaison 6.1 User Manual 13

frozen (0/0). Define ligands section, ensure that Selected entries in Project Table is selected. gand-protein complexes to be simulated have now been specified. Next, some sim- parameters must be set to reduce the time taken for the simulation.

Parameters tab, change the Maximum minimization steps to 100 in both the Ligandtion and the Complex Simulation tabs.

tarting and Monitoring the Liaison Jobes approximately 15 minutes on a 2.8 GHz Xeon processor. The Liaison simula-t need to be run to continue with the tutorial. If you prefer, you may continue theting with Section 2.3.

ands and receptor defined and Liaison simulation parameters set, the Liaison simu-e started.

the Settings button.

b Settings dialog box opens.

the Incorporate option menu, choose Append new entries.

e the Job Name to 2boh_sar_series.

the host where the Liaison simulations are to be run from the Host option menu.

on the local machine ensure that localhost is selected. If the host is a multipro- machine, specify the number of available CPUs in the Total N Processors text box,ise leave its value at one. If you distribute the job over 5 processors, each subjob

ke about 3 minutes.

Save and Run.

s of the job can be monitored in the Monitor panel. While the job is in progress, themn in the Jobs tab for this job displays the text running. When the job finishes,anges to incorporated : finished.


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Before the job is launched the following input files are written:

When the LProject Tabthe followin

If you wantthe project

2.3 GA

Before you as describednow. You m

A Strike lic

2.3.1 I

You will bethe Liaison descriptors

1. If the dow.

The Li

2. In the

A file

3. Navig

This fi

2boh_sar_series.inp Command file2boh_sar_series_pv.maegz Ligand structure file

2boh_sar_2boh_sar_r Software Release 2013-3

iaison simulation finishes, the calculated Liaison results are incorporated into thele along with the input ligand geometries, and the working directory will containg job output files:

to stop working on the tutorial now, choose Close Project from the Project menu. Ifis a scratch project, you will be prompted to save it or delete it.

enerating and Validating an LIA Model of Binding ffinitybegin the exercises shown below, you must first have created a working directory, in Section 2.1 on page 9. If you have not yet set up your working directory, do soust also complete the exercise in Section 2.2 on page 11.

ense is required for these exercises.

mporting Liaison Results into Strike for Model Creation importing the Liaison descriptors that will be used to create the LIA model throughpanel. The data could also be imported directly into the Project Table. The Liaisonare stored in 2boh_sar_series-out.mae.gz.

Liaison panel is not already open, choose Applications Liaison in the main win-

aison panel opens with the Systems tab displayed.

Analysis tab, click Browse.

selector opens.

ate to and import the file 2boh_sar_series-out.mae.gz.

le should be in your working directory.

series.log Log summary file series-out.mae.gz Structure file of final complex geometries with calcu-

lated Liaison results


4. In the

The mProjec

5. Close

2.3.2 CThe experimused for theLIA equatiousing , , and terms from Liaison.

cise, you will create an LIA model for the five molecules for which you generated Five molecules is a bare minimum for generating a model, but this is sufficient foron purposes.

Select descriptors to be included in the model table, select Uele, Uvdw, and Ucav.

ntrol-click to select the second and third of these descriptors. These are the termse used for an LIA model, and will be the independent variables in the model.

the Regression method option menu, choose Multiple Linear Regression.

that Use all selected is selected.

Figure 2.2. The Analysis tab of the Liaison panel.


Schrdinge16

4. Click

The C

5. Select

This ppredic

6. Enter

7. Click

The Strike incorporaterow with nar Software Release 2013-3

Choose, to the right of the Activity Property text box.

hoose Activity Property dialog box opens.

the delta G assoc (297 K kcal/mol) property and click OK. roperty is the response or dependent variable that a model will be created tot.

2boh_lrm_model as the job name.Run to begin the Strike job.job should finish in a matter of seconds and the predicted binding affinities ared in the Project Table as Predicted Activity1.1. In the Build QSAR Model panel, ame lrm_model.1.1 is added to the Results table that corresponds to the LIA model.

Figure 2.3. The Strike Build QSAR Model panel.


2.3.3 Analyzing the LIA Binding Affinity ModelOnce the LIA model has been created, it must be analyzed to see if it makes intuitive sense andpossesses predictive power that does not arise by chance. From the Build QSAR Model panelwe will viewmodel, and

The basics oprovide an these includrial we are log unit, ancoefficientsOPLS_2005not need tothe fundam

First, you w

1. In thelrm_m

Since thing.

2. Click

The Pfound propertrainin

From Worksthe ful

Next, you w

3. Click

The Vmodelbasic rdepeninformLiaison 6.1 User Manual 17

a plot of predicted versus experimental activities, analyze the fundamentals of theassess its predictive power prior to making predictions on test set molecules.

f each model are displayed in the Results table in the Build QSAR Model panel andat-a-glance overview of a model. For a multiple linear regression (MLR) modele the standard deviation, R2, F-statistic, and P-value. For the purposes of this tuto-

interested in models with an R2 greater than 0.6, a standard deviation lower than 1d a P-value less than 0.05. For an LIA model to make intuitive sense the , , and calculated when using the OPLS_2001 force-field should all be positive. For the cavity term is calculated in a different fashion, and the gamma coefficient does

be positive for the LIA model to make intuitive sense. For further information onental metrics of an MLR model see the Strike User Manual.

ill display a plot of predicted versus experimental activities.

Build QSAR Model panel, ensure that the LIA model, which is namedodel.1.1, is selected in the Results table.

there is only one model and it is selected already, you should not have to do any-If there was more than one model, you would have to select the model.

Plot.

lot XY panel opens with a plot of the predicted binding affinity from the LIA modelin property Predicted Activity1.1 versus the experimental binding affinities found inty Activity (kcal/mol), which was used as the dependent or response variable ing the MLR model.

this plot you can select points and view the selected molecules in the Maestropace, or select groups of molecules in the Project Table. For further information onl capabilities of the plotting tool see Chapter 11 of the Maestro User Manual.

ill view all the available information on the LIA model.

View in the Build QSAR Model panel.

iew QSAR Model panel opens. This panel displays the Strike output from LIA creation. From this display all the information on the model is available, fromegression statistics to validation tests such as the results of the leave-group-out anddent variable randomization testing results. When you have finished examining theation, close the panel.


Schrdinge18

2.3.4 P

Once the Lbinding affito predict blated througthey can be

For this parcourse this and a test se

1. Click

2. In theclick O

The st

3. In the

The P

Figure 2.4r Software Release 2013-3

redicting Binding Affinities with the LIA ModelIA model has been analyzed and found to be suitable, it may be applied to predictnities for molecules in a test set. In a similar fashion the LIA model may be appliedinding affinities for any molecule for which the LIA descriptors have been calcu-h Liaison. To do this, the molecules must be imported into the Project Table where

acted upon by Strike.

t of the tutorial, you will reuse the molecules you used to develop the model. Ofshould give the same results as for the model. For a tutorial on using a training sett, see the Strike Tutorial.

the Import button on the Project toolbar.

Import dialog box, select the Maestro file 2boh_sar_series-out.mae.gz, andpen.

ructures are imported and selected in the Project Table. Build QSAR Model panel, click Predict.

redict based on QSAR model panel opens, and the Build QSAR Model panel closes.

. The Scatter Plot panel showing the experimental vs. predicted activity plot.


4. In the

This s

5. Enter

6. Click

The Strike the LIA mStrikePredic

2.3.5 M

Once an LIAities may bThe steps ar

1. Run a

2. Impor

You ca

3. Open

4. Ensure

5. Click

The geityX.1 Liaison 6.1 User Manual 19

Select model to use for prediction table ensure that the LIA model is selected.

hould be the model named 2boh_lrm_model.1.1.

2boh_lrm_pred as the job name. Run.

job should finish in a matter of seconds, and the predicted binding affinities fromodel are incorporated into the Project Table as delta G assoc (297 K kcal/mol)tion.

aking Predictions for Additional Molecules model predicting binding affinities has been created and validated, binding affin-

e predicted for any molecule for which the three LIA terms have been generated.e the same as was done for the test set above.

Liaison calculation to generate the three LIA descriptors for your own ligands.

t the molecules into the Project Table and ensure that they are selected.n import them using either the Liaison panel or the Import panel.

the Strike Predict Based on QSAR Model panel.

that the LIA model is selected in the Results table.

Run.

nerated predictions are added automatically to the Project Table as Predicted Activ-where X is the original model number for the LIA model.

Figure 2.5. The Strike Predict based on QSAR model panel.

Chapter 3

Liaison User Manual

Chapter 3: Protein and Ligand Preparation

The qualitythe ligand. Saration Wizstructures foligand prepligand struc

3.1 PA typical Pmetal ions, or charges. ysis cannot atom force states must

This sectionbe performmenu on thePreparation

After proceand the ligamost cases,to determin

You may ondescribed in

1. Impor

The pligand

2. Simpl

For costructuLiaison 6.1 User Manual 21 of Liaison results depends on reasonable starting structures for both the protein andchrdinger offers a comprehensive protein preparation facility in the Protein Prep-ard, which is designed to ensure chemical correctness and to optimize proteinr use with Glide and other products. Likewise, Schrdinger offers a comprehensive

aration facility in LigPrep. It is strongly recommended that you process protein andtures with these facilities in order to achieve the best results.

rotein PreparationDB structure file consists only of heavy atoms, can contain waters, cofactors, andand can also be multimeric. The structure generally has no information on bondingTerminal amide groups can also be misaligned, because the X-ray structure anal-usually distinguish between O and NH2. For Liaison calculations, which use an all-field, atom types and bond orders must be assigned, the charge and protonationbe corrected, side chains reoriented if necessary, and steric clashes relieved.

provides an overview of the protein preparation process. The entire procedure caned in the Protein Preparation Wizard panel, which you open from the Workflows main toolbar. This tool and its use is described in detail in Chapter 2 of the Protein Guide.

ssing, you will have files containing refined, hydrogenated structures of the ligandnd-receptor complex. The prepared structures are suitable for use with Liaison. In not all of the steps outlined need to be performed. See the descriptions of each stepe whether it is required.

occasion want to perform some of these steps manually. Detailed procedures are Chapter 3 of the Protein Preparation Guide.

t a ligand/protein cocrystallized structure, typically from PDB, into Maestro.

reparation component of the protein preparation facility requires an identified.

ify multimeric complexes.

mputational efficiency it is desirable to keep the number of atoms in the complexre to a minimum. If the binding interaction of interest takes place within a single


Schrdinge22

subunit, you should retain only one ligand-receptor subunit to prepare for Liaison. If twoidentical chains are both required to form the active site, neither should be deleted.

Determine whether the protein-ligand complex is a dimer or other multimer con-taining duplicate binding sites and duplicate chains that are redundant.

Is

3. Locate

Waterjudgedthey amore

makin

Theseattachwatersare keprepar

4. AdjusProbleIncomare dishould

Metal roModtypes thermoGC, et

It mayreceptassignbenefimust bGlu 14the cotallizeligandr Software Release 2013-3

f the structure is a multimer with duplicate binding sites, remove redundant bindingites and the associated chains by picking and deleting molecules or chains.

any waters you want to keep, then delete all others.

molecules in the crystallographic complex are generally not used unless they are critical to the functioning of the proteinligand interaction. When waters are used,

re later included in the protein as structural waters. Keeping structural waters islikely to be important for Liaison than for other programs such as Glide, whereg a site more accessible by removing all waters may be necessary for docking.

waters are identified by the oxygen atom, and usually do not have hydrogensed. Generally, all waters (except those coordinated to metals) are deleted, but that bridge between the ligand and the protein are sometimes retained. If waterspt, hydrogens will be added to them by the preparation component of the proteination job. Afterwards, check that these water molecules are correctly oriented.t the protein, metal ions, and cofactors.

ms in the PDB protein structure may need to be repaired before it can be used.plete residues are the most common errors, but may be relatively harmless if theystant from the active site. Structures that are missing residues near the active site be repaired.

ions in the protein complex cannot have covalent bonds to protein atoms. The Mac-el atom types for metal ions are sometimes incorrectly translated into dummy atom

(Du, Z0, or 00) when metal-protein bonds are specified in the input structure. Fur-re, isolated metal ions may erroneously be assigned general atom types (GA, GB,c.). be necessary to adjust the protonation of the protein, which is crucial when theor site is a metalloprotein such as thermolysin or an MMP. In such a case, Glides a special stability to ligands in which anions coordinate to the metal center. Tot from this assignment, groups such as carboxylates, hydroxamates, and thiolatese anionic. The protein residues that line the approach to the metal center (such as3 and His 231 in thermolysin) need to be protonated in a manner compatible with

ordination of an anionic ligand such as a carboxylate or hydroxamate. The co-crys-d complex therefore needs to be examined to determine how the protein and thes should be protonated. In some cases, two or more protonation states of the protein


may need to be used in independent docking experiments to cover the range of physicallyreasonable ligand dockings.

Cofactors are included as part of the protein, but because they are not standard residues itis sometimes necessary to use Maestros structure-editing capabilities to ensure that mul-tiple b

F C I

t

S S

5. AdjusIf the they minteracfound

If yousites, t

6. Run a

This ipotent

7. Review

Ip

Eo

3.2 CAfter you hprotein struLiaison 6.1 User Manual 23

onds and formal charges are assigned correctly.

ix any serious errors in the protein.heck the protein structure for metal ions and cofactors.

f there are bonds to metal ions, delete the bonds, then adjust the formal charges ofhe atoms that were attached to the metal as well as the metal itself. et charges and correct atom types for any metal atoms, as needed.et bond orders and formal charges for any cofactors, as needed.

t the ligand bond orders and formal charges.

complex structure contains bonds from the ligand or a cofactor to a protein metal,ust be deleted. Glide models such interactions as van der Waals plus electrostatictions. Glide cannot handle normal covalent bonds to the ligand, such as might bein an acyl enzyme.

are working with a dimeric or large protein and two ligands exist in two activehe bond orders have to be corrected in both ligand structures.

restrained minimization of the protein structure.

s done with impref, and should reorient side-chain hydroxyl groups and alleviateial steric clashes.

the prepared structures.

f problems arise during the restrained minimization, review the log file, correct theroblems, and rerun.xamine the refined ligand/protein/water structure for correct formal charges, bondrders, and protonation states and make final adjustments as needed.

hecking the Protein Structuresave completed the protein preparation, you should check the completed ligand andctures.


Schrdinge24

3.2.1 Checking the Orientation of Water MoleculesYou only need to perform this step if you kept some structural waters. Reorienting the hydro-gens is not strictly necessary, as their orientation should have been changed during refinement,but it is use

If the orienSection 3.9

When you refinement

3.2.2 CYou shouldrestraint-op

Steric clashContacts fodefines badthe van der ugly contacand display

If steric claprocedure, bdefault of 0the prepared

3.2.3 R

You shouldthe ligand ointerveningacceptor-ac

Some of theThe preparacally occursone or more

reasonable representedr Software Release 2013-3

ful to check that the orientation is correct.

tation is incorrect, reorient the molecules by using the procedure outlined in of the Protein Preparation Guide.

have corrected the orientation of the retained water molecules, you should run aon the adjusted protein-ligand complex.

hecking for Steric Clashes make sure that the prepared site accommodates the co-crystallized ligand in thetimized geometry obtained from the structure preparation.

es can be detected by displaying the ligand and protein in Maestro and using thelder in the H-Bonds and Contacts panel to visualize bad or ugly contacts. Maestro contacts purely on the basis of the ratio of the interatomic distance to the sum ofWaals radii it assigns. As a result, normal hydrogen bonds are classified as bad orts. By default, Maestro filters out contacts that are identified as hydrogen bonds,s only the genuine bad or ugly contacts.

shes are found, repeat the restrained optimization portion of the protein preparationut allow a greater rms deviation from the starting heavy-atom coordinates than the

.3 . Alternatively, you can apply an additional series of restrained optimizations to ligand-protein complex to allow the site to relax from its current geometry.

esolving H-Bonding Conflicts look for inconsistencies in hydrogen bonding to see whether a misprotonation ofr the protein might have left two acceptor atoms close to one another without an

hydrogen bond. One or more residues may need to be modified to resolve such anceptor or donor-donor clash.

se clashes are recognized by the preparation process but cannot be resolved by it.tion process may have no control over other clashes. An example of the latter typi- in an aspartyl protease such as HIV, where both active-site aspartates are close to atoms of a properly docked ligand. Because these contact distances fall within any

cavity radius, the carboxylates are not subject to being neutralized and will both be as negatively charged by the preparation process. However, when the ligand inter-


acts with the aspartates via a hydroxyl group or similar neutral functionality, one of the aspar-tates is typically modeled as neutral.

If residues need to be modified, follow these steps:

1. Place

2. Exami

3. Use yotomeri

4. Use ththe Pr

5. Re-mi

It is usuallyzation to colarge-scale without daninal complechanged theit is best to

3.3 LiTo give the ligand structures suppli

1. They m

2. They m

3. They with n

4. They m

5. They m

For exprotonacceptincurramineLiaison 6.1 User Manual 25

the refined protein-ligand complex in the Workspace.

ne the interaction between the ligand and the protein (and/or the cofactor).ur judgment and chemical intuition to determine which protonation state and tau-c form the residues in question should have.

e structure-editing capabilities in Maestro to resolve the conflict (see Section 3.8 ofotein Preparation Guide for procedures).nimize the structure.

sufficient to add the proton and perform about 50 steps of steepest-descent minimi-rrect the nearby bond lengths and angles. Because this optimizer does not make

changes, the partial minimization can be done even on the isolated ligand or proteinger of altering the conformation significantly. However, if comparison to the orig-x shows that the electrostatic mismatch due to the misprotonation has appreciably positions of the ligand or protein atoms during the protein-preparation procedure,reprotonate the original structure and redo the restrained minimization.

gand Preparationbest results, the structures that are used must be good representations of the actualtures as they would appear in a protein-ligand complex. This means that the struc-ed to Liaison must meet the following conditions:

ust be three-dimensional (3D).ust have realistic bond lengths and bond angles.

must each consist of a single molecule that has no covalent bonds to the receptor,o accompanying fragments, such as counter ions and solvent molecules.

ust have all their hydrogens (filled valences). ust have an appropriate protonation state for physiological pH values (around 7).

ample, carboxylic acids should be deprotonated and aliphatic amines should beated. Otherwise a neutral aliphatic amine could improperly act as a hydrogen-bondor in the docking calculations, or could occupy a hydrophobic region withouting the large desolvation penalty that XP Glide docking would have assessed if the had been properly protonated.


Schrdinge26

Protonation states are particularly crucial when the receptor site is a metalloprotein suchas thermolysin or a MMP. If the metal center and its directly coordinated protein residueshave a net charge, Glide assigns a special stability to ligands in which anions coordinateto the metal center. To benefit from this assignment, groups such as carboxylates, hydrox-amateto anio

6. They m

Maeststro foformamat be

All of the aLigPrep is d

3.3.1 UThe Schrdatom 3D strin SD, Maeline. For de

To run LigPbmin requirof commancommand li

The LigPrethe structurmize the strthe LigPrep

1. Conve

2. Select

3. Add h

4. Remo

5. Neutra

6. Generr Software Release 2013-3

s, and thiolates must be anionic. If there is no net charge, Glide gives no preferencens over neutral functional groups.

ust be supplied in Maestro, SD, Mol2, or PDB format.

ro transparently converts SD, MacroModel, Mol2, PDB, and other formats to Mae-rmat during structure import. However, Glide has no direct support for other

ts, so you should ensure that your structures are in Maestro, SD, Mol2, or PDB for-fore starting Liaison jobs.bove conditions can be met by using LigPrep to prepare the structures. Use ofescribed in the next section.

sing LigPrep for Ligand Preparationinger ligand preparation product LigPrep is designed to prepare high quality, all-uctures for large numbers of drug-like molecules, starting with 2D or 3D structuresstro, or SMILES format. LigPrep can be run from Maestro or from the commandtailed information on LigPrep, see the LigPrep User Manual.

rep, you must have a LigPrep license. The MacroModel commands premin ande LigPrep licenses when run in a LigPrep context, and are limited to a restricted setds when run using a LigPrep license. LigPrep can be run from Maestro or from thene.

p process consists of a series of steps that perform conversions, apply corrections toes, generate variations on the structures, eliminate unwanted structures, and opti-uctures. Many of the steps are optional, and are controlled by selecting options in panel or specifying command-line options. The steps are listed below.

rt structure format.

structures.

ydrogen atoms.

ve unwanted molecules.

lize charged groups.

ate ionization states.


7. Generate tautomers.

8. Filter structures.

9. Generate alternative chiralities.

10. Gener

11. Remo

12. Optim

13. Conve

The LigPreLigPrep to LigPrep Us

The simplesfor each sutures from ering conformor specified

The defaultminimize thon panel op

The Ionizatfound in the

RetainNeutra

Generate sevwith atings cstates.

Desalt is se

Generate taligand, seleinput structthen the taLiaison 6.1 User Manual 27

ate low-energy ring conformations.

ve problematic structures.

ize the geometries.

rt output file.

p panel allows you to set up LigPrep jobs in Maestro. Choose Applications >open the panel. For details of panel options and operation, see Chapter 2 of theer Manual.

t use of LigPrep produces a single low-energy 3D structure with correct chiralitiesccessfully processed input structure. LigPrep can also produce a number of struc-ach input structure with various ionization states, tautomers, stereochemistries, andations, and eliminate molecules using various criteria including molecular weight

numbers and types of functional groups present.

options in the LigPrep panel remove unwanted molecules, add hydrogens, ande ligand structure (performing a 2D-3D conversion, if necessary). Below are notestions that produce more than one output structure per input structure.

ion options allow you to generate all the ligand protonation states that would be specified pH range. The Ionization options are:

original statelize

ate possible states at target pH target +/- range. This is the default, and can gener-eral different output structures for each input structure. The default pH target is 7.0 +/- range of 2.0, so the default pH range is 5.0 9.0. Both the target and range set-an be changed. You can use either the ionizer or Epik to generate ionization

Epik is a separate product, so you must purchase this product to use it.

lected by default.

utomers is selected by default. The tautomerizer generates up to 8 tautomers percting the most likely tautomers if more than 8 are possible. If you are sure that theures are already in the correct tautomeric form for docking to a particular target,utomerizer should be turned off by deselecting Generate tautomers.


Schrdinge28

The stereoizer can generate two stereoisomers per chiral center in the ligand, up to a speci-fied maximum. There are three Stereoisomers options.

The first two options, Retain specified chiralities (the default) and Determine chiralitiesfrom 3D structure, generate both isomers only at chiral centers where chirality is unspeci-fied orthat Rwhile ity inf

Gener

For allified b

Generate lolowest ener

3.3.2 UIf you prefeinstallationsThese utilitligands in th

Hydro

or the

Hydrodescri

Structstrucmanuar Software Release 2013-3

indeterminate; centers with known chirality retain that chirality. The difference isetain specified chiralities takes its chirality data from the input file (SD or Maestro),Determine chiralities from 3D structure ignores input file chiralities and takes chiral-ormation from the 3D geometry.

ate all combinations varies the stereochemistry at all chiral centers.

choices, the stereochemistry is varied up to a maximum number of structures spec-y Generate at most max per ligand. The default maximum is 32.

w energy ring conformations: number per ligand. The default is to generate only thegy conformation.

sing Other Programs for Ligand Preparationr to prepare the ligands with other programs, you can do so. Schrdinger software include a number of utilities that can be used to perform some of the above tasks.ies are also used by LigPrep. One of these, the Ionizer, can be used to preparee required protonation states. Some of the other tasks can be performed as follows:

gen atoms can be added in Maestro with either the Add hydrogens toolbar button:

Hydrogen Treatment panel (select Hydrogen Treatment from the Edit menu).gen atoms can also be added (or removed) using the utility applyhtreat, which isbed in Section 4.1 of the General Utilities manual.

ure file format conversion can be done from the command line with utilities such astconvert, pdbconvert, and sdconvertsee Section 1 of the General Utilitiesl.

Chapter 4

Liaison User Manual

Chapter 4: Running Liaison

Liaison is abeen fitted tpredicting s

The LiaisonBased Descperformed uthe Strike U

4.1 OBefore youproperly prfile include

To run a Li

1. SpecifThe reTable

2. Speciftab.

3. Set coters ta

4. Click

5. In the sors.

If youthe cuten to from a

6. Click Liaison 6.1 User Manual 29 method of predicting ligand-protein binding free energies using a model that haso known binding energy values. The process involves two steps, a fitting step and atep. Each step is carried out as two tasks, a simulation task and an analysis task.

panel is used to set up and run the simulation tasks. It runs the Ligand & Structure-riptors script (lsbd) to set up and run the Liaison job. The analysis tasks aresing the Build QSAR Model panel of Strike. For more information on Strike, seeser Manual. A tutorial introduction to the Liaison tasks is given in Chapter 2.

verview of Liaison Tasks run a Liaison simulation, you should ensure that the receptor and the ligands areepared, as described in Chapter 3. You should also ensure that the ligand structures the known binding energies.

aison simulation:

y the systems to be simulated in the Specify structures section of the Systems tab.ceptor is taken from the Workspace. The ligands can be taken from the Project

or a file.

y the kind of system to be simulated in the Job options section of the Parameters

nstraints if required in the Specify restrained/frozen shells section of the Parame-b.

the Settings button.

Job Settings dialog box, set the job name and select the host and number of proces-

want to choose a remote machine or batch queue as the host for the job, ensure thatrrent working directory is mounted on the remote host. Liaison input files are writ-the current working directory. Liaison does not have the ability to copy input files local directory to a remote scratch directory.

Save and Run.


Schrdinge30

When the job finishes, the results are incorporated into the Project Table. The scores and thevarious components that are used in the analysis task are added as properties. If the job doesnot incorporate, select it in the Monitor panel and click Monitor.

To run a Li

1. Select

Ia

Is

ILo

The B

2. Select

F

3. Choos

4. For De

5. Click

If the you m

6. Click

To run a Li

1. Selectenergy

2. Choos

3. Select

4. Click

When the joadded to ther Software Release 2013-3

aison fitting job: the results of a Liaison simulation:

f the simulation results are already in the Project Table, select the relevant entries,nd choose Build QSAR Model from the Strike submenu of the Applications menu.

f the simulation results include both the training set and the test set, you shouldelect the training set for the fitting.

f the simulation results are not incorporated, click Browse in the Analysis tab of theiaison panel, navigate to and select the file jobname-final.mae.gz, and click Fitr Predict in Strike.

uild QSAR Model panel of Strike opens, with the Liaison results loaded.

the descriptors required for the fit from the list (click, shift-click, control-click):or an LRM model, select Uvdw, Uele, and Ucav.

e Multiple Linear Regression from the Regression method option menu.

scriptors, ensure that Use all selected is selected.

Choose to choose the activity property.

activity property is not in the Project Table, you can import it from a CSV file, butust do this before clicking Choose.

Run.

aison prediction job: the results of a Liaison simulation for the test set (the ligands whose binding you want to predict) in the Project Table.e Applications Strike Predict in the main window.

the model you want to apply from the list.

Run.

b finishes, you can view the results by clicking View. The predicted values are also Project Table.


4.2 The Liaison Panel The main part of the Liaison panel consists of three tabs:

System Param Analys

Below thesebutton, for button, whi

To open the

4.2.1 SThis tab con

4.2.1.1

In the Defintreated flexible proteinyou must sligand is ideprotein regiit is markedLiaison 6.1 User Manual 31

s tabeters tabis tab

tabs on the left are the Start button, for starting the Liaison simulation, the Writewriting the Liaison input files for later use from the command line, and the Resetch resets all settings in the panel to their default values.

Liaison panel, choose Applications Liaison in the main window.

ystems Tabtains two sections, one for defining the protein, and one for defining the ligands.

Defining the Proteine Protein section, you define the protein and specify which portions of it are to beibly. The protein must be displayed in the Workspace. If you want to specify flex- regions, you must also display a ligand. If a ligand is included in the Workspace,elect Pick to identify ligand and pick a ligand atom in the Workspace so that thentified. Identifying the ligand serves two purposes: it can be used to define flexible

ons, and it is excluded from the protein structure. You can select Mark ligand so that when you pick it.

Figure 4.1. The Systems tab of the Liaison panel.


Schrdinge32

If you want to treat regions of the protein as flexible, you can do so by selecting either a prede-termined set of shells or by choosing the atoms to be treated flexibly. To do so, select one of theoptions described below:

Size of flexible protein regionChoose a region from this option menu. The regions areseparashells that hadefine

Flexibopen tother You ca

Note: Youwhe

4.2.1.2

In the Defin

Select

File

4.2.2 P

This tab pro

The optionsOptions thalation in thebelow.

Sampling m

Choose theMolecular D

Minimization

Choose an methods. ADescent.r Software Release 2013-3

ted into three shells: a flexible shell, a restrained shell, and a frozen shell. Theare defined by two distances from the displayed ligand in angstroms. All residuesve atoms within the specified distance are included in the inner of the two shells

d by the radius.

le protein atomsSelect this option to specify the flexible atoms. Click Select tohe Atom Selection dialog box to set up the protein atoms to be treated flexibly. Allatoms are frozen. The ASL expression for the atoms is displayed in the text box.n type in an ASL expression instead of using the Atom Selection dialog box.

should make sure that you make the same choice of restrained and frozen shellsn you run Liaison for a particular system, otherwise the results will be invalid.

Defining the Ligandse ligands section, you specify the source of the ligands. There are two options:

ed entries in Project TableUse the entries that are selected in the Project Table.Enter the file name in the text box, or click Browse and navigate to the file.

arameters Tab

vides options for setting the simulation parameters.

that apply to both the complex and the free ligand are in the upper part of the tab.t apply to one or the other are in tabs labeled Ligand Simulation and Complex Simu- lower part of the tab. The controls in these tabs are identical, and are described

ethod option menu

method for performing the simulation, from Minimization, Hybrid Monte Carlo, orynamics.

algorithm option menu

algorithm for performing the minimization steps in any of the three samplingvailable algorithms are Truncated Newton, Conjugate Gradient, and Steepest


Simulation t

Specify thezation samp

Temperatur

Specify the10 ps Not a

Residue-ba

Set the valutions of an apair list if a

Force field o

Select the fLiaison simSelect the Ononpolar m

Use ligand i

Select this free and theLiaison 6.1 User Manual 33

emperature text box

temperature of the simulation in K. Default: 300 K Not available with the Minimi-ling method.

e relaxation time text box

time scale, in picoseconds, on which heat is exchanged with the heat bath. Default:vailable with the Minimization sampling method.

sed cutoff distance text box

e (in ) for the cutoff distance of non-bonded interactions. All pairwise interac-tom in one residue with an atom in another residue are included on the non-bonded

ny such pair of atoms is separated by this distance or less. Default: 15 .ption menu

orce field. The force field options are OPLS_2005 (the default) and OPLS_2001.ulations are run using Surface Generalized Born (SGB) continuum solvation.PLS_2005 force field if you want the calculation to use the improved parametrized

odel instead of the default SGB terms that are used with OPLS_2001.

nput partial charges (if they exist) optionoption to use the input charges for the ligand in Liaison calculations (for both the bound state).

Figure 4.2. The Parameters tab of the Liaison panel.


Schrdinge34

Maximum minimization steps text box

Specify the maximum steps to take during any minimization. Can be set independently forligands and complexes. Default: 1000.

Heating tim

Set the timeHMC or MD

Simulation t

Set the simages for the

4.2.3 A

This tab proanalysis. Yothat containthis file are are selectedStrike BuildManual.r Software Release 2013-3

e text box

in picoseconds over which the system is heated before the LIA task is started, in an simulation. Default: 10 ps.

ime text box

ulation time for the LIA task, in an HMC or MD simulation. In this task the aver- van der Waals, Coulombic, reaction field and cavity terms are determined.

nalysis Tabvides an interface to Strike for performing the fit and predict steps of the Liaisonu can use Strike independently. If you use these controls, you must specify the files the results of the Liaison simulation, named jobname-final.mae. The structures inimported into the Project Table; when you click Fit or Predict in Strike, these entries in the Project Table and used as input to Strike. Clicking this button opens the QSAR Model panel. For more information, see Chapter 3 of the Strike User

Figure 4.3. The Analysis tab of the Liaison panel.


4.3 Liaison FilesWhen you run a Liaison job, the following input files are written to the launch directory:

When the LProject Tabthe followin

4.4 ROnce you hthen run the

$SCHRODINThe requireoptions, deWAIT and

jobname.ijobname_p

jobname.ljobname-o

Table 4.1. O

Argument

-v[ersion

-h[elp]

-s strfile | --str=strf-i infile |--cmd=infi-w | --wri-c | --co

-NJOBS n Liaison 6.1 User Manual 35

iaison simulation finishes, the calculated Liaison results are incorporated into thele along with the input ligand geometries, and the working directory will containg job output files:

unning Liaison From the Command Lineave set up a Liaison job in Maestro, you can click Write to write out the input file, Liaison simulation job from the command line with the following command:GER/liaison [options] [job-options] -i infile -s strfile d arguments and options are described in Table 4.1. The standard Job Control

scribed in the Table 2.1 of the Job Control Guide, are accepted, as well as the-LOCAL options described in Table 2.2 of the Job Control Guide.

np Command input filev.maegz Receptor and ligand structure input

og Log summary file ut.mae.gz Structure file containing the final geometries of the

complexes with the calculated Liaison results

ptions for the liaison command.

Description

] Show the program version and exit.

Show usage information and exit.

ile Input structure file in Maestro pose viewer format This file contains the receptor as the first entry, followed by the ligands.

le Liaison command input file

te Write input files for running simulation, but do not run job.mpile Compile results from previous simulations. Must specify -NJOBS, -s, and -i

arguments from original simulation

Number of subjobs to split job into


Schrdinge36

You can run the job on a multiprocessor host, and split the job into a specified number ofsubjobs.r Software Release 2013-3

Liaison User Manual

Getting Help

Information

The dPDF d

The Shttp://dinger

FindingMaestro pro

To get info

Pause informmain w

If the GenerNot al

Click about brows

Choosbrows

Whenside b

ChoosmentsLiaison 6.1 User Manual 37 about Schrdinger software is available in two main places:

ocs folder (directory) of your software installation, which contains HTML andocumentation. Index pages are available in this folder.

chrdinger web site, http://www.schrodinger.com/, particularly the Support Center,www.schrodinger.com/supportcenter, and the Knowledge Base, http://www.schro-.com/kb.

Information in Maestrovides access to nearly all the information available on Schrdinger software.

rmation:

the pointer over a GUI feature (button, menu item, menu, ...). In the main window,ation is displayed in the Auto-Help text box, which is located at the foot of theindow, or in a tooltip. In other panels, information is displayed in a tooltip.

tooltip does not appear within a second, check that Show tooltips is selected underal Appearance in the Preferences panel, which you can open with CTRL+, (,).l features have tooltips.

the Help button in the lower right corner of a panel or press F1, for informationa panel or the tab that is displayed in a panel. The help topic is displayed in yourer. The button may have text or an icon:

e Help Online Help or press CTRL+H (H) to open the default help topic in yourer.

help is displayed in your browser, use the navigation links or search the help in thear.

e Help Manuals Index, to open a PDF file that has links to all the PDF docu-. Click a link to open the document.

Getting Help

Schrdinge38

Choose Help Search Manuals to search the manuals. The search tab in Adobe Readeropens, and you can search across all the PDF documents. You must have Adobe Readerinstalled to use this feature.

For informa

Probleprodu

New s

Script

Python

Utility

Keybo

Install

Runni

Using

Maest

ContacIf you have using the in

E-maiUSPSPhoneFax:WWWFTP:

Generally, eWhen sendi

All rel Liaiso Prima Installr Software Release 2013-3

tion on:

ms and solutions: choose Help Knowledge Base or Help Known Issues ct.

oftware features: choose Help New Features.

s available for download: choose Scripts Update.

scripting: choose Help Python Module Overview.

programs: choose Help About Utilities.

ard shortcuts: choose Help Keyboard Shortcuts.

ation and licensing: see the Installation Guide.

ng and managing jobs: see the Job Control Guide. Maestro: see the Maestro User Manual.

ro commands: see the Maestro Command Reference Manual.

ting Technical Supportquestions that are not answered from any of the above sources, contact Schrdingerformation below.

l: [email protected]: Schrdinger, 101 SW Main Street, Suite 1300, Portland, OR 97204: (503) 299-1150

(503) 299-4532: http://www.schrodinger.com

ftp://ftp.schrodinger.com

-mail correspondence is best because you can send machine output, if necessary.ng e-mail messages, please include the following information:

evant user input and machine outputn purchaser (company, research institution, or individual)ry Liaison useration, licensing, and machine information as described below.

Getting Help

Gathering Information for Technical SupportThe instructions below describe how to gather the required machine, licensing, and installationinformation, and any other job-related or failure-related information, to send to technicalsupport. Wh

For genera

1. Open

M W M C

2. When

A dial

3. Attach

If your job 1. Open

M B E

2. Select

The P

3. If youAutom

4. Click

An arcthe na

5. Attach

6. Copy into th

WcLiaison 6.1 User Manual 39

ere the instructions depend on the profile used for Maestro, the profile is indicated.

l enquiries or problems:

the Diagnostics panel.

aestro: Help Diagnostics indows: Start All Programs Schrodinger-2013-3 Diagnostics ac: Applications Schrodinger2013-3 Diagnostics ommand line: $SCHRODINGER/diagnostics

the diagnostics have run, click Technical Support.

og box opens, with instructions. You can highlight and copy the name of the file.

the file specified in the dialog box to your e-mail message.

failed:

the Monitor panel.

aestro: Applications Monitor Jobs or Tasks Monitor JobsioLuminate: Tasks Job Monitorlements: Tasks Monitor Jobs

the failed job in the table, and click Postmortem.ostmortem panel opens.

r data is not sensitive and you can send it, select Include structures and deselectatically obfuscate path names.

Create.

hive file is created in your working directory, and an information dialog box withme of the file opens. You can highlight and copy the name of the file.


and paste any log messages from the window used to start the interface or the jobe email message, or attach them as a file.

indows: Right-click in the window and choose Select All, then press ENTER toopy the text.

Getting Help

Schrdinge40

Mac: Start the Console application (Applications Utilities), filter on the applica-tion that you used to start the job (Maestro, BioLuminate, Elements), copy the text.

If Maestro failed:

1. Open

W M L

2. When

A dial

3. Attach

4. Attach

The fi

Wind(ChooAttach

Mac: (Go Attach

LinuxAttach

r Software Release 2013-3

the Diagnostics panel.

indows: Start All Programs Schrodinger-2013-3 Diagnostics ac: Applications SchrodingerSuite2013-3 Diagnostics

inux/command line: $SCHRODINGER/diagnostics the diagnostics have run, click Technical Support.

og box opens, with instructions. You can highlight and copy the name of the file.


the error files your e-mail message.

les should be in the following location:

ows: %LOCALAPPDATA%\Schrodinger\appcrash se Start Run and paste this location into the Open text box.) maestro_error_pid.txt and maestro.exe_pid_timestamp.dmp.

$HOME/Library/Logs/CrashReporter Home Library Logs CrashReporter) maestro_error_pid.txt and maestro_timestamp_machinename.crash.

: $HOME/.schrodinger/appcrash maestro_error_pid.txt and crash_report_pid.txt.

IndexAactive-site cavity ................................................. 1adding hydrogens .............................................. 28all-atom force field.............................................. 1analysis task

Bbinding energbonds, coval

Ccavity, activeclose contactcommand linconventions,

Ddirectory

installatiMaestro

Eenvironment

SCHRODI

Ffitting task ...

example.overview

force field ....format convefree energy p

Hhydrogen tre

Iidentical cha

LLiaison pane

AnalysisParamete

Systems tab........................................... 12, 31license, LigPrep ................................................ 26LigPrep ....................................................... 2627linear-response (LR) methods............................. 2Liaison 6.1 User Manual 41

...................................................... 29

y model ......................................... 4ent, to receptor .............................. 25

site ................................................. 1s .................................................... 24e, running Liaison from ............... 35 document........................................ v

on .................................................... 5working........................................... 5

variableNGER .............................................. 5

........................................................ 1

...................................................... 15..................................................... 30.................................................. 1, 33rsion, to Maestro .......................... 28erturbation (FEP) ........................... 2

atment ........................................... 28

ins ................................................. 22

l tab .......................................... 15, 34rs tab ............................................ 33

LRM binding energy model................................ 4

Mmetalloproteins, charge and protonation states. 26metals

adjusting charges ........................................ 22coordination of ligands to........................... 26covalent bonds to protein............................ 22

multimeric protein structures ............................ 21

OOPLS-AA force fields ........................................ 1overview of protein preparation........................ 21

PParameters tab, Liaison panel ........................... 33Plot XY panel ................................................... 18prediction task..................................................... 1

example ...................................................... 18overview ..................................................... 30

product installation ........................................... 38protein

adjustment of structure ............................... 22misprotonation of ....................................... 24

protein preparation, overview ........................... 21protonation state................................................ 25

SSchrdinger contact information ...................... 38simulation method ............................................ 32simulation task .................................................. 29solvation model............................................. 4, 33Strike....................................................... 1, 29, 34

Build QSAR Model panel .......................... 16Predict based on QSAR model panel ......... 19

structuresformat conversion ....................................... 28requirements ............................................... 25

Surface Generalized Born (SGB) solvent model 4Systems tab, Liaison panel ............................... 31

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