the computational method
Post on 15-Jul-2015
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introduction
The three-dimensional structure of a molecule is closely related to
a large variety of chemical, physical and biological properties.
The need for computer-generated 3D molecular structures has
clearly been recognized in drug design and many other areas.
Since the number of experimentally determined molecular
geometries is limited—about 600,000 X-ray structures
are presently contained in the Cambridge Structural Database ,
there is a need for methods to predicting 3D coordinates directly
from the constitution of a molecule.
intro. cont .
As a consequence, in the last three decades a number of programs
for automatic 2D-to-3D conversion have been reported , Among
them,
CORINA (Coordinates) CONCORD CHEM-X etc…
automatically generates three-dimensional coordinates for the
atoms of a molecule purely from its constitution of a molecule,
The program scope, its reliability, robustness and speed as well as
some special features for handling large rings and metal
complexes make it extremely useful for any study or modeling
purpose that requires 3D information of the molecules under
investigation
GENERATE ACCURATE 3D COORDINATES:CONCORDHistory: (Texas, 1987)
Concord is productivity tool useful for molecular modeling and QSAR/QSPR research
Concord is the oldest program generates 3Dstructures which are 100% consistent with the stereo-chemical specifications in the 2D input.
Advantages :
Fast, Accurate Structures : extremely rapid
Fast, Complete Conversions :• providing complete control regarding the quality of
structuresin 3D databases.
• Concord allows researchers to specify limits on molecular size, number of rotatable bonds, etc. and exclude compounds from the “conversion domain
• Concord typically converts over 99% of the structures in its conversion domain at an average rate of just 0.2 cpu_seconds per compound .
Concord provides many advantageous input/output options
MDL SD-files, SYBYL® mol and mol2 files, and Tripos’ SLNformats are supported.
The highly compact and easy-to-learn SMILES line-notation isanother very popular input format. Additional output formatsinclude
MOPAC, MM4, GAUSSIAN,PDB, CSSR, ORTEP, and customformats. To save time, two or more formats can be outputsimultaneously.
Concord requires a Concord software
license, and is accessible through the SYBYL
expert molecular modeling environment or
standalone. Concord runs on workstations
operating under IRIX® (SGI®) or Linux® (x86).
GASPTM
StereoPlex®
GeneFold®
FlexXTM
:StereoPlex
,
when coupled with Concord, enables the intelligent stereochemical diversification of a database.
•CORINA is applicable to the entire range of organic chemistry
•CORINA generates by default one low-energy conformation for each input structure. For rings consisting of less than nine atoms, multiple conformations can be generated—a useful feature for flexible 3D database search
Conversion Rate. CORINA rate (100%
Correctness of StereochemistryAll programs
except Chem-X (23 failures) retained
the stereochemistry of almost all stereocenters
Computation Time. CONCORD requires extremely short computation times (0.14s/mol), whereas MOLGEO, and COBRA need substantially larger times (3.49-8.98 s/mol). All other programs need times of less than 1 s/mol. The computationtimes refer to the number of structures converted by the different programs
:These quantity-qualitycharacteristics show again the different suitability of the seven programs for automatic2D-to-3D conversion.
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