helen m. berman, rutgers university embo practical course section: searching structure databases...
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Helen M. Berman, Rutgers UniversityEMBO Practical Course
Section: Searching Structure Databases
September 26, 2008
PSI Structural Genomics Knowledgebase
Kn
ow
ledg
ebase
SGKB
Knowledgebase Vision
The PSI Structural Genomics Knowledgebase (PSI SGKB) will turn the products of the PSI effort into major advances in knowledge that can be used to understand living systems and human disease.
It will be a key resource for the advancement of biology, biochemistry, functional genomics, pharmacology, bioinformatics, chemistry, education and clinical medicine.
SGKB
Knowledgebase Goals
To provide a “marketplace of ideas” that connects protein sequence information to 3D structures and
homology models enhances functional annotations provides access to new experimental protocols and materials
To kick start and enable advancements in structural genomics by communicating and providing visibility and accessibility of
information and technology advances of the PSI through presentation and discussion of the most provocative
challenges with the general community by fostering community collaborations
SGKB
PSI SGKB features
Database searchable by sequence, text, and PDB ID Search results include aggregate reports and
inventories Links to PSI projects, external resources, and
publications SG Gateway with Nature delivers featured articles,
PSI news and events, featured molecules and technologies, molecules of unknown function and broader SG content
Notification to public about recently solved PSI structures or new editorial content
SGKB
To capture, make accessible, and highlight elements of the high-throughput pipelines for use by various scientific communities
To leverage such information through the generation of molecular models and functional annotation
Scope
GenomicBased Target
Selection
DataCollection
StructureDetermination
Isolation, Expression,Purification,
Crystallization
PDB Deposition & Release
ModelsAnnotationsPublications
Metrics
Technology
Experimental Tracking
Target Selection Materials
SGKB
Knowledgebase Users
Biologists Biochemists Functional Genomicists Pharmacologists Bioinformatics Chemists Clinical Researchers and
Physicians Teachers and Students
A Tour of the PSI SGKB
SGKB1
PSI SGKB Homepage
Receive e-mail alerts
Explore structures
of unknown function
View latest structures
& statistics
Teasers for this month’s editorial content
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Structural Genomics Update
Editorial content: Research Advances Featured Molecule Research Library News Events Calendar
Search Box
available
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About this site Additional help content (getting started), site map, contact
information, and terms of use
About PSI Information about the Protein Structure Initiative and the
PSI SGKB
PSI centers Links to the PSI Large-Scale and Specialized Centers
PSI Resources Links to a list of our Biomedical Protein Target themes,
Target Selection documentation, and the Modeling, Technology, Experimental Data Tracking, Materials, and Publications Resources
NPG Resources Links to the other Nature gateways, journals and other
resources provided by the Nature Publishing Group
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E-alerts: Receive news of PSI SGKB updates by email or RSS feed Updates to editorial content (monthly) Newly released structures (weekly)
Functional Sleuth: explore protein structures solved by the PSI whose functions are unknown
Latest PSI statistics
Provides current tallies of structures solved View detailed reports of which structures have
solved by the PSI (“Metrics”) View the latest structures solved by the PSI
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Functional Sleuth
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Metrics
I.1.A Number of novel experimental PSI-2 structures 1219
I.1.B Number of distinct experimental PSI-2 structures non-redundant sequences 1714
I.1.D Total number of experimental PSI-2 structures 1933
I.1.E Numbers of experimentally determined distinct residues 385746
Numbers of experimentally determined novel residues 268559
I.2.J Number of experimental structures of human proteins 71
I.2.K Number of experimental structures of eukaryotic proteins 206
I.2.M Number of experimental structures of membrane proteins 10
I.2.N Number of experimental structures determined at the atomic level using x-ray crystallography
1753
Number of experimental structures determined at the atomic level using NMR methods
180
PSI-2 Summary Statistics Updated Sept 5, 2008
novel structures - structures with less than 30% sequence identity to an existing structure at the time of PDB deposition distinct proteins - structures with non-redundant sequences less than 98% sequence identity
SGKB
See latest structures…
Searching the PSI SGKB
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Searching the PSI SGKB
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Searching the PSI SGKB
1
Begin your search here: By protein sequence By keyword (plain text) By structure (PDB ID)
All PSI SGKB data and resources are accessible from one central Search Box
SGKB
Sequence/PDBid search
Available structures of proteins with similar/identical amino acid sequences
Any structural and functional properties (annotation) determined from these protein structures
Available theoretical/homology models created with amino acid sequences similar to your query
Any information about similar protein sequences (targets) studied by the PSI structural genomics efforts
The protocols used during those PSI research efforts Ordering information to obtain DNA clone materials, if
available.
SGKB
Sequence/PDBid search
SGKB
Structures
In the Structures tab, experiment and reference information about the structure is displayed:
View matching sequence alignment and sequence identity Link to RCSB PDB’s Structure Explorer to learn more about
the structure View information about chemical substrates in the experiment
(bound ligands and substrates) Download the 3D atomic coordinates for the molecule If published, connect to its citation and abstract at PubMed.
SGKB
Structures
SGKB
Annotations
Genomic features: gene identifier, name and synonyms, operon/regulon mappings from databases Protein sequence features: amino acid sequence, taxonomy & phylogeny, isoforms, single nucleotide polymorphisms, post-translational modifications, and sequence families.Structure features: secondary structure, oligomeric state, structure and functional domains, DNA binding motifs, sites of interactionLigands: information about bound ligands Functional/Biochemical classifications: enzyme class, substrate specificity and catalysis, epitope mapping, cellular location, organ location Protein Networks and Biological Systems: enzymatic pathways and networks informationLiterature: synonyms for protein names, links to PubMed by database identifier and related text and authors
Information from more than 50 external annotation resources
SGKB
Annotations every annotation provided is a link to more content
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Future Annotations Layout
Quick Annotations Summarywill indicate available information
annotations will be organized by scientific category
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Models
In the Models tab, a list of the homology models available from the integrated Protein Models Portal are displayed
view the structural model, and interact with it in a Java window (AstexViewer)
download the model’s atomic coordinates view predicted domain annotations from databases such as
InterPro view sequence/domain annotations related to the template
structure, such as SCOP and CATH
SGKB
Models
AstexViewerlets you viewthe model
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Experimental Data Tracking
TargetDB contains worldwide structural genomics protein target information.
Search by sequence, Target ID, project site, status, update date, protein name, and source organism
Links to other sequence databases, domain databases, other structural genomics centers, and the RCSB PDB
Download target data Target statistics summary
PepcDB contains all the functionality of TargetDB plus
Experimental protocols Detailed status history of experimental trials Information on failed experiments
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TargetDB Search
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Experimental TrackingPepcDB search form
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Protocols from PepcDB
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Materials Repository
Directly order targets of interest
SGKB
Text Search
With a plain text search, find information from:
PSI Center web pages Publications resource Technology resource Annotation database
SGKB
Text Search
Site Search access web sites and files from10 PSI centers and the Technology Portal
SGKB
Text Search
Structure Publications records displays the PDB ID and the link to the RCSB PDB Structure Explorer page their doi and Pubmed identifier a link to the abstract
SGKB
Text Search
Annotations Text search may findannotations from the database if the text query is biological term
SGKB
Text Search
Methodology Publications their doi and Pubmed identifier a link to the abstract
SGKB
Technology Module
PSI Centers are actively developing technologies and methodologies for all aspects of the structure determination pipeline
FunctionalAnnotation
PublicationsGenomic
Based Target Selection
DataCollection
StructureDetermination
Isolation, Expression,Purification,
Crystallization
PDB Deposition & Release
SGKB
Technologies
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Publications to Date
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Acknowledgements
KB Group PSI Resources Wendy Tao Andrei Kouranov (Exp. Data Tracking)Raship Shah Torsten Schwede (Models)James Chun Paul Adams (Technology) Margaret Gabanyi Josh La Baer (Materials)Tom Oldfield Wladek Minor (Publications) John Westbrook
Access Informationhttp://kb.psi-structuralgenomics.org
NatureMatthew Day
Boyana Konforti
KB Steering CommitteeChair, Eaton Lattman