Helen M. Berman, Rutgers UniversityEMBO Practical Course

Section: Searching Structure Databases

September 26, 2008

PSI Structural Genomics Knowledgebase

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ow

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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

SGKB1

Structural Genomics Update

Editorial content: Research Advances Featured Molecule Research Library News Events Calendar

Search Box

available

SGKB1

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

SGKB1

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

SGKB

Functional Sleuth

SGKB1

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

SGKB

Searching the PSI SGKB

SGKB

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

SGKB

Future Annotations Layout

Quick Annotations Summarywill indicate available information

annotations will be organized by scientific category

SGKB

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

SGKB

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

SGKB

TargetDB Search

SGKB

Experimental TrackingPepcDB search form

SGKB

Protocols from PepcDB

SGKB

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

SGKB

Publications to Date

SGKB

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