SGKB

2009 NIGMS Workshop:Enabling Technologies for Structural Biology

Section on Structural AnalysisHelen M. Berman

March 4, 2009

How to use the PSI Structural Genomics Knowledgebase for Research

Part I: Introduction

Kn

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ebase

The PSI Structural Genomics Knowledgebase will turn the products of the PSI effort into major advances in knowledge that can be used to understand living systems and human disease.

Knowledgebase Goals

It will 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

It will 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

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

Knowledgebase Users

Biologists Biochemists Functional Genomicists Pharmacologists Bioinformatics Chemists Clinical Researchers and

Physicians Teachers and Students

Navigating the PSI SGKB Homepage

Database searchable by sequence, text, and PDB ID and delivers aggregate reports, inventories

Links to PSI projects, external resources, and publications

Link to central Community-Nominated Targets Proposal system

SG Gateway with Nature delivers research findings, technologies, news and events related to the PSI and structural genomics

Publicizes recently solved PSI structures or new editorial content

Tour of the PSI SGKB

In today’s tutorial, we will demonstrate:

How to navigate the site and its interactive features

How to search the PSI SGKB for information

How to find walkthroughs and exercises about this site

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)John Westbrook Wladek Minor (Publications)

Access Informationhttp://kb.psi-structuralgenomics.org

NatureMatthew Day

Boyana Konforti

SGKB

PSI SGKB Steering CommitteeEaton E. Lattman, Chair