how to use the psi structural genomics knowledgebase for research part ii: demonstration

SGKB

2009 NIGMS Workshop: Enabling Technologies for Structural Biology

Section on Structural Analysis Margaret J. Gabanyi

March 4, 2009

How to Use the PSI Structural Genomics Knowledgebase for Research

Part II: Demonstration

The PSI SGKB homepage makes many features available from one central place.

The Structural Genomics Update provides a collection of PSI and broader research highlights, news, and events in collaboration with the Nature Publishing Group

About this site

About this site contains instructions, FAQs, and also academic exercises on how to use the SGKB.

URL: http://kb.psi-structuralgenomics.org/KB/KB-Tour.html

About PSI

PSI Policies, Reports, administrative, and funding opportunities are located on the About PSI site.

PSI Centers

The PSI centers menu shows information about the PSI-2 Network centers, their objectives, and a link to their homepages.

PSI Resources

In addition to the search function, you can visit each of the PSI resources individually. Links point to more information about the resource and its homepage.

PSI Resource: Technology Portal

NPG Resources

Links to Nature resources, such as the Nature Gateways, NPG Journals, and bookmarking and blog tools are also made available here.

Subscribe to RSS feeds

Users can subscribe to E-alerts and RSS (Really Simply Syndication) feeds to automatically receive notice of PSI SGKB content and latest structure updates

Functional Sleuth

In Functional Sleuth, we present protein structures determined by the PSI structural genomics efforts whose further functional analysis is required.

Functional Sleuth

Community-Nominated Targets

The greater scientific community is invited to submit protein target nominations for structure determination using the Community-Nominated Targets proposal system.

You can see latest structures solved by the PSI Centers; this list can also be delivered to your browser weekly using a (Really Simple Syndication) RSS feed.

Latest PSI Structures and Statistics

Latest PSI Statistics

Structural Genomics Update

Research Advances Editorials about recent structure and technological results

Featured Molecule Detailed explanation about a PSI structure

Research Library Catalog of PSI and other papers about the protein production and structural determination pipeline

News

Events Calendar

Research Advances

Editorials about recent Research Advances such as new structures and technical highlights are provided by the Nature Publishing Group

Research Advances

Research Advances editorials contain links that directly query the PSI SGKB, and the main search box is available to query other topics.

Featured PSI Molecule

Each month, the Featured PSI Molecule gives a detailed portrait of a biological molecule solved by the PSI structural genomics efforts.

Featured PSI Molecule

The Featured PSI Molecule is an article about a PSI structure written by David Goodsell in his easily accessible style.

Research Library

The Research Library is a catalog of all PSI and other publications to date related to the protein production and structure determination pipeline. Structural and functional reports are found here as well.

Research Library

News and Events Calendar

To present a broader update on recent scientific advances, we provide the latest News from the Protein Structure Initiative, Nature News and other NPG publications.

An Events Calendar keeps the community in touch with upcoming conferences, events, and workshops that promote a structural view of biology.

Available structures of proteins with similar/identical amino acid sequences

Any structural and functional properties (annotation) determined from these protein structures

Homology models created for/with your query sequence

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

Sequence/PDB ID search and results

Structures Tab

Annotations Tab

Models Tab

Targets Tab

Protocols Tab

Materials Tab

Text Search

With a plain text search, gain access to information from: PSI Center web pages Publications resource Technology resource Annotation database

Text search results

For Further Information

PSI SGKB

http://kb.psi-structuralgenomics.org

PSI SGKB Tutorial

http://kb.psi-structuralgenomics.org/KB/KB-Tour.html

PSI SGKB Tutorial with classroom exercises

http://kb.psi-structuralgenomics.org/KB/KB-Tutorial.html