Transcript 17_Gabanyi_pt2

How to Use the PSI Structural Genomics
Knowledgebase for Research
Part II: Demonstration
2009 NIGMS Workshop:
Enabling Technologies for Structural Biology
Section on Structural Analysis
Margaret J. Gabanyi
March 4, 2009
SGKB
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.
Latest PSI Structures and Statistics
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 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.
Sequence/PDB ID search and results
 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
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