PSI Structural Genomics Knowledgebase
Search online for protein sequences,
structures, functions, methods, and more
Margaret Gabanyi, PhD
comments@psi-structuralgenomics.org
SGKB
http://kb.psi-structuralgenomics.org/KB/
Knowledgebase
The Structural Genomics Knowledgebase is a free online
resource that integrates the products of SB and SG efforts with
key biological resources to enable a structural view of biology.
A Gateway to SB and SG information
  Database
searchable by
sequence, text, and
PDB ID
  Structural
Genomics Gateway
with Nature delivers
research advances,
technologies, news
and events related
to the structural
genomics and
biology
What’s in the SGKB?
SGKB
I. Searching the PSI SGKB
for protein information
SGKB
http://kb.psi-structuralgenomics.org/KB/
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
  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
Matching/Similar Structures
In the Structures tab:
  View matching
sequence alignment
  View structure entry
details
  ‘Mouse-over’ Chain
ID to view which
sources have
information
  Launch FirstGlance
to view the protein
structure
  Explore protein
annotations list
SGKB
Structures Tab - Annotations List
Gene-level features: gene identifiers and synonyms,
operon/regulon mappings, model organism databases
Protein-level features: amino acid sequence, taxonomy &
phylogeny, SNPs, post-translational modifications, and
sequence families and motifs.
Structure features: secondary structure, oligomeric state, structure and
functional domains, sites of interaction, experimental details (source/host)
Functions: enzyme class, substrate specificity and catalysis, epitope
mapping
Localizations: cellular location, organ location, 2D-PAGE databases
Pathways: protein interaction, pathway, and network databases
Medicine: pharmacological and medical databases
References: links to PubMed by database identifier and related text and
authors, keywords
Information from more than 150 resources
SGKB
Models Tab
data from www.proteinmodelportal.org (SIB)
SGKB
Protein Models Portal
PMP calculates and stores over
3.2M pre-built theoretical models
www.proteinmodelportal.org
SGKB
Targets Tab
data from targetdb.pdb.org
Protocols Tab
data from pepcdb.pdb.org
Materials Tab
PSI Material Repository, psimr.asu.edu
Conducting a Text Search
Searching by text returns:
  Annotation database
  Highlights from NPG
  Publications portal
  PSI Center web pages
  Structures and associated articles   Technology portal (improved)
kb-beta.psi-structuralgenomics.org/KB/
Text Search Results
SGKB
Search from any SG Update Page
  Research Advances
Editorials about
recent structure and
technological results
  Featured Molecule
A PSI structure
highlight with
interactive views
  Research Library
Catalog of papers
about the structural
determination
pipeline
  News
  Events Calendar
Other tools and features
  The Structural Genomics Update provides a collection
of PSI and broader research highlights, news, and
events in collaboration with the Nature Publishing Group
(tutorial)
  RSS feeds (via the Nature e-alert service)
  Target Sequence Comparison and Analysis tools
  Functional Sleuth – gallery of protein structures with
uncharacterized functions
  Technology Portal – lists of useful servers for your
research
SGKB
Homework: Tutorial to explore the 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
For Further Information
Protein Structure Initiative
http://www.nigms.nih.gov/initiatives/PSI
PSI Material Repository
http://psimr.asu.edu
PSI Structural Genomics Knowledgebase
http://kb.psi-structuralgenomics.org/KB/
http://kb-beta.psi-structuralgenomics.org/KB/
PSI SGKB Tutorial
http://kb.psi-structuralgenomics.org/KB/KB-Tour.html
Questions? comments@psi-structuralgenomics.org