Download SGKB

PSI Structural Genomics Knowledgebase
Helen M. Berman, Rutgers University
EMBO Practical Course
Section: Searching Structure Databases
September 26, 2008
Knowledgebase
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
Scope
Experimental Tracking
Target Selection
Materials
Genomic
Based Target
Selection
Isolation,
Expression,
Purification,
Crystallization
Data
Collection
Structure
Determination
PDB Deposition
& Release
Models
Annotations
Publications
Technology
Metrics
 To capture, make accessible, and highlight elements of the highthroughput pipelines for use by various scientific communities
 To leverage such information through the generation of molecular
models and functional annotation
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Knowledgebase Users
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Biologists
Biochemists
Functional Genomicists
Pharmacologists
Bioinformatics
Chemists
Clinical Researchers and
Physicians
 Teachers and Students
SGKB
A Tour of the PSI SGKB
PSI SGKB Homepage
Receive
e-mail
alerts
Explore
structures
of unknown
function
Teasers for this
month’s editorial
content
View latest
structures
& statistics
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SGKB
Structural Genomics Update
Search
Box
available
Editorial content:
 Research Advances
 Featured Molecule
 Research Library
 News
 Events Calendar
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SGKB
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
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SGKB
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
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SGKB
Functional Sleuth
SGKB
Metrics
PSI-2 Summary Statistics
Updated Sept 5, 2008
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
 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
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than 98% sequence identity
SGKB
See latest structures…
SGKB
Searching the PSI SGKB
Searching the PSI SGKB
SGKB
Searching the PSI SGKB
All PSI SGKB data and resources are
accessible from one central Search Box
Begin your search here:
 By protein sequence
 By keyword (plain text)
 By structure (PDB ID)
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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.
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Sequence/PDBid search
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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.
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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 interaction
Ligands: 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 information
Literature: 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
 annotations will be
organized by scientific
category
Quick Annotations Summary
will indicate available information
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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
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Models
AstexViewer
lets you view
the 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
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TargetDB Search
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Experimental Tracking
PepcDB search form
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Protocols from PepcDB
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Materials Repository
Directly order
targets of interest
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Text Search
With a plain text search,
find information from:
 PSI Center web pages
 Publications resource
 Technology resource
 Annotation database
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Text Search
Site Search
access web sites and
files from
10 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
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Text Search
Annotations
Text search may find
annotations 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
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Technology Module
PSI Centers are actively developing technologies and
methodologies for all aspects of the structure determination
pipeline
Genomic
Based Target
Selection
Isolation,
Expression,
Purification,
Crystallization
Data
Collection
Structure
Determination
PDB Deposition
& Release
Publications
Functional
Annotation
SGKB
Technologies
SGKB
Publications to Date
SGKB
Acknowledgements
Access Information
http://kb.psi-structuralgenomics.org
KB Group
Wendy Tao
Raship Shah
James Chun
Margaret Gabanyi
Tom Oldfield
John Westbrook
PSI Resources
Nature
Matthew Day
Andrei Kouranov (Exp. Data Tracking)
Boyana Konforti
Torsten Schwede (Models)
Paul Adams (Technology)
KB Steering Committee
Josh La Baer (Materials)
Chair, Eaton Lattman
Wladek Minor (Publications)
SGKB