PSI Structural Biology Knowledgebase

PSI | Structural Biology Knowledgebase
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PSI and PSI SBKB Frequently Asked Questions

What is Structural Genomics (SG)?

Structural Genomics is the systematic determination of three-dimensional structures of proteins representative of the range of protein structure and function found in nature. The aim, ultimately, is to build a body of structural information that will facilitate prediction of a reasonable structure and potential function for almost any protein from knowledge of its coding sequence. Such information will be essential for understanding the functioning of the human proteome.

What is the Protein Structure Initiative (PSI)?

The Protein Structure Initiative (PSI) is a national research program in the emerging field of structural genomics. The PSI is a large-scale, high-throughput effort to increase the number of structures of unique, non-redundant proteins, permitting the study of a broad range of protein structures. This will be accomplished by a coordinated effort of federal, university, and industrial scientists to reduce costs, increase efficiency and success rates, and decrease the time for the production and determination of the three-dimensional atomic-level structures of proteins.

The third phase of this project, PSI:Biology, is a 5-year endeavor to join protein structure with biological function.

What is the PSI SBKB?

The Protein Structure Initiative Structural Biology Knowledgebase (PSI SBKB) is Resource Center within the PSI:Biology Program. The goal of the PSI SBKB is to integrate protein structures with all of the freely available biological information to enable a better understanding living systems and disease. The PSI SBKB web portal, this web site, is the top-level entry point for the Knowledgebase. This portal site integrates information from the PSI centers and a set of component modules focused key aspects of the PSI program. These include: protein target selection, experimental data tracking, materials archiving, comparative models, annotation, progress metrics, and technology developments.

What information is available from the PSI SBKB Portal and where does it come from?

PSI SBKB is an online portal to the resources of the Protein Structure Initiative program and the greated biological community. The portal provides:

  • A Structural Biology Update section which highlights recent developments in the field of structural biology and structural genomics
  • A query feature that integrates information from protein production and structure determination pipelines of the PSI Centers providing one-stop search and reporting functions for this information. Queries are provided for keyword, protein and nucleotide sequence, and PDB ID code.
  • Featured PSI molecules, written and illustrated by David Goodsell
  • Entry points to each of the PSI SBKB Modules for protein target selection, experimental data tracking, DNA materials archiving, comparative modeling, annotation, progress metrics, technology developments, and publications
  • A Functional Sleuth section which collects PSI structures that require further functional characterization and annotation 
  • Entry points to the PSI Center sites and general information about PSI programs
  • Entry points for PSI outreach, education and publications

What is the organization of the PSI Program?

As mentioned previously, the PSI:Biology Network is a joint government, academic, and industry effort. Adminstration of PSI:Biology, headed by PSI Director Ward Smith, PhD, resides at the National Institute of General Medical Sciences - one of the National Institutes of Health. The PSI network consists of three types of centers charged with different research themes - visit the PSI Centers page for more information.

What are the PSI SBKB Modules?

The SBKB is not an archive nor database, but a PORTAL to many publicly available databases.  Since there are many varied types of scientific data (seqeunce vs. methods vs. structures), several portal modules have been developed using the state-of-the-art techniques in their fields. 

These modules are:

  • Target Selection: The selection of protein targets for the PSI-2 program is coordinated by the Intercenter Bioinformatics team.
  • Experimental data tracking: TargetTrack tracks the progress of protein targets studied by PSI Centers. TargetTrack gives the status of each target, and also provides information about the protocols used for protein production and the reasons for stopping work on any target.
  • Archiving DNA Materials: The PSI Material Repository is responsible for storing and distributing clones. When the repository is fully operational, it will be possible to determine whether clones are available for any particular target.
  • Comparative Modeling: For every structure determined by the PSI Centers, hundreds of models can be made using a variety of computational methods. The Protein Model Portal gives access to pre-built models from PSI centers and also to models calculated from the contents of UniProt. The module is in collaboration with the Swiss Institute for Bioinformatics at the University of Basel.
  • Annotation: For each target, many different annotations are possible: structure determination and validation details; sequence information, including possible domain assignments; structure information, including surface characteristics, cavities, potential and actual active sites; fold classification; protein-protein interactions; protein-ligand interactions; structure function-relationships; and many others. Many of these annotations are available through the PSI centers and integrated into the SBKB.
  • Technology Innovation: The PSI Technology Portal provides summaries of key PSI technology innovations along with links to publications and detailed information about technologies within the PSI centers.
  • Progress Metrics: The Metrics Module calculates and distributes a variety success measures for the Protein Structure Initiative projects. This module provides a standardized means of counting experimental structures, assessing the impact of these experimental structures in the community, measuring the value of experimental structures in terms of structural models for related proteins, and estimating structural coverage for specific proteomes. These values, updated at the beginning of each month, can be viewed on the Metrics Summary Table.

Where can I find more information about the biomedical focus of the PSI Centers?

Each PSI Center is pursuing protein targets with a particular biomedical emphasis. Summaries of the biomedical themes for each PSI center can be found from the top-level Biomedical Themes menu item. The summaries for each center include lists of target protein sequences being pursued that are related to the biomedical focus area.

How do I find out if my protein of interest has an experimental structure?

Try the SBKB sequence search option. This search will identify similar sequences in experimental structures in the Protein Data Bank (PDB). Structures with matching or similar sequences will be reported, along with links to download the coordinate data files for the structures.

How do I find out if my protein of interest has a comparative model structure?

Try the SBKB sequence search option. This search will identify similar sequences in structures created by comparative modeling methods. Search results will provide links to the SBKB Proteing Model Portal, which provides further methodological details for each matching model structure and the coordinate download options.

How do I find out if my protein of interest is under investigation by one of PSI centers?

Try the SBKB sequence search option. This search will identify similar sequences in the protein production and structure determination pipelines of the PSI Centers. Experimental tracking information from TargetTrack for similar sequences is included in search results. This information will describe the experimental progress such as whether the protein has been expressed and purified. If experimental protocol information has been reported for the protein then links to this information will also be provided.

Can I suggest protein sequences to the PSI Centers for structural determination?

The PSI encourages target nominations for structure determination, which are vetted for feasibility and consistency with the overall PSI goals. Investigators can create an account and submit their target proposals using the Community Targets feature on the PSI SBKB, and a decision is usually received within one month. Proposals accepted for structure determination must adhere to the PSI rules, most notably that structural data, including, must be deposited in the public database, the PDB, within 4 weeks of completion of the structure.

Who do I contact about obtaining clones or protein samples?

The PSI Material Repository (PSI-MR) has the overall goal to take in, process, and sequence all PSI plasmid clones along with relevant information and distribute them via an ordering process that is easily accessible on-line.

How do I find out about the technologies developed by the PSI program?

Technology highlights from the PSI program are regularly featured on the SBKB home page. The PSI Technology Portal provides summaries of key PSI technology innovations along with links to publications and detailed information about technologies within the PSI centers.

How can I find publications from the PSI program?

Lists of publications from PSI Centers and publications related to the PSI program are regularly updated by the SBKB. You can visit the PSI Publications portal for a full list.

What can I find out about my protein by querying the PSI SBKB site?

The SBKB portal can be searched by protein sequence, PDB ID, or a keyword. Sequence and PDB ID query reports contain: experimental progress for the protein target, the protocols that have been used for protein production; characteristics of structures that have been determined; comparative models that have been generated or could be predicted; domain classifications using a variety of methods; functional and biomedical annotations. When a keyword query is performed, the reports contain links to documents at PSI Centers, PSI Modules, and the SBKB portal.

What future developments are planned for the SBKB?

Improvements to the way we handle queries and present the results is coming for SBKB and TargetTrack.  A protocol search will also become available before the end of 2013. 

Structural Biology Knowledgebase ISSN: 1758-1338
Funded by a grant from the National Institute of General Medical Sciences of the National Institutes of Health