Margaret Gabanyi

The protein structure initiative structural genomics knowledgebase

The Protein Structure Initiative Structural Genomics Knowledgebase (PSI SGKB, http://kb.psi-structuralgenomics.org) has been created to turn the products of the PSI structural genomics effort into knowledge that can be used by the biological research community to understand living systems and disease. This resource provides central access to structures in the Protein Data Bank (PDB), along with functional annotations, associated homology models, worldwide protein target tracking information, available protocols and the potential to obtain DNA materials for many of the targets. It also offers the ability to search all of the structural and methodological publications and the innovative technologies that were catalyzed by the PSIs high-throughput research efforts. In collaboration with the Nature Publishing Group, the PSI SGKB provides a research library, editorials about new research advances, news and an events calendar to present a broader view of structural biology and structural genomics. By making these resources freely available, the PSI SGKB serves as a bridge to connect the structural biology and the greater biomedical communities.

The Structural Biology Knowledgebase: a portal to protein structures, sequences, functions, and methods.

The Protein Structure Initiative’s Structural Biology Knowledgebase (SBKB, URL: http://sbkb.org) is an open web resource designed to turn the products of the structural genomics and structural biology efforts into knowledge that can be used by the biological community to understand living systems and disease. Here we will present examples on how to use the SBKB to enable biological research. For example, a protein sequence or Protein Data Bank (PDB) structure ID search will provide a list of related protein structures in the PDB, associated biological descriptions (annotations), homology models, structural genomics protein target status, experimental protocols, and the ability to order available DNA clones from the PSI:Biology-Materials Repository. A text search will find publication and technology reports resulting from the PSI’s high-throughput research efforts. Web tools that aid in research, including a system that accepts protein structure requests from the community, will also be described. Created in collaboration with the Nature Publishing Group, the Structural Biology Knowledgebase monthly update also provides a research library, editorials about new research advances, news, and an events calendar to present a broader view of structural genomics and structural biology.

The Protein Structure Initiative Structural Biology Knowledgebase Technology Portal: a structural biology web resource

The Technology Portal of the Protein Structure Initiative Structural Biology Knowledgebase (PSI SBKB; http://technology.sbkb.org/portal/) is a web resource providing information about methods and tools that can be used to relieve bottlenecks in many areas of protein production and structural biology research. Several useful features are available on the web site, including multiple ways to search the database of over 250 technological advances, a link to videos of methods on YouTube, and access to a technology forum where scientists can connect, ask questions, get news, and develop collaborations. The Technology Portal is a component of the PSI SBKB (http://sbkb.org), which presents integrated genomic, structural, and functional information for all protein sequence targets selected by the Protein Structure Initiative. Created in collaboration with the Nature Publishing Group, the SBKB offers an array of resources for structural biologists, such as a research library, editorials about new research advances, a featured biological system each month, and a functional sleuth for searching protein structures of unknown function. An overview of the various features and examples of user searches highlight the information, tools, and avenues for scientific interaction available through the Technology Portal.

Data to knowledge: how to get meaning from your result

This paper presents a variety of techniques and technologies aimed at the transformation of crystallographic data into information and knowledge.

Protein Structure Annotation Resources

A key reason three-dimensional (3-D) protein structures are annotated with supporting or derived information is to understand the molecular basis of protein function. To this end, protein structure annotation databases curate key facts and observations, based on community-accepted standards, about the ~100,000 3-D experimental protein structures to date. This review will introduce the primary structure repositories, databases, and value-added structural annotation databases, as well as the range of information they provide. The different levels of annotation data (primary vs. derived vs. inferred) and how they should all be considered accordingly will also be described.

BioSync: an online resource for X-ray facilities worldwide

The BioSync website (biosync.sbkb.org) has served as a technical resource for the structural biology community for over 25 years. BioSync provides curated information on 150+ worldwide high-energy (synchrotron) beamlines that support measurements on biological samples. BioSync also serves as an important annotation resource for the PDB by helping connect released PDB entries to the facilities from which the data were collected. BioSync is used by researchers, beamline scientists, and funding agencies from around the world.

Structural Biology Knowledgebase: An Integrated Resource for Modern Biologists

1 Rutgers University, Center for Integrative Proteomics Research, Piscataway, NJ, USA, 2 Lawrence Berkeley National Laboratory, Physical Biosciences Division, Berkeley, CA, USA, 3 The Commonwealth Medical College, Basic Sciences Department, Scranton, PA, USA, 4 University of Basel & Swiss Institute of Bioinformatics, BioZentrum, Basel, Switzerland, 5 University of Virginia, Department of Molecular Physiology and Biological Physics, Charlottesville, VA, USA

The Structural Biology Knowledgebase - search Online for Protein Sequences, Structures, Functions, Methods and More

The Structural Biology Knowledgebase (SBKB, URL: http://sbkb.org) is a free online resource designed to combine all protocols and results of the structural genomics and structural biology efforts with information from the biological community in order to have a better understanding living systems and disease. We will present examples of how to navigate the SBKB and how to use it to enable biological research. For example, a protein sequence or PDB ID search will provide a list of protein structures from the Protein Data Bank, associated biological descriptions (annotations), homology models, structural genomics protein target information, experimental protocols, and the ability to order available DNA clones. A text search will find technology reports and publications that were created by the Protein Structure Initiatives high-throughput research efforts. Web tools that aid in bench top research, such as the Sequence Comparison and Analysis tool for protein construct design, will also be demonstrated. Created in collaboration with the Nature Publishing Group, the Structural Biology Knowledgebase Gateway provides a research library, editorials about new research advances, news, and an events calendar also present a broader view of structural genomics and structural biology.The SBKB is funded by the Protein Structure Initiative/NIGMS.