Veerasamy Ravichandran

The Protein Data Bank

The Protein Data Bank (PDB; http://www.rcsb.org/pdb/ ) is the single worldwide archive of structural data of biological macromolecules. This paper describes the goals of the PDB, the systems in place for data deposition and access, how to obtain further information, and near-term plans for the future development of the resource.

The Protein Data Bank: unifying the archive

The Protein Data Bank (PDB; http://www.pdb.org/) is the single worldwide archive of structural data of biological macromolecules. This paper describes the progress that has been made in validating all data in the PDB archive and in releasing a uniform archive for the community. We have now produced a collection of mmCIF data files for the PDB archive (ftp://beta.rcsb.org/pub/pdb/uniformity/data/mmCIF/). A utility application that converts the mmCIF data files to the PDB format (called CIFTr) has also been released to provide support for existing software.

The PDB data uniformity project

The Protein Data Bank (PDB; http://www.rcsb.org/pdb/) is the single worldwide archive of structural data of biological macromolecules. This paper describes the data uniformity project that is underway to address the inconsistency in PDB data.

Toward data standards for proteomics.

Biologists have traditionally worked with relatively small data sets and shared results only with others working on similar biological systems. With the advent of genomics, and now proteomics, they are faced with exponentially growing sets of highly interrelated, heterogeneous, complex and rapidly evolving types of data. The lack of cohesion between heterogeneous proteomics data, resulting from the diverse structure and organization of independently produced data sets, poses a serious problem for progress in the field. We argue here that the adoption of consensus standards for the interpretation, handling and dissemination of specific types of protein data should be a priority for the proteomics community.

HIV protease structural database

HIV Protease Database (HIVdb) is a repository for those structures of HIV protease that have never been released or deposited to the Protein Data Bank (PDB). Together with the official PDB data, HIVdb provided a unique source of information in a statistical sense. The database contains 207 structures; 148 taken from PDB, and 59 that are unique entries in HIVdb. Query tools in terms of the creation of ensembles for statistical analysis were designed. We present a new form, location, tools and data form of the HIV Protease Database. The new tools utilize a standard PDB user interface, but provide extra capabilities connected exclusively with this one protein and its ligands. We also present a design strategy for a specific subset or sub-database of the PDB with the aim of pointing out the statistical dimension of the problem related to a single protein structure. We are currently annotating the ligands in order to include their chemical properties. This approach emphasises large scale databases and scalability.