 |
 |
Protein Data Bank in Europe : Site mapDepositing data at the PDBeThe primary role we perform as a member of the wwPDB is as a deposition site for structural biologists. We therefore provide services for depostion of different experiments : Macromolecular crystallography PDB AutoDep Electron microscopy EMDep Looking for information about our resourcesYou are reading our site map page, we also have various web pages on Documentation and Resources of the PDBe. You might find a number of tutorial pages useful too, these have a number of worked examples for both different services and real research analysis. The PDBe groupThe PDBe group is a member of of the wwPDB and is involved with collecting data, storing the data and services to return information. Other partners of the wwPDB are RCSB, PDBj and the BMRB for NMR data; EM data being part of a new initiative handled at the PDBe. Underlying our work is the PDBe database but also we are involved with standards such as mmCIF dictionary , XML standards for macromolecules, and OraCIF data exchange.How to use our servicesWe have a huge array of services so have a number of documentation resources on using these.What search services we provideWe provide an array of different services for the analysis of protein structure data. General searchIf you are looking for a general search of structure data then we recommend you try PDBelite which is a simple text based search system. If this is too limited then PDBepro provides a graphical interface based on a logical AND, OR and NOT queries for the general structure search.ChemistryIf you are interested in the interaction of ligands (drugs, inhibitors and other small molecules) bound to macrmolecular structure (active sites) then we recommend you use PDBeMotif. This service also includes a vast array of other functionality based on protein structure motifs, ligands and sequences. Please note, these services only acts on data actually deposited and do not provide drug design functionality. If your interest is chemistry entities we provide a rich data dictionary PDBechem of small molecules found within the PDB archive. We also have a much broader searchable chemical library of about 1 million molecules that is cross references to many external resources as PDBeChemSearch. In addition we provide a research-lead tool based on active sites found using discovery driven data mining; or your own spatial arrangement of amino acids PDBeTemplate. You can search the PDB for an arrangment of residues (template) or label protein molecules with templates.Protein Fold and AssembliesWe provide a number of services on protein structures and their interactions. The first, PDBeFold is a fast and sensitive tool for structure alignment that returns similar structure(s) to the query structure. Second we have services that look at protein quartinary structure. These are based on the native deposited data, i.e. structures determined by crystallography which are deposited as an assymmetric unit are converted to assemblies using mathematical analysis of interfaces - hypothetical in vivo protein quartinary structure. PQS PQS is an older, but still useful service which we are in the process of replacing with PDBePisa that uses an improved energy function. The Pisa service additional provides information on interfaces between protein chains.Statistical analysis of structureIf you wish to look at statistical properties of macromolecular structure data then we provide tools that look directly at our relational database. There services are collected together under PDBeAnalysis and include methods to validate protein structure, to view entry, residue and atomic statistics. Additional to these a tool is provided is to directly query the PDBe relational DB using SQL PDBeDatabase; to help you get started the SQL cross compiler from the PDBeAnalysis tools will drop the SQL from the analysis tools directly into PDBeDatabase for you to view and edit.Links to sequence, and new PDB dataWe have mapping services PDBeMapQuick that allows you to find how to go between protein structure and other databases/data (UNPROT, CATH, SCOP, GO, PFAM, EC, InterPro, NCBI-taxonomy). Ths is made possible by weekly analysis done by the PDBe and UNIPROT groups which maps data at the residue level for every protein structure to the sequence data (results where available). We also provide detail of the release cycle of new structures PDBstatus, what are the new structures this week PDB New Entries, NMR data analysis Olderado and a useful tool bar for you browser to quickly return structure data references BIObar.Funding and other adminstration informationWe are funded by a number of different organisations since all data and information is provided to anyone at no cost; this funds not just our core deposition work and services but also a number of projects. We have written a number of publications that cover various aspects of the work done at the PDBe. Finally, we have presented a number of workshops while future events and news can be viewed in these linked pages.
Document mantained by: Gaurav Sahni |
|