The PDB-Preview database: a repository of in-silico models of 'on-hold' PDB entries
نویسندگان
چکیده
UNLABELLED The PDB-Preview database is a dynamic web repository of in-silico predicted three-dimensional (3D) models of experimentally determined structures that are deposited into the PDB but are not yet publicly released, and are kept 'on-hold'. The PDB-Preview database is automatically generated on a weekly basis by the bioinfo.pl meta-server, which uses top-of-the-line fold-recognition methods. The PDB-Preview provides biologists with preliminary fold assignments well before the experimentally determined 3D structures are released. AVAILABILITY http://bioinfo.pl/PDB-Preview/.
منابع مشابه
BALBES: a molecular-replacement pipeline
The number of macromolecular structures solved and deposited in the Protein Data Bank (PDB) is higher than 40 000. Using this information in macromolecular crystallography (MX) should in principle increase the efficiency of MX structure solution. This paper describes a molecular-replacement pipeline, BALBES, that makes extensive use of this repository. It uses a reorganized database taken from ...
متن کاملMapping PDB chains to UniProtKB entries
MOTIVATION UniProtKB/SwissProt is the main resource for detailed annotations of protein sequences. This database provides a jumping-off point to many other resources through the links it provides. Among others, these include other primary databases, secondary databases, the Gene Ontology and OMIM. While a large number of links are provided to Protein Data Bank (PDB) files, obtaining a regularly...
متن کاملPDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003
PDB-REPRDB is a database of representative protein chains from the Protein Data Bank (PDB). Started at the Real World Computing Partnership (RWCP) in August 1997, it developed to the present system of PDB-REPRDB. In April 2001, the system was moved to the Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST) (http://www.cbrc.jp/); ...
متن کاملThe ConSurf-DB: pre-calculated evolutionary conservation profiles of protein structures
ConSurf-DB is a repository for evolutionary conservation analysis of the proteins of known structures in the Protein Data Bank (PDB). Sequence homologues of each of the PDB entries were collected and aligned using standard methods. The evolutionary conservation of each amino acid position in the alignment was calculated using the Rate4Site algorithm, implemented in the ConSurf web server. The a...
متن کاملProteins of Unknown Function in the Protein Data Bank (PDB): An Inventory of True Uncharacterized Proteins and Computational Tools for Their Analysis
Proteins of uncharacterized functions form a large part of many of the currently available biological databases and this situation exists even in the Protein Data Bank (PDB). Our analysis of recent PDB data revealed that only 42.53% of PDB entries (1084 coordinate files) that were categorized under "unknown function" are true examples of proteins of unknown function at this point in time. The r...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
عنوان ژورنال:
- Bioinformatics
دوره 20 15 شماره
صفحات -
تاریخ انتشار 2004