PDB-REPRDB
PDB-REPRDB is a reorganized database of protein chains from PDB(Protein Data Bank), and provides 'the list of the representative protein chains' and 'the list of similar protein chain groups'.
Description
More detailed information about this field from each metasource.
PDB-REPRDB is a reorganized database of protein chains from PDB(Protein Data Bank), and provides 'the list of the representative protein chains' and 'the list of similar protein chain groups'.
metasource: Fairsharing.orgversion: FAIRsharing.org: PDB-REPRDB; PDB-REPRDB; DOI: https://doi.org/10.25504/FAIRsharing.k4sp7m; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
PDB-REPRDB is a database of representative protein chains from the Protein Data Bank (PDB) (1). Criteria used to select representatives are: a) quality of atomic co-ordinate data, b) sequence uniqueness, and c) conformation uniqueness. The system of PDB-REPRDB (2,3) is designed so that the user may obtain a quick selection of representative chains from PDB. System operation can be divided into two stages: 1) calculation of similarities between all pairs of protein chains, 2) classification of those chains and selection of representative chains according to priorities specified by the user. Similarities are calculated beforehand, and selection of representative chains can be dynamically configured according to the user's requirement. The WWW interface provides a large degree of freedom in setting parameters, such as cut-off scores of sequence and structural similarity. Users can eliminate unnecessary chains from the PDB chain list by setting threshold values and can also change priority of nine factors: resolution, R-factor, number of chain breaks, ratio of non-standard amino acid residues, ratio of residues with only Ca co-ordinates, ratio of residues with only backbone co-ordinates, number of residues, whether mutant or wild, and whether complex or not. Moreover, users can select whether or not to include entries by NMR experimental techniques and whether or not to include membrane protein chains by setting a flag of NMR and membrane, respectively. The membrane flag was introduced into the system in September 2002. One can obtain a representative list and classification data of protein chains from the system. The representative list includes information about factors mentioned above, EC number, and compound in PDB. The 'eID' sections are hyper-linked to data on classified groups, and a graphic representation of three-dimensional structure can be displayed using the RasMol program by clicking on 'e'. Furthermore, 'eEcnumber' sections are hyper-linked to the Ligand chemical database for enzyme reactions (LIGAND) (4). The system is available at the new PDB-REPRDB WWW server (http://www.cbrc.jp/pdbreprdb/).
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
Webpage:
http://www.cbrc.jp/pdbreprdb/Webpage
More detailed information about this field from each metasource.
http://www.cbrc.jp/pdbreprdb/
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
http://mbs.cbrc.jp/pdbreprdb-cgi/reprdb_menu.pl
metasource: Fairsharing.orgversion: FAIRsharing.org: PDB-REPRDB; PDB-REPRDB; DOI: https://doi.org/10.25504/FAIRsharing.k4sp7m; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Licence:
Name: NIH Web Policies and NoticesLicence name
More detailed information about this field from each metasource.
NIH Web Policies and Notices
metasource: Fairsharing.orgversion: FAIRsharing.org: PDB-REPRDB; PDB-REPRDB; DOI: https://doi.org/10.25504/FAIRsharing.k4sp7m; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Licence URL
More detailed information about this field from each metasource.
https://www.nih.gov/web-policies-notices
metasource: Fairsharing.orgversion: FAIRsharing.org: PDB-REPRDB; PDB-REPRDB; DOI: https://doi.org/10.25504/FAIRsharing.k4sp7m; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Publications:
Publications
More detailed information about this field from each metasource.
PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003
PMID: 12520060
metasource: Fairsharing.org
version: FAIRsharing.org: PDB-REPRDB; PDB-REPRDB; DOI: https://doi.org/10.25504/FAIRsharing.k4sp7m; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
Publications
More detailed information about this field from each metasource.
PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003
PMID: 12520060
metasource: Fairsharing.org
version: FAIRsharing.org: PDB-REPRDB; PDB-REPRDB; DOI: https://doi.org/10.25504/FAIRsharing.k4sp7m; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
-
PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003
PubMed citations: 27.
27 articles citing: PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB) in 2003
Data Mining and Systems Pharmacology to Elucidate Effectiveness and Mechanisms of Chinese Medicine in Treating Primary Liver Cancer. PMID:34432201
Gaussian network model can be enhanced by combining solvent accessibility in proteins. PMID:28790346
Expressing Redundancy among Linear-Epitope Sequence Data Based on Residue-Level Physicochemical Similarity in the Context of Antigenic Cross-Reaction. PMID:27274725
Proposal for a new therapy for drug-resistant malaria using Plasmodium synthetic lethality inference. PMID:24533301
Sequence-based Gaussian network model for protein dynamics. PMID:24336646
On the meaning of affinity limits in B-cell epitope prediction for antipeptide antibody-mediated immunity. PMID:23209458
pKNOT v.2: the protein KNOT web server. PMID:22693223
PredyFlexy: flexibility and local structure prediction from sequence. PMID:22689641
Deciphering the Arginine-binding preferences at the substrate-binding groove of Ser/Thr kinases by computational surface mapping. PMID:22125489
A series of PDB related databases for everyday needs. PMID:21071423
Effect of using suboptimal alignments in template-based protein structure prediction. PMID:21058297
Prediction of inter-residue contact clusters from hydrophobic cores. PMID:20802820
Intrinsically disordered regions may lower the hydration free energy in proteins: a case study of nudix hydrolase in the bacterium Deinococcus radiodurans. PMID:20657662
Prediction of protein long-range contacts using an ensemble of genetic algorithm classifiers with sequence profile centers. PMID:20487509
Prodepth: predict residue depth by support vector regression approach from protein sequences only. PMID:19759917
Protein elastic network models and the ranges of cooperativity. PMID:19617554
Translationally optimal codons associate with structurally sensitive sites in proteins. PMID:19349643
Sequence based residue depth prediction using evolutionary information and predicted secondary structure. PMID:18803867
Sequence-similar, structure-dissimilar protein pairs in the PDB. PMID:18004789
A reduced amino acid alphabet for understanding and designing protein adaptation to mutation. PMID:17565494
pKNOT: the protein KNOT web server. PMID:17526524
oGNM: online computation of structural dynamics using the Gaussian Network Model. PMID:16845002
Better prediction of protein contact number using a support vector regression analysis of amino acid sequence. PMID:16221309
Nh3D: a reference dataset of non-homologous protein structures. PMID:16011803
The N-terminal to C-terminal motif in protein folding and function. PMID:15657118
Mining frequent patterns in protein structures: a study of protease families. PMID:15262784
A Hidden Markov Model method, capable of predicting and discriminating beta-barrel outer membrane proteins. PMID:15070403
Tags:
Tags
More detailed information about this field from each metasource.
protein
metasource: Fairsharing.org
version: FAIRsharing.org: PDB-REPRDB; PDB-REPRDB; DOI: https://doi.org/10.25504/FAIRsharing.k4sp7m; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
protein structure
metasource: Fairsharing.org
version: FAIRsharing.org: PDB-REPRDB; PDB-REPRDB; DOI: https://doi.org/10.25504/FAIRsharing.k4sp7m; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
structure
metasource: Fairsharing.org
version: FAIRsharing.org: PDB-REPRDB; PDB-REPRDB; DOI: https://doi.org/10.25504/FAIRsharing.k4sp7m; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
polypeptide_region
metasource: Fairsharing.org
version: FAIRsharing.org: PDB-REPRDB; PDB-REPRDB; DOI: https://doi.org/10.25504/FAIRsharing.k4sp7m; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
structure databases
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
Tags
More detailed information about this field from each metasource.
protein
metasource: Fairsharing.orgversion: FAIRsharing.org: PDB-REPRDB; PDB-REPRDB; DOI: https://doi.org/10.25504/FAIRsharing.k4sp7m; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
protein structure
metasource: Fairsharing.orgversion: FAIRsharing.org: PDB-REPRDB; PDB-REPRDB; DOI: https://doi.org/10.25504/FAIRsharing.k4sp7m; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
metasource: Nucleic Acid Research database catalogue
version: extracted_at: 2022-11-04T11:16:25.468657
structure
metasource: Fairsharing.orgversion: FAIRsharing.org: PDB-REPRDB; PDB-REPRDB; DOI: https://doi.org/10.25504/FAIRsharing.k4sp7m; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
polypeptide_region
metasource: Fairsharing.orgversion: FAIRsharing.org: PDB-REPRDB; PDB-REPRDB; DOI: https://doi.org/10.25504/FAIRsharing.k4sp7m; Last edited: Jan. 8, 2019, 1:17 p.m.; Last accessed: Jan 03 2022 7:07 p.m.
structure databases
metasource: Nucleic Acid Research database catalogueversion: extracted_at: 2022-11-04T11:16:25.468657
protein protein structure structure polypeptide region structure
Need help integrating and/or managing biomedical data?