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Unique identifier OMICS_21345
Name PDBSite
Restrictions to use None
Community driven No
Data access Browse
User data submission Not allowed
Version 1.0
Maintained Yes

Documentation


Maintainers


  • person_outline Vladimir A Ivanisenko
  • person_outline Nikolay Kolchanov

Publication for PDBSite

PDBSite citations

 (4)
library_books

Single‐residue posttranslational modification sites at the N‐terminus, C‐terminus or in‐between: To be or not to be exposed for enzyme access

2015
Proteomics
PMCID: 4745020
PMID: 26038108
DOI: 10.1002/pmic.201400633

[…] t” from UniProtKB provide comprehensive lists of known residue modifications. There are also databases for access to information about modified residues observed in 3D structures of proteins such as PDBsite , , AMASS and PTM‐SD . Software tools for analyzing the role of modified residues within the protein's 3D structure in molecular simulations are also available , , . Unrivalled, UniProtKB all […]

library_books

Predicting conserved protein motifs with Sub HMMs

2010
BMC Bioinformatics
PMCID: 2879284
PMID: 20420695
DOI: 10.1186/1471-2105-11-205

[…] and functionally insightful information about known or predicted active sites is provided by protein structure-based resources, such as the Catalytic Site Atlas (CSA), CASTp, ActSitePred, ConSurf and PDBSite [,-]. The utility spectrum of these structure-based resources is typically restricted to proteins that share sequence similarity with proteins of known 3D structure. This requirement of struct […]

library_books

FLORA: A Novel Method to Predict Protein Function from Structure in Diverse Superfamilies

2009
PLoS Comput Biol
PMCID: 2721411
PMID: 19714201
DOI: 10.1371/journal.pcbi.1000485

[…] otein structures being deposited in the PDB . Resources such as the Catalytic Site Atlas are carefully curated by hand and restricted to residues directly involved in catalysis, whereas MSDSite and PDBSite , generate templates based on active site residues defined in the PDB file by the authors. Although these resources are undoubtedly extremely valuable, it is questionable whether sufficient co […]

call_split

pi Turns: types, systematics and the context of their occurrence in protein structures

2008
BMC Struct Biol
PMCID: 2559839
PMID: 18808671
DOI: 10.1186/1472-6807-8-39
call_split See protocol

[…] lt conditions. To identify if a residue in a π-turn was important for the function of the protein we used the annotations in PDBSUM [], which uses CSA [] for the identification of catalytic residues, PDBSITE [] for the active-site residues and CONSURF [] for sequence conservation. CONSURF uses a color code based on the conservation score in the range 9 to 1 (9 being the most conserved and 1 the le […]

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PDBSite institution(s)
Institute of Cytology and Genetics SBRAS, Novosibirsk, Russia
PDBSite funding source(s)
Partly supported by the Russian Fund for Basic Research (03-04-48506-a, 03-07-90181-b and 03-07-96833-p2003); the Siberian Branch of the Russian Academy of Sciences (Integration Project No. 119); Russian Ministry of Industry, Science and Technologies (43.073.1.1.1501); the US Civilian Research & Development Fund for the Independent States of the former Soviet Union (CRDF); Rup2-2629-NO-04; the Basic Research and Higher Education (BRHE) program NO- 008-X1; Siberian Branch of the Russian Academy of Sciences (Project No. 10.4); and the State Contract of Federal agency on a science and innovations (01.106.11.0002).

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