PCDB: a database of protein conformational diversity

Juritz, Ezequiel; Alberti, Sebastián; Parisi, Gustavo

doi:10.1093/nar/gkq1181

Cited by 26 publications

(22 citation statements)

References 43 publications

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“…Very few servers with similar functionality can be found in literature, such as the now defunct PCDB database of the same protein in multiple conformations ( 9 ) and its new incarnation, the CoDNaS database ( 10 ). However, neither PCDB nor CoDNaS provide any visualization nor any ways of analyzing the flexibility, providing only RMSD between different sets of coordinates.…”

Section: Introductionmentioning

confidence: 99%

PDBFlex: exploring flexibility in protein structures

Hrabe

Sedova

et al. 2015

Nucleic Acids Res

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The PDBFlex database, available freely and with no login requirements at http://pdbflex.org, provides information on flexibility of protein structures as revealed by the analysis of variations between depositions of different structural models of the same protein in the Protein Data Bank (PDB). PDBFlex collects information on all instances of such depositions, identifying them by a 95% sequence identity threshold, performs analysis of their structural differences and clusters them according to their structural similarities for easy analysis. The PDBFlex contains tools and viewers enabling in-depth examination of structural variability including: 2D-scaling visualization of RMSD distances between structures of the same protein, graphs of average local RMSD in the aligned structures of protein chains, graphical presentation of differences in secondary structure and observed structural disorder (unresolved residues), difference distance maps between all sets of coordinates and 3D views of individual structures and simulated transitions between different conformations, the latter displayed using JSMol visualization software.

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Section: Introductionmentioning

confidence: 99%

PDBFlex: exploring flexibility in protein structures

Hrabe

Sedova

et al. 2015

Nucleic Acids Res

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“…The approach employed in PeptiSite shares some similarity with those of PCDB,[59] PepX,[7] PepSite[6] or IEDB-3D[60], however, PeptiSite specifically focuses on the detailed analysis of the peptide binding sites. Besides identifying the constituents of the receptor-peptide binding sites, the subsequent processing of the PeptiSite ensembles creates accurate interaction maps between the binding site and the peptide ligand residues, quantifies cross-compatibility between pockets and ligands from different structures.…”

Section: Introductionmentioning

confidence: 99%

PeptiSite: A structural database of peptide binding sites in 4D

Acharya

Kufareva

Ilatovskiy

et al. 2014

Biochemical and Biophysical Research Communications

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We developed PeptiSite, a comprehensive and reliable database of biologically and structurally characterized peptide-binding sites, in which each site is represented by an ensemble of its complexes with protein, peptide and small molecule partners. The unique features of the database include (1) the ensemble site representation that provides a fourth dimension to the otherwise three dimensional data, (2) comprehensive characterization of the binding site architecture that may consist of a multimeric protein assembly with cofactors and metal ions (3) analysis of consensus interaction motifs within the ensembles and identification of conserved determinants of these interactions. Currently the database contains 585 proteins with 650 peptide-binding sites. http://ablab.ucsd.edu/~chayan/PeptiSite link allows searching for the sites of interest and interactive visualization of the ensembles using the ActiveICM web-browser plugin. This structural database for protein-peptide interactions enables understanding of structural principles of these interactions and may assist the development of an efficient peptide docking benchmark.

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“…Previous efforts to this end include compilation of databases of conformational changes (Gerstein and Krebs, 1998;Juritz et al, 2011;Li et al, 2015;Monzon et al, 2013) and their analysis (Kosloff and Kolodny, 2008). In addition, homologymodeling tools, such as Swiss-Model (Biasini et al, 2014) and ModBase (Pieper et al, 2014), use various templates and may capture a given query at different conformations.…”

Section: Introductionmentioning

confidence: 99%

ConTemplate Suggests Possible Alternative Conformations for a Query Protein of Known Structure

et al. 2015

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Protein function involves conformational changes, but often, for a given protein, only some of these conformations are known. The missing conformations could be predicted using the wealth of data in the PDB. Most PDB proteins have multiple structures, and proteins sharing one similar conformation often share others as well. The ConTemplate web server (http://bental.tau.ac.il/contemplate) exploits these observations to suggest conformations for a query protein with at least one known conformation (or model thereof). We demonstrate ConTemplate on a ribose-binding protein that undergoes significant conformational changes upon substrate binding. Querying ConTemplate with the ligand-free (or bound) structure of the protein produces the ligand-bound (or free) conformation with a root-mean-square deviation of 1.7 Å (or 2.2 Å); the models are derived from conformations of other sugar-binding proteins, sharing approximately 30% sequence identity with the query. The calculation also suggests intermediate conformations and a pathway between the bound and free conformations.

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PCDB: a database of protein conformational diversity

Cited by 26 publications

References 43 publications

PDBFlex: exploring flexibility in protein structures

PDBFlex: exploring flexibility in protein structures

PeptiSite: A structural database of peptide binding sites in 4D

ConTemplate Suggests Possible Alternative Conformations for a Query Protein of Known Structure

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