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Protocols

pdbFun specifications

Information


Unique identifier OMICS_10543
Name pdbFun
Interface Web user interface
Restrictions to use None
Input data Users can select any residue subset (even including any number of PDB structures) by combining the available features. Selections can be used as probe and target in multiple structure comparison searches.
Output data The output is a list of aligned structural matches offered in tabular and also graphical format.
Computer skills Basic
Stability No
Maintained No

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Publication for pdbFun

pdbFun citations

 (4)
library_books

Phosphate binding sites identification in protein structures

2010
Nucleic Acids Res
PMCID: 3045618
PMID: 20974634
DOI: 10.1093/nar/gkq987

[…] site in unbound protein structures makes it an ideal tool for functional annotation and for complementing docking and drug design methods. the pfinder program is available at http://pdbfun.uniroma2.it/pfinder., many important chemical reactions and molecular interactions that occur in the cell involve ligands containing the phosphate group., more than half of known proteins […]

library_books

De Orphaning the Structural Proteome through Reciprocal Comparison of Evolutionarily Important Structural Features

2008
PLoS One
PMCID: 2362850
PMID: 18461181
DOI: 10.1371/journal.pone.0002136

[…] specificity., alternative strategies also rely on comparisons of sequence or structure, either in whole or just in part. examples include sequence motifs , ; global fold (dali , vast , ssm , grath , pdbfun , tops , sumo , , cm ); and small structural motifs—the object of this study. in contrast to all these techniques, which seek elements of sequence or structure that are intrinsically […]

library_books

Prediction of enzyme function based on 3D templates of evolutionarily important amino acids

2008
BMC Bioinformatics
PMCID: 2219985
PMID: 18190718
DOI: 10.1186/1471-2105-9-17

[…] individual method., these other methods exploit other types of functionally relevant similarities between proteins: one such is general structural similarity (dali [], vast [], ssm [], grath [], pdbfun [], tops [], sumo [,], cm []); another is local sequence similarity of a few residues that are highly specific to function, such as pre-defined sequence motifs [,]. such motifs […]

library_books

Overview of BITS2005, the Second Annual Meeting of the Italian Bioinformatics Society

2005
BMC Bioinformatics
PMCID: 1866399
DOI: 10.1186/1471-2105-6-S4-S1

[…] together, and secondary structure guided sequence alignment is improved., ausiello et al. [] describe the query 3d program for local comparison of protein structures. query 3d is at the core of the pdbfun server [] for the identification of local structural similarities between annotated residues in proteins., d'ursi et al. [] used a flexible docking approach to characterize the molecular […]


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pdbFun institution(s)
Centre for Molecular Bioinformatics, Department of Biology, University of Rome Tor Vergata Via della Ricerca Scientifica, Rome, Italy

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