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Citations per year

Number of citations per year for the bioinformatics software tool PatchFinder
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This map represents all the scientific publications referring to PatchFinder per scientific context
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Protocols

PatchFinder specifications

Information


Unique identifier OMICS_06944
Name PatchFinder
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for PatchFinder

PatchFinder citations

 (8)
library_books

The Carboxy Terminal Domain of Erb1 Is a Seven Bladed ß Propeller that Binds RNA

2015
PLoS One
PMCID: 4400149
PMID: 25880847
DOI: 10.1371/journal.pone.0123463

[…] Erb1 is known to bind rRNA as shown by UV-crosslinking experiments. It is possible that the β-propeller is involved in such a binding due to its highly positive charge (). We used the PatchFinder Plus algorithm [] to identify the biggest positive patch on the surface of the domain. Indeed, as seen for the electrostatic surface analysis, the tool found a big region of basic residues […]

library_books

An association adjusted consensus deleterious scheme to classify homozygous Mis sense mutations for personal genome interpretation

2013
BioData Min
PMCID: 3892026
PMID: 24365473
DOI: 10.1186/1756-0381-6-24

[…] are likely to alter the binding capability for ligand(s). As disease-causing mutations that do not occur in binding sites or buried sites are predominantly found on protein interfaces [], we used the PatchFinder program [,] to computationally predict the most significant cluster of conserved residues on a protein’s surface that may indicate possible functional sites of the protein; i.e., sites of […]

library_books

Prediction of DNA binding proteins from relational features

2012
Proteome Sci
PMCID: 3579737
PMID: 23146001
DOI: 10.1186/1477-5956-10-66

[…] classifier for identifying DNA-binding proteins among proteins with known 3D structures. First, their method detects clusters of evolutionarily conserved regions on the surface of proteins using the PatchFinder algorithm. Next, a classifier is trained using features like the electrostatic potential, cluster-based amino acid conservation patterns, the secondary structure content of the patches and […]

library_books

Prediction of DNA binding propensity of proteins by the ball histogram method using automatic template search

2012
BMC Bioinformatics
PMCID: 3382442
PMID: 22759427
DOI: 10.1186/1471-2105-13-S10-S3

[…] classifier for identifying DNA-binding proteins among proteins with known 3D structures. First, their method detects clusters of evolutionarily conserved regions on the surface of proteins using the PatchFinder algorithm. Next, a classifier is trained using features like the electrostatic potential, cluster-based amino acid conservation patterns, the secondary structure content of the patches and […]

library_books

Functional region prediction with a set of appropriate homologous sequences an index for sequence selection by integrating structure and sequence information with spatial statistics

2012
BMC Struct Biol
PMCID: 3533907
PMID: 22643026
DOI: 10.1186/1472-6807-12-11

[…] larger thresholds.Secondly, in order to evaluate the performance of LMIC as a detection method for conserved residue clusters, we compared the performances of the predictions with LMIC and those with PatchFinder. PatchFinder finds the patch of residues with the lowest probability of occurring by chance [,]. At first, PatchFinder sets a minimal average conservation cutoff for a patch, to generate t […]

call_split

From face to interface recognition: a differential geometric approach to distinguish DNA from RNA binding surfaces

2011
Nucleic Acids Res
PMCID: 3177183
PMID: 21693557
DOI: 10.1093/nar/gkr395
call_split See protocol

[…] hich we had structures available in both holo and apo forms (for details, see Supplementary Data S1).Interface residues were calculated using the Intervor web server () excluding water molecules. The PatchFinder algorithm () was applied to extract all continuous positive patches on the protein surface with a cutoff of 2 kT/e. The patches were sorted based on the number of grid points included with […]


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PatchFinder institution(s)
Department of Biochemistry, George S Wise Faculty of Life Sciences, Tel Aviv University Ramat Aviv, Israel

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