PatchFinder protocols

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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 in pipeline

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

[…] 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 […]


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PatchFinder in publications

 (9)
PMCID: 5753473
PMID: 29298701
DOI: 10.1186/s12989-017-0238-9

[…] with a fluorescent dna intercalating dye sybrgreen®. dna strand breaks determined as the % of dna in the comet tail (%tdna) and as the comet tail length (tl) were scored by the fully automated patchfinder™ system (imstar, france). in order to control the day-to-day variation and to ensure equal electrophoresis efficiency both negative (a549 human lung epithelial cell line treated with pbs […]

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 […]

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

[…] 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 […]

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 […]

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 […]


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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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