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HotPatch specifications

Information


Unique identifier OMICS_15455
Name HotPatch
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data A partial information about the function type of the protein of interest.
Operating system Unix/Linux
Programming languages C++
Computer skills Advanced
Version 4.0
Stability No
Maintained No

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Publication for HotPatch

HotPatch in publications

 (7)
PMCID: 4649501
PMID: 26577048
DOI: 10.1038/srep16828

[…] is broken since asp113 participates in ion coordination; the rearrangement of the ef3 loop causes also the exposure of arg116 (, panel b)., we further analysed the casor structure using the hotpatch server (http://hotpatch.mbi.ucla.edu/) in order to identify unusual hydrophobic patches likely mediating protein-protein interactions between sorcin and its molecular partners. the hotpatch […]

PMCID: 3644405
PMID: 23183826
DOI: 10.1007/s00109-012-0976-y

[…] in the figures were built using pymol. calculation of continuous molecular surface properties was performed using vasco software []. polar patches on the protein surfaces were located by using hotpatch software []., bifc data were analyzed with prism 5 (graphpad), using the kruskal–wallis test followed by post hoc analysis with a dunn test. p < 0.05 is considered significant for any set […]

PMCID: 3113577
PMID: 21325267
DOI: 10.1093/nar/gkr060

[…] super-imposing the ybey structure () with the structures of complete ago protein and mid/piwi domain () using the crystallographic object-oriented toolkit [coot; (,)]. ybey structure was analyzed by hotpatch server (http://hotpatch.mbi.ucla.edu/) () for the dna/rna binding properties and for finding functionally important patches on its surface. ybey (pdb id: 1xm5; chain a) and 4mer rna […]

PMCID: 3017548
PMID: 21249130
DOI: 10.1371/journal.pone.0014500

[…] online servers. structure analysis was carried out using swisspbd viewer and pymol (www.pymol.org). pdb2pqr , propka and apbs packages were used for charge surface calculations and the hotpatch web server for hydrophobicity calculations. for protein-protein dockings the gramm package was used in hydrophobic mode ., pet28a vectors containing orf of xtgadd45a and mutants […]

PMCID: 3064807
PMID: 21062824
DOI: 10.1093/nar/gkq923

[…] stereochemical analysis () were used to select a model for further analysis. electrostatic characteristics of the model were explored with apbs () and putative protein–protein interfaces sought with hotpatch (). dna-binding ability was tested with db-mom () and pro-dna (). further protein structure superpositions were done with ssm () and displayed in pymol (), which was also used to produce […]


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