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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 citations

 (7)
library_books

Structural basis of Sorcin mediated calcium dependent signal transduction

2015
Sci Rep
PMCID: 4649501
PMID: 26577048
DOI: 10.1038/srep16828

[…] interaction 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 a […]

call_split

Parkinson’s disease associated mutations in DJ 1 modulate its dimerization in living cells

2012
PMCID: 3644405
PMID: 23183826
DOI: 10.1007/s00109-012-0976-y
call_split See protocol

[…] picted 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 []. […]

library_books

A highly conserved protein of unknown function in Sinorhizobium meliloti affects sRNA regulation similar to Hfq

2011
Nucleic Acids Res
PMCID: 3113577
PMID: 21325267
DOI: 10.1093/nar/gkr060

[…] nteracts with the Arg59, Lys61 (E–F). The docking results suggest a probable RNA binding site in the YbeY protein. We further subjected the YbeY structure to analysis of surface binding properties by Hotpatch webserver (). HotPatch finds unusual patches on the surface of proteins, and statistically computes how unusual they are (patch rareness), and how likely each patch is to be of functional imp […]

library_books

Gadd45a Is an RNA Binding Protein and Is Localized in Nuclear Speckles

2011
PLoS One
PMCID: 3017548
PMID: 21249130
DOI: 10.1371/journal.pone.0014500

[…] i.ucla.edu) 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 . […]

library_books

Characterization of the relationship between integrase, excisionase and antirepressor activities associated with a superinfecting Shiga toxin encoding bacteriophage

2010
Nucleic Acids Res
PMCID: 3064807
PMID: 21062824
DOI: 10.1093/nar/gkq923

[…] some Xis proteins—demonstrated or predicted ()—to self-interact and form DNA-bound micronucleoprotein filaments, potential sites of protein–protein interaction on the Φ24B Xis model were sought with HotPatch (). For protein–protein interactions, exposed hydrophobic residues constitute the most reliable predictor of interaction sites. The model of Φ24B Xis produces a single, strong prediction comp […]

call_split

The transcriptional co activator LEDGF/p75 displays a dynamic scan and lock mechanism for chromatin tethering

2010
Nucleic Acids Res
PMCID: 3045605
PMID: 20974633
DOI: 10.1093/nar/gkq933
call_split See protocol

[…] omain of LEDGF/p75 using the latest available version of Modeller (), with the NMR structure (PDB 2B8A) of the HDGF-PWWP as a template (). Second, we predicted putative DNA binding residues using the HotPatch algorithm (). This analysis indicated residues K56 and R74 to be solvent exposed and not required for the stabilization of the tertiary structure of the protein, minimizing the chance of pert […]


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