BeAtMuSiC protocols

View BeAtMuSiC computational protocol

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BeAtMuSiC specifications

Information


Unique identifier OMICS_11225
Name BeAtMuSiC
Interface Web user interface
Restrictions to use None
Input data The main input of the webserver is the structure of the protein–protein complex, in PDB format. The user may either upload his own structure file, or provide the 4-letter PDB code of the structure, which will then be automatically downloaded from the Protein Data Bank.
Output data The main output of the webserver is the change in binding free energy resulting from each mutation. The webserver also reports the solvent accessibility of the mutated residue, in the complex and in the individual partners. The results may be downloaded as a plain text file, or browsed interactively on the website.
Computer skills Basic
Version 1.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline Yves Dehouck <>

Publication for BeAtMuSiC

BeAtMuSiC in pipeline

2014
PMCID: 3985714
PMID: 24803870
DOI: 10.1021/ct401022c

[…] correlation with experimental values. to calculate binding energy by foldx, we used eq and calculated the unfolding free energy of the whole complex and each monomer separately., the second method, beatmusic is specifically trained to calculate the change in binding affinity produced by single missense mutations. it uses residue based statistical potentials that were previously optimized […]


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BeAtMuSiC in publications

 (10)
PMCID: 5862610
PMID: 29568389
DOI: 10.18632/oncotarget.24459

[…] a protein-protein complex upon mutation of amino acid residue to alanine. we have scanned all interface residue with schrodinger module bioluminate [], and two other web servers drugscoreppi [] and beatmusic []. we performed alanine scanning of all interface residues in both gata4 and nkx2.5 to find hotspot residues. we found that in all the cases bioluminate, drugscoreppi and beatmusic, […]

PMCID: 5500802
PMID: 28539360
DOI: 10.1074/jbc.M117.789883

[…] structure (pdb code 1cf4) () and thermodynamic data (). the same structure was used to inform computational predictions of the contribution of specific residues using mcsm (), robetta (), and beatmusic (). the outputs from the programs were quite different, so only those residues that produced a predicted shift in δδg that was in the top quartile in at least two programs were selected. […]

PMCID: 5340008
PMID: 28264645
DOI: 10.1186/s12858-017-0077-1

[…] therefore, we were interested to examine how computational methods compared to our experimental results. the same mutagenesis experiment was performed computationally on blip position 50 with the beatmusic server, which computes theoretical δδg values based on a set of statistical potentials derived from known protein structures []. the tem-1-blip (pdb code: 1jtg) and kpc-2-blip (pdb code: […]

PMCID: 4872100
PMID: 26980279
DOI: 10.1093/nar/gkw185

[…] some of the amino acid residues in the binding to hsv and human udg, and also an attempt at modifying the strength of saugi's inhibition of these two udgs. the saugi mutants were designed using the beatmusic server (http://babylone.ulb.ac.be/beatmusic/query.php). the predicted energy loss at the mutated interfaces in the saugi/human udg and saugi/hsvudg complexes suggested that the three […]

PMCID: 4730321
PMID: 26761001
DOI: 10.3390/ijms17010077

[…] webservers and stand-alone computer programs were applied to assess monomer folding free energy change and dimer affinity change due to mutations. the webservers used for energy calculation included beatmusic [], neemo [], popmusic [], i-mutant 2.0 [], sdm [], duet [] and cupsat []. also a computer algorithm, foldx 3.0 β3 [,] was used to predict the folding free energy changes and dimer affinity […]


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BeAtMuSiC institution(s)
Department of BioModelling, BioInformatics and BioProcesses, Université Libre de Bruxelles (ULB), Brussels, Belgium
BeAtMuSiC funding source(s)
Belgian Fonds de la Recherche Scientifique (F.R.S.-FNRS) through an FRFC grant

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