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Protocols

mCSM specifications

Information


Unique identifier OMICS_00133
Name mCSM
Alternative name mutation Cutoff Scanning Matrix
Interface Web user interface
Restrictions to use None
Input format PDB
Computer skills Basic
Stability Stable
Maintained Yes

Subtool


  • mCSM–NA

Maintainers


  • person_outline Douglas E. V. Pires
  • person_outline Tom Blundell

Additional information


http://structure.bioc.cam.ac.uk/mcsm_na

Publications for mutation Cutoff Scanning Matrix

mCSM citations

 (28)
library_books

Accurate prediction of functional, structural, and stability changes in PITX2 mutations using in silico bioinformatics algorithms

2018
PLoS One
PMCID: 5903617
PMID: 29664915
DOI: 10.1371/journal.pone.0195971

[…] (http://melolab.org/anolea). for structure predictions of pitx2, sequence in fasta format was obtained from ncbi database (np_001191327.1)., eight different protein stability programs (duet, sdm, mcsm i-mutant3.0, mupro, iptree-stab, cupsat, and istable) were used to predict the effects of missense mutations on the stability of pitx2 protein. duet is a web server that uses integrated […]

library_books

Structural Implications of Mutations Conferring Rifampin Resistance in Mycobacterium leprae

2018
Sci Rep
PMCID: 5864748
PMID: 29567948
DOI: 10.1038/s41598-018-23423-1

[…] environments where substitution probabilities are calculated from analysis of families of protein homologues. later we used a machine learning approach called mutation cut-off scanning matrix (mcsm), that uses the pharmacophore properties of the mutating residues and calculates the changes in stability of protein-protein, protein-nucleic acid and protein-ligand interactions. finally, […]

library_books

Evolution of carbapenem resistance in Acinetobacter baumannii during a prolonged infection

2018
Microb Genom
PMCID: 5885017
PMID: 29547094
DOI: 10.1099/mgen.0.000165

[…] of the missense variants were analysed to account for all the potential effects of the mutations []. the effects of the mutations upon the stability of the proteins was predicted using sdm [], mcsm-stability [] and duet []. the effect of the mutations upon the binding affinity for meropenem were predicted using mcsm-lig []. these computational approaches represent the wild-type residues […]

library_books

BEST1 protein stability and degradation pathways differ between autosomal dominant Best disease and autosomal recessive bestrophinopathy accounting for the distinct retinal phenotypes

2018
Hum Mol Genet
PMCID: 5905664
PMID: 29668979
DOI: 10.1093/hmg/ddy070

[…] for computational stability analysis we relied on the recently solved 3d protein structure of chicken best1 (cbestcryst) (), which was implemented into the structure-based prediction tools mutation cutoff scanning matrix (mcsm), site-directed mutator (sdm), duet and the three-state predictor i-mutant 2.0. accordingly, the analyzed pathologic mutations were all classified […]

library_books

Computational Investigation of the Missense Mutations in DHCR7 Gene Associated with Smith Lemli Opitz Syndrome

2018
Int J Mol Sci
PMCID: 5796090
PMID: 29300326
DOI: 10.3390/ijms19010141

[…] the effect of mutations on protein stability (folding free energy change (∆∆g)) using the generated homology model of dhcr7 protein. the webservers used in this study include duet [], eris [], mcsm [], sdm [], foldx [] and saafec []. the sasa were calculated using vmd []. as dhcr7 is a transmembrane protein, the membrane was also included when calculating the sasa. thus, only the amino […]

library_books

Analyses of Tissue Culture Adaptation of Human Herpesvirus 6A by Whole Genome Deep Sequencing Redefines the Reference Sequence and Identifies Virus Entry Complex Changes

2017
Viruses
PMCID: 5795429
PMID: 29301233
DOI: 10.3390/v10010016

[…] the gb hcmv trimer strain ad169 (pdb id: 5cxf) with each of its subunits. the free energy predictions of the thr193ala mutation on the subunit-subunit interaction stability was done using web server mcsm [], which predicts stability changes of a wide range of mutations from graph-based signatures encoding distance patterns between atoms., illumina deep sequencing was conducted deriving hhv-6a […]


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mCSM institution(s)
Department of Biochemistry, University of Cambridge, Cambridge, UK; ACRF Rational Drug Discovery Centre and Biota Structural Biology Laboratory, St Vincents Institute of Medical Research, Fitzroy, VIC, Australia
mCSM funding source(s)
Supported by Brazilian agency Conselho Nacional de Desenvolvimento Cientıfico e Tecnologico (CNPq), Brazil Victoria Fellowship from the Victorian Government and the Leslie (Les) J. Fleming Churchill Fellowship from the The Winston Churchill Memorial Trust and University of Cambridge and The Wellcome Trust.

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