mCSM protocols

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mCSM specifications


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


  • mCSM–NA


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

Additional information

Publications for mutation Cutoff Scanning Matrix

mCSM in pipelines

PMCID: 4806318
PMID: 27009368
DOI: 10.1038/srep23743

[…] ebola virus trimer., the coulombic electrostatic potential for the proteins was calculated using delphi, with default parameters. the electrostatics map was visualized and analyzed using chimera., mcsm was used to predict the effect of each individual sdp on the stability of the protein. the ebola virus structures were used as input and the relevant amino acid changed to the one present […]

PMCID: 5093252
PMID: 27840822
DOI: 10.1155/2016/2023803

[…] obtained from the pymol mutagenesis tool. structure refinement was carried out using kobamin which is based on knowledge based potential refinement for proteins protocol []., the approach called mutation cutoff scanning matrix (mcsm) uses the concept of graph-based structural signatures to study and predict the impact of single-point mutations on protein stability and protein-protein […]

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mCSM in publications

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

[…] ( 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 […]

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, […]

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 […]

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 […]

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 […]

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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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