mCSM statistics

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Citations per year

Number of citations per year for the bioinformatics software tool mCSM
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Tool usage distribution map

This map represents all the scientific publications referring to mCSM per scientific context
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Associated diseases

This word cloud represents mCSM usage per disease context
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Popular tool citations

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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

 (36)
library_books

Computational Protein Phenotype Characterization of IL10RA Mutations Causative to Early Onset Inflammatory Bowel Disease (IBD)

2018
Front Genet
PMCID: 5934427
PMID: 29755507
DOI: 10.3389/fgene.2018.00146

[…] e position of mutation site, residues codes of wild-type and mutant in one-letter format were provided as an input for this server. The collective predictions of SDM (Site Directed Mutator) and mCSM (mutation Cutoff Scanning Matrix) methods are obtained in a non-linear regression fashion. Predictions reveal variation in Gibbs free energy (DDG) wherein positive values denote stabilized mutations an […]

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

[…] with the functional characterization of PITX2 missense variants.The results from our molecular modeling analysis were also compared to the predictions of eight stability predictor methods (DUET, SDM, mCSM, I-mutant3.0, MUpro, iPTREE-STAB, CUPSAT, and iStable). Based on our analyses, it appears that CUPSAT performs the best of the seven methods evaluated here in predicting the effect of missense mu […]

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

[…] ctural 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, we use […]

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

[…] uences 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 str […]

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

[…] prediction of protein stability changes upon single-site variations from the protein structure or sequence (http://folding.biofold.org/i-mutant/i-mutant2.0.html; date last accessed December 2017) (). mCSM relies on graph-based signatures. Distance patterns between atoms are used to train predictive models and to represent the protein residue environment (). SDM is based on knowledge of observed su […]

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

[…] redict 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 acid […]


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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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