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Citations per year

Number of citations per year for the bioinformatics software tool McBASC
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This map represents all the scientific publications referring to McBASC per scientific context
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Popular tool citations

chevron_left Multiple nucleotide sequence alignment Amino acid sequence homology search Assembly scaffolding Gene design Protein-coding gene prediction Conventional primer design Sequence annotation visualization Multiplex primer design Nucleotide sequence homology search Co-evolving residue prediction Primer design DNA design Restriction site detection chevron_right
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Protocols

McBASC specifications

Information


Unique identifier OMICS_29039
Name McBASC
Alternative name McLachlan Based Substitution Correlation
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Advanced
Version 1.1
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Richard Aldrich

Publications for McLachlan Based Substitution Correlation

McBASC citations

 (13)
call_split

Protein sites with more coevolutionary connections tend to evolve slower, while more variable protein families acquire higher coevolutionary connections

2017
F1000Res
PMCID: 5506539
PMID: 28751967
DOI: 10.5256/f1000research.12138.r21733
call_split See protocol

[…] ein families. Altogether we identified 19,736 (out of total 36,616) coevolved site pairs located within 10Å spatial distance from the 753 family alignments, with a MIp Z-score cutoff of 4.0 or higher.McBASC ( http://fodorwebsite.appspot.com//covariance1_1.zip) was used to calculate the simple inter-position coevolution for the 753 protein family alignments. McBASC provides high score for non-cons […]

library_books

Emerging Computational Methods for the Rational Discovery of Allosteric Drugs

2016
PMCID: 4901368
PMID: 27074285
DOI: 10.1021/acs.chemrev.5b00631

[…] Some work has been done to competitively benchmark the performance of these methods. In 2004, Fodor and Aldrich compared OMES, MI, SCA, and McBASC in a variety of tests. In short, the study found that performance is largely dependent on the way that different methods determine background residue probabilities and handle positional conserv […]

library_books

Progress and challenges in predicting protein interfaces

2015
Brief Bioinform
PMCID: 4719070
PMID: 25971595
DOI: 10.1093/bib/bbv027

[…] ediction [], scoring of docking decoys [] as well as in protein–protein interface prediction [, ] (E).Early applications of co-evolution to protein interface prediction include OMES [], MI [] SCA [], McBASC [], ELSC [] and the more recent i-Patch [] and EVComplex []. The earlier methods generally suffer from low precision (20–25% precision at 20% recall) []. The more recent method, i-Patch, achiev […]

library_books

Multiple Co Evolutionary Networks Are Supported by the Common Tertiary Scaffold of the LacI/GalR Proteins

2013
PLoS One
PMCID: 3877293
PMID: 24391951
DOI: 10.1371/journal.pone.0084398

[…] ifferent algorithms rank different pairs as the most strongly co-evolving , with no single algorithm clearly more “correct” than others. Thus, for this work, we used five common methods – ZNMI, OMES, McBASC, ELSC and SCA – that employ divergent strategies to detect evolutionary constraints. ZNMI uses information theory ; OMES calculates a goodness-of-fit-like statistical parameter , ; McBASC detec […]

library_books

Computational enzyme design approaches with significant biological outcomes: progress and challenges

2012
Comput Struct Biotechnol J
PMCID: 3962085
PMID: 24688648
DOI: 10.5936/csbj.201209007

[…] ss this, Fodor et al. [] assessed the performance of four different methods in detecting coevolutionary site, namely Statistical Coupling Analysis (SCA) [], Observed Minus Expected Squared (OMES) [], McLachlan Based Substitution correlation (McBASC) [] and Mutual Information (MI) []. In their research, OMES and McBASC were found to outperform the other two algorithms in favoring poorly conserved r […]

library_books

Accurate Simulation and Detection of Coevolution Signals in Multiple Sequence Alignments

2012
PLoS One
PMCID: 3473043
PMID: 23091608
DOI: 10.1371/journal.pone.0047108

[…] ing Analysis (DCA) , , and the three binary methods (db, dgb, and nbZPX2) described above.We have also tested several non-MI algorithms including Observed Minus Expected Squared Covariance (OMES) , , McLachlan Based Substitution Correlation (McBASC) , , Explicit Likelihood of Subset Co-variation (ELSC) , Statistical Coupling Analysis (SCA) , , . Sparse Inverse Covariance (PSICOV) could not be tes […]


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McBASC institution(s)
Department of Molecular and Cellular Physiology, and Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA, USA
McBASC funding source(s)
Supported by the Mathers Foundation.

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