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CMASA specifications


Unique identifier OMICS_22006
Alternative name Contact MAtrix based local Structural Alignment algorithm
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C, C++
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Stability No
Maintained No


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Publication for Contact MAtrix based local Structural Alignment algorithm

CMASA citations


Proteome wide prediction of targets for aspirin: new insight into the molecular mechanism of aspirin

PMCID: 4793309
PMID: 26989626
DOI: 10.7717/peerj.1791

[…] The overall structures of the 23 putative targets of aspirin identified in this study are very different (). However, the 23 targets have similar local structures. It indicates the power of the CMASA for detecting and comparing binding sites similarities from whole structures of proteins. Further, the CMASA is not only highly accurate but also sensitive and fast for detecting the binding poc […]


An assessment of catalytic residue 3D ensembles for the prediction of enzyme function

BMC Bioinformatics
PMCID: 4634577
PMID: 26538500
DOI: 10.1186/s12859-015-0807-6

[…] []. Alternatively, the catalytic site identification server provides users with protein annotations based on structural matches with entries of the PDB []. For the more recently introduced algorithm CMASA, which uses a similar approach, the authors reported the detection of 166 putative catalytic sites []. Methods like ProFunc [] or ASSIST [] combine analysis of protein sequence and structure usi […]


A Simple Extension to the CMASA Method for the Prediction of Catalytic Residues in the Presence of Single Point Mutations

PLoS One
PMCID: 4182483
PMID: 25268770
DOI: 10.1371/journal.pone.0108513

[…] The computational experiments are divided into four scenarios. The first scenario is aimed at reproducing the results reported in . The second scenario assesses the predictions obtained by xCMASA in the case when there are not mutations. The third scenario assesses the CMASA performance when a single point mutation is applied to the catalytic sites. The fourth scenario analyzes the perfo […]


A comparative analysis of protein targets of withdrawn cardiovascular drugs in human and mouse

J Clin Bioinforma
PMCID: 3413526
PMID: 22548699
DOI: 10.1186/2043-9113-2-10

[…] An accurate algorithm for detecting local protein structural similarity, CMASA [] was applied to detect local structural similarities of drug-binding sites in non-redundant structure database from SCOP database []. The binding sites detected above were used as queries. Sub […]


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CMASA institution(s)
State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China; Graduate School of Chinese Academy of Sciences, Beijing, China; Kunming Institute of Zoology-Chinese University of Hongkong Joint Research Center for Bio-resources and Human Disease Mechanisms, Kunming, China
CMASA funding source(s)
Supported by the National Basic Research Program of China (Grant No. 2007CB815705; 2009CB941300), the National Natural Science Foundation of China (Grant No. 30623007) and Chinese Academy of Sciences (Grant No. 2007211311091).

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