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MatAlign specifications


Unique identifier OMICS_03660
Name MatAlign
Alternative name Matrix Alignment
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Protein information
Input format PDB
Output data PDBID, number of residues in the given chain of protein, number of residues that are matched/ aligned/ equivalent, percent of aligned residues, alignment lenght, RMSD, alignment score, normalized alignment scoreLinux, WindowsAdvanced
Operating system Unix/Linux, Windows
Computer skills Advanced
Version 1.1
Stability Stable
C Clustering
Maintained Yes




No version available



  • person_outline Zeyar Aung

Publication for Matrix Alignment

MatAlign citations


CoMOGrad and PHOG: From Computer Vision to Fast and Accurate Protein Tertiary Structure Retrieval

Sci Rep
PMCID: 4543952
PMID: 26293226
DOI: 10.1038/srep13275

[…] our CoMOGrad feature vector. With this feature, we can simply take Euclidean distance to compare structures rather than using the alignment technique of α carbon distance matrices used by MASASW and MatAlign. As anticipated, introduction of this feature makes the comparison method much simpler and faster. […]


Conserved Motifs and Prediction of Regulatory Modules in Caenorhabditis elegans

PMCID: 3337475
PMID: 22540038
DOI: 10.1534/g3.111.001081

[…] e redundancy of the whole genome motif profile set, we used the average log likelihood ratio (ALLR) statistic () to determine the similarity between motif profiles. ALLR statistics are implemented in MatAlign-v4a (Wang and Stormo; Similarity of two motif profiles is determined by the ALLR scores of each pair of motif profiles and the length of the aligned part o […]


Dynamics based alignment of proteins: an alternative approach to quantify dynamic similarity

BMC Bioinformatics
PMCID: 2868010
PMID: 20398246
DOI: 10.1186/1471-2105-11-188

[…] tions of the same protein (PSD-95 PDZ3) using different random seeds for the initial atomic velocities. The similarities of each pairs of DFMs resulted from the different MD runs were measured by the matrix alignment algorithm. Naturally, the five DFMs were not perfectly the same, but the similarity between each pair was highly significant (see Table ). Most importantly, comparing different simula […]


A simple and fast heuristic for protein structure comparison

BMC Bioinformatics
PMCID: 2335283
PMID: 18366735
DOI: 10.1186/1471-2105-9-161

[…] of queries over the NH3D database [] to evaluate the capability of a nearest neighbor classification to detect similarity at CATH's architecture level. Comparisons are then made against DaliLite and MatAlign. […]


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MatAlign institution(s)
Institute for Infocomm Research, Singapore; School of Computing, National University of Singapore, Singapore

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