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MATRAS specifications


Unique identifier OMICS_03655
Alternative name MArkovian TRAnsition of Structure evolution
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes


  • person_outline Takeshi Kawabata

Publications for MArkovian TRAnsition of Structure evolution

MATRAS citations


Population Size and the Rate of Language Evolution: A Test Across Indo European, Austronesian, and Bantu Languages

Front Psychol
PMCID: 5934942
PMID: 29755387
DOI: 10.3389/fpsyg.2018.00576

[…] nfluence rates of language change (Greenhill, ) including population density, social structure (Nettle, ; Labov, ; Ke et al., ; Trudgill, ), degree of contact, and connectedness with other languages (Matras, ; Bowern, ), degree of language diffusion within a speech community (Wichmann et al., ), degree of bilingualism or multilingualism (Lupyan and Dale, ; Bentz and Winter, ), language group diver […]


In Vitro and in Silico Evidence of Phosphatase Diversity in the Biomineralizing Bacterium Ramlibacter tataouinensis

Front Microbiol
PMCID: 5768637
PMID: 29375498
DOI: 10.3389/fmicb.2017.02592

[…] imal multiple templates were automatically built using MODELLER (Šali and Blundell, ). The quality of the models was checked by Verify3D (Lüthy et al., ). Structures and models were superimposed with Matras (Kawabata, ). The 3D coordinate files of the protein models are provided in Supplementary Data Sheet .Electrostatic potential maps of 3D structures and models were computed and drawn using the […]


Platelets and Their Pathways in Dentistry: Systematic Review

PMCID: 5682705
PMID: 29184829
DOI: 10.4103/jispcd.JISPCD_284_17

[…] nding and remain in the central dead space of the wound until repair is complete. Macrophages produce growth factors that stimulate neovascularization, fibroblast proliferation, and migration. It was Matras in 1972 who had first used platelets as sealants to promote homeostasis for surgical procedures. He also had demonstrated the importance of fibrin in reuniting human nerves with the aid of conc […]


Potyvirus virion structure shows conserved protein fold and RNA binding site in ssRNA viruses

Sci Adv
PMCID: 5606705
PMID: 28948231
DOI: 10.1126/sciadv.aao2182

[…] r the CPs in flexuous filamentous plant viruses, we searched for structural homologs for the core region of WMV CP (excluding the extended N- and C-terminal regions) using the web servers Dali () and Matras (). The hits with higher scores by both methods are indeed the CPs from potexviruses ( and figs. S3 and S4), but additional homologs are detected in nucleoproteins (NPs) from members of Orthomy […]


A novel rare variant R292H in RTN4R affects growth cone formation and possibly contributes to schizophrenia susceptibility

PMCID: 5611737
PMID: 28892071
DOI: 10.1038/tp.2017.170

[…] lar to that of RTN4R, with 33.5% sequence identity, and both the LINGO1 and PTPRD proteins have an immunoglobulin (Ig)-like domain with weak sequence similarity (sequence identity=19.5%). The program MATRAS was used for the superimposition. The model was then refined using three programs: MODELLER, UCSF Chimera and myPresto. Details of the modeling procedure are provided in the and . […]


Rare genetic variants in CX3CR1 and their contribution to the increased risk of schizophrenia and autism spectrum disorders

PMCID: 5611740
PMID: 28763059
DOI: 10.1038/tp.2017.173

[…] Bound structures of membrane, fractalkine and heterotrimeric G protein were modeled by 3D superimpositions. 3D structures of GPCR in complexes were superimposed on the CX3CR1 model using the program MATRAS, and bound molecules in the complexes were also transformed with their GPCRs. The membrane model used was taken from a molecular dynamics study of GPCRs. The fractalkine structure was obtained […]


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MATRAS institution(s)
Center for Information Biology, National Institute of Genetics, Yata, Mishima, Shizuoka, Japan

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