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Protocols

M4T specifications

Information


Unique identifier OMICS_24771
Name M4T
Alternative name Multiple Mapping Method with Multiple Templates
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data A raw sequence.
Output data A full atom model(s) and the alignment(s) used to build the model.
Output format PDB
Programming languages C++, Javascript, Perl
Computer skills Basic
Version 3.0
Stability Stable
Maintained Yes

Maintainer


  • person_outline András Fiser <>

Publications for Multiple Mapping Method with Multiple Templates

M4T citations

 (19)
library_books

Three dimensional spatial analysis of missense variants in RTEL1 identifies pathogenic variants in patients with Familial Interstitial Pneumonia

2018
PMCID: 5781290
PMID: 29361909
DOI: 10.1186/s12859-018-2010-z

[…] determined, so we constructed a computationally derived homology model. to begin, we applied nine computational modeling algorithms to the protein sequence: genesilico [], hhpred [], i-tasser [], m4t [], pcons5 [], phyre2 [], raptorx [], robetta [], and swiss-model []. raptorx produced the highest-coverage model, which consisted of two well-folded domains spanning residues 1–769 and 881–1151. […]

library_books

Mycobacterium tuberculosis universal stress protein Rv2623 interacts with the putative ATP binding cassette (ABC) transporter Rv1747 to regulate mycobacterial growth

2017
PMCID: 5549992
PMID: 28753640
DOI: 10.1371/journal.ppat.1006515

[…] conserved non-surface fha1 residues, gly69 and his88, are thought to stabilize the structure of the binding site [,,] (). the homology model of the fha i domain of rv1747 was generated utilizing the m4t server ver 3.0 [] based on comparative modeling using a combination of 2 templates (pdb codes 2lc1 and 1uht). the homology model of the rv1747 fha domain was then superimposed onto the rad53 fha […]

library_books

Metagenomic mining for thermostable esterolytic enzymes uncovers a new family of bacterial esterases

2016
PMCID: 5171882
PMID: 27991516
DOI: 10.1038/srep38886

[…] predict the three-dimensional structure of estdz2 were performed by selected automated web-servers for protein structure homology modelling included in “protein model portal”, such as swiss-model, m4t, infold2, phyre2 and i-tasser, by applying standard protocols. comparison of the overall structures generated by the different models, showed that the architecture of the catalytic domain […]

library_books

Functional and structural characterization of a novel putative cysteine protease cell wall modifying multi domain enzyme selected from a microbial metagenome

2016
PMCID: 5146660
PMID: 27934875
DOI: 10.1038/srep38031

[…] the pcp amino acid sequence was fragmented into four different parts which were submitted individually to four automated protein structure modeling servers: lomets, swiss-model, quark and m4t 3.0. tridimensional models comprising these fragments were generated using the homologous domains from protein databank (pdb) entries 2b9k, 3fn2, 3pbi, 2krs, 2kt8, 2xiv, 4q4g, 3a2y, 3npf, 3ne0, […]

library_books

Amyotrophic Lateral Sclerosis Type 20 In Silico Analysis and Molecular Dynamics Simulation of hnRNPA1

2016
PMCID: 4945010
PMID: 27414033
DOI: 10.1371/journal.pone.0158939

[…] [] and provean []., the tridimensional structures were created based on comparative and ab initio modeling. for the comparative modeling, the following algorithms were used: intfold [], phyre2 [], m4t [], swissmodel [], ps2 [], raptorx [] and modeller []. for the ab initio modeling, the algorithms rosetta [,] and i-tasser [] were used. the generated structures were then structurally aligned […]

library_books

The GH51 α l arabinofuranosidase from Paenibacillus sp. THS1 is multifunctional, hydrolyzing main chain and side chain glycosidic bonds in heteroxylans

2016
PMCID: 4939007
PMID: 27398094
DOI: 10.1186/s13068-016-0550-x

[…] entering uniprot sequence b1a0t7 in fasta format as the query., for protein modeling, a structural model of thsabf (genbank abz10760) was generated by homology modeling using m4t, which selects and optimally combines multiple template structures benefitting from the unique contribution of each template []. selected templates were the gh51 α-l-arabinofuranosidases […]


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M4T institution(s)
Department of Systems and Computational Biology, Albert Einstein College of Medicine, Bronx, NY, USA; Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
M4T funding source(s)
Supported by NIH GM62519-04.

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