M4T statistics

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Citations per year

Number of citations per year for the bioinformatics software tool M4T
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Tool usage distribution map

This map represents all the scientific publications referring to M4T per scientific context
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Associated diseases

This word cloud represents M4T usage per disease context
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Popular tool citations

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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

 (22)
library_books

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

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

[…] lly 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

Structural and functional characterization of the Helicobacter pylori cytidine 5′ monophosphate pseudaminic acid synthase PseF: molecular insight into substrate recognition and catalysis mechanism

2017
PMCID: 5638570
PMID: 29062238
DOI: 10.2147/AABC.S139773

[…] The HpPseF model was predicted with the following servers: IntFOLD, I-TASSER, SWISS-MODEL, RaptorX, Phyre2 and M4T. The quality of the predicted models was determined by the protein structure and model assessment tools in the SWISS-MODEL workspace., The best model was selected according to the QMEAN4 Z-score, […]

library_books

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

2017
PLoS Pathog
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 d […]

library_books

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

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

[…] performed by employing a variety of automated web-servers for protein structure homology modelling and applying standard protocols as implemented in “Protein Model Portal”. These include SWISS-MODEL, M4T, InFOLD2, Phyre2 and I-TASSER. Model structures of EstDZ2, were created based on templates derived from previously determined structures that exhibited esterolytic and/or other activities, i.e. an […]

library_books

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

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

[…] redictions, 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, 2E […]

library_books

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

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

[…] 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 to […]


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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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