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Matt specifications


Unique identifier OMICS_03644
Name Matt
Alternative name Multiple Alignment with Translations and Twists
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for Multiple Alignment with Translations and Twists

Matt citations


Resculpting the binding pocket of APC superfamily LeuT fold amino acid transporters

PMCID: 5809530
PMID: 29058016
DOI: 10.1007/s00018-017-2677-8

[…] a C score of -1.87 and a TM score of 0.49 (scores improved to − 0.83 and 0.61 if only the core 5 + 5, TM1-10 inclusive, sequence was submitted) []. Multiple pairwise structure–structure alignments in Matt [] identified that F159 (in the I-TASSER top PAT2 model), V104 (LeuT), G100 (AdiC), and W117 (Mhp1), were in equivalent positions, consistent with the predictions from I-TASSER, HHPred/Modeller, […]


Bioinformatics comparisons of RNA binding proteins of pathogenic and non pathogenic Escherichia coli strains reveal novel virulence factors

BMC Genomics
PMCID: 5571608
PMID: 28836963
DOI: 10.1186/s12864-017-4045-3

[…] ectrostatics) using SYBYL7.2 (Tripos Inc.). Structural alignment of the modelled PELOTA_1 domain and the L7Ae K-turn binding domain from Archaeoglobus fulgidus (PDB code: 4BW0: B) was performed using Multiple Alignment with Translations and Twists (Matt) []. The same kink-turn RNA from H. marismortui, found in complex with the L7Ae K-turn binding domain from A. fulgidus, was docked onto the model, […]


An efficient algorithm for protein structure comparison using elastic shape analysis

PMCID: 5041553
PMID: 27708689
DOI: 10.1186/s13015-016-0089-1

[…] d algorithm are comparable with ESA of all backbone atoms.In another experiment, the computing time of the different methods of protein structure comparison [], viz., combinatorial extension (CE) [], Matt [], MUSTANG [] and ESA [, ] have been recorded for varying number of residues along with the proposed algorithm. The computing time of the existing and proposed algorithm are given in Table . In […]


An effective sequence alignment free superpositioning of pairwise or multiple structures with missing data

PMCID: 4915111
PMID: 27330544
DOI: 10.1186/s13015-016-0079-3

[…] ons in proteins. While our method is designed for the full structure superposition (see more examples in Additional file : Tables S2 and S3).We also benchmark the performance of PSSM against DALI and MATT using Fischer’s benchmark dataset (Table ). Fischer’s dataset is a popular benchmark for testing protein structure alignment programs, and they contain 68 pairs of protein structures. In Table , […]


Identification and classification of small molecule kinases: insights into substrate recognition and specificity

BMC Evol Biol
PMCID: 4702295
PMID: 26738562
DOI: 10.1186/s12862-015-0576-x
call_split See protocol

[…] sed for structural alignment (PDB ids are given in Fig. ). Pairwise structural alignments of each ELK and EPK representative PDB structure with Rio kinase (pdbid : 1zp9) were generated using MASS [], Matt [] and DeepAlign []. Secondary structure elements and Hanks and Hunter subdomain motifs were aligned manually. These structural and motif landmarks ensured correct placement of intervening region […]


Insights into Substrate Specificity of NlpC/P60 Cell Wall Hydrolases Containing Bacterial SH3 Domains

PMCID: 4600125
PMID: 26374125
DOI: 10.1128/mBio.02327-14

[…] otation) refinement with one TLS group per molecule in the ASU (asymmetric unit), and NCS (noncrystallographic symmetry) restraints. Structural comparison and clustering analysis were performed using Matt (). Molecular graphics were prepared using PyMOL (Schrödinger LLC, USA), and electrostatic potential was calculated using Delphi (). […]


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Matt institution(s)
Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA

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