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TM-align specifications

Information


Unique identifier OMICS_03646
Name TM-align
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for TM-align

TM-align citations

 (209)
library_books

Characterization of a novel organic solute transporter homologue from Clonorchis sinensis

2018
PLoS Negl Trop Dis
PMCID: 5942847
PMID: 29702646
DOI: 10.1371/journal.pntd.0006459

[…] Structure Analysis and Verification Server (http://services.mbi.ucla.edu/SAVES/). Other OST subunits were also modeled using the same methods. Overall structural comparisons were performed using the TM-align structure alignment server []. The TM-score value indicates the overall fold similarity. It is protein size-independent and less sensitive to local structural variations. TM-score ranges from […]

library_books

Comparative systems analysis of the secretome of the opportunistic pathogen Aspergillus fumigatus and other Aspergillus species

2018
Sci Rep
PMCID: 5919931
PMID: 29700415
DOI: 10.1038/s41598-018-25016-4

[…] filtered proteins in A. fumigatus Af293 were compared to the structure of their corresponding sequence-based homolog among the known drug target proteins in DrugBank based on TM score computed using TM Align (https://zhanglab.ccmb.med.umich.edu/TM-align/) and root-mean-square deviation (RMSD) value between locally aligned atoms computed using PyMOL (The PyMOL Molecular Graphics System, Version 1. […]

call_split

A Legionella pneumophila amylase is essential for intracellular replication in human macrophages and amoebae

2018
Sci Rep
PMCID: 5910436
PMID: 29679057
DOI: 10.1038/s41598-018-24724-1
call_split See protocol

[…] latform. Branch length was determined by aLRT,. Predicted structures were generated via I-TASSER (https://zhanglab.ccmb.med.umich.edu/I-TASSER/). Structures generated from I-TASSER were aligned using TM-align to generate a TM-score of structural similarity (https://zhanglab.ccmb.med.umich.edu/TM-align/). […]

library_books

Evolutionary convergence and divergence in archaeal chromosomal proteins and Chromo like domains from bacteria and eukaryotes

2018
Sci Rep
PMCID: 5906684
PMID: 29670199
DOI: 10.1038/s41598-018-24467-z

[…] te the position of knuckles in ZnRs. Similar results were obtained by automated pairwise structural alignment of Cren7 (PDB: 3KXT_A) and ZnRs (e.g. sarcosine oxidase delta subunit, PDB: 1VRQ_D) using TM-align and Fr-TM-align which gave a TM score of 0.52 (normalised by the length of 3KXT_A), indicating a ‘fold level’ similarity between the two.To investigate if this structural relationship to ZnRs […]

call_split

Application of alignment free bioinformatics methods to identify an oomycete protein with structural and functional similarity to the bacterial AvrE effector protein

2018
PLoS One
PMCID: 5895030
PMID: 29641586
DOI: 10.1371/journal.pone.0195559
call_split See protocol

[…] propeller-domain amino acids and the AvrE1 1513–1578 region were predicted using I-TASSER (structural templates are listed in ). The predicted structures of DspA/E and AvrE1 region were aligned using TM-align []. […]

library_books

Genome Wide Identification of the Alba Gene Family in Plants and Stress Responsive Expression of the Rice Alba Genes

2018
Genes
PMCID: 5924525
PMID: 29597290
DOI: 10.3390/genes9040183

[…] are mentioned in .The amino acid sequences were submitted to LOMETS [] to generate 3D structures. The 3D structures predicted for OsAlba proteins () were aligned to their respective templates in the TM-align server []. The predicted model was further analyzed in Chimera 1.2 [], which showed different number of α-helices, β-strands, and coils (). The OsAlba proteins showed the presence of 2–4 α-he […]

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TM-align institution(s)
Center of Excellence in Bioinformatics, University at Buffalo, Buffalo, NY, USA

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