TM-align protocols

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TM-align specifications

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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 in pipelines

 (9)
2017
PMCID: 5786184
PMID: 29087246
DOI: 10.1080/19336950.2017.1393131

[…] microscope (zeiss, germany)., the structures of the wild-type and a28v hkir6.2 were predicted by i-tasser and the rat kir6.2 (pdb: 5wua) was used as a template for de novo structure prediction. tm-align was used to align wild-type and a28v hkir6.2. predicted structures were generated in pymol., imaging data from the immunostained cells were analyzed using zen software (zeiss, germany). […]

2016
PMCID: 5158031
PMID: 27977773
DOI: 10.1371/journal.pone.0168271

[…] recognition engine v2.0, phyre2, http://www.sbg.bio.ic.ac.uk/phyre2/html/page.cgi?id=index, []; iterative threading assembly refinement, i-tasser, http://zhanglab.ccmb.med.umich.edu/i-tasser/, []; tm-align, http://zhanglab.ccmb.med.umich.edu/tm-align/, []). the pymol molecular graphics system, version 1.7.x schrödinger, llc, was used to model gnat1 interactions with gdp (pdb code 1got), gtp […]

2014
PMCID: 3981765
PMID: 24718683
DOI: 10.1371/journal.pone.0094126

[…] using the i-tasser program on the basis of crystal structure of previously resolved human mterfs , –, . superimposing 3d structures of maize mterfs with that of human mterfs was performed in the tm-align program . pymol v1.6.0.0 was used to display and analyze the tertiary structure of maize mterfs., promoter sequences (2-kb upstream of the translation start codon) for maize mterf genes […]

2014
PMCID: 4131471
PMID: 25147569
DOI: 10.1155/2014/918143

[…] using clustal omega []. protein tertiary structure prediction was conducted via hhpred by the max-planck institute for developmental biology. superposition of protein structures was done by tm-align []. the structure of tlr1-tir (1fyv) was downloaded from the protein data bank (http://www.rcsb.org/pdb/home/home.do). the presentations of the 3d tir domain structures were accomplished […]

2013
PMCID: 3846731
PMID: 24312616
DOI: 10.1371/journal.pone.0081979

[…] crystallographic structure of human sod1 as the template. the tm-scores and root mean square deviations (rmsds) of the mutant structures with respect to the wild-type structure were calculated using tm-align []., a human-curated database was developed using the server side include in java, jmol. the database at http://bioinfogroup.com/database contains the results obtained from this work. […]


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TM-align in publications

 (137)
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 […]

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 […]

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

[…] 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 […]

PMCID: 5895030
PMID: 29641586
DOI: 10.1371/journal.pone.0195559

[…] 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 []., harxl23 was amplified from genomic dna extracted from arabidopsis oy-1 plants, infected with hpa isolate emoy2, using proofreading polymerase (pfu, invitrogen). forward and reverse […]

PMCID: 5924525
PMID: 29597290
DOI: 10.3390/genes9040183

[…] 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 […]


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

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