Fr-TM-align statistics

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Fr-TM-align specifications

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Unique identifier OMICS_03670
Name Fr-TM-align
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability No
Source code URL http://cssb.biology.gatech.edu/skolnick/files/FrTMalign/frtmalign.tar.bz2
Maintained Yes

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Publication for Fr-TM-align

Fr-TM-align in publications

 (11)
PMCID: 5906684
PMID: 29670199
DOI: 10.1038/s41598-018-24467-z

[…] 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 also […]

PMCID: 5847522
PMID: 29560273
DOI: 10.1038/s41540-018-0050-7

[…] by the annotation of ligand-binding sites with efindsite (fig. ). next, drug-target complexes are constructed for drugbank proteins with a two-step similarity-based docking procedure employing fr-tm-align and kcombu (fig. ). this protocol generates drug-bound structures for drugbank and unbound structures for orphanet proteins (fig. ). subsequently, all drugbank pockets are compared […]

PMCID: 4678705
PMID: 26666296
DOI: 10.1186/s13062-015-0099-9

[…] ring finger of non-smc element 1 homolog (pdbid 3nw0_b) with an rmsd of 1.3 å over 35 pairs of backbone cα atoms (fig. ). automated pairwise protein structure superimposition using tm-align [] and fr-tm-align [] produced similar results with a tm-score >0.5, indicating a fold level similarity of α-cop β-sheet domain with other ring domains., zinc finger domains occur in several proteins […]

PMCID: 4506424
PMID: 26185100
DOI: 10.1186/s13062-015-0066-5

[…] ubr-box (pdb identifiers 3ny1, 3ny2, 3ny3, 3nih, 3nii, 3nij, 3nik, 3nil, 3nim, 3nin, 3nis and 3nit) and other treble clef domains were retrieved from the pdb. dali [], topsearch [], tm-align [] and fr-tm-align [] tools were used to evaluate structural similarity of the ubr-box with other proteins. the structures were visualized, compared and manually superimposed in the molecular visualization […]

PMCID: 4468813
PMID: 26082804
DOI: 10.1186/s13321-015-0067-5

[…] were detected by meta-threading using ethread []. we note that weak homology is defined by the maximum sequence identity of 40 %, and the structural similarity of ≥0.4 tm-score [] as reported by fr-tm-align []. furthermore, only non-covalently bound small organic compounds with 6–100 heavy atoms were selected. as the result, a representative and non-redundant pdb-bench comprises 3,659 […]


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Fr-TM-align institution(s)
Center for the Study of Systems Biology, School of Biology, Georgia Institute of Technology, Atlanta, USA
Fr-TM-align funding source(s)
This research was supported in part by NIH grant No. GM-48845.

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