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Citations per year

Number of citations per year for the bioinformatics software tool TM-Score
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This map represents all the scientific publications referring to TM-Score per scientific context
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Protocols

TM-Score specifications

Information


Unique identifier OMICS_16759
Name TM-Score
Interface Web user interface
Restrictions to use None
Input data The template/model structure, the experimental structure.
Input format .PDB
Output data The TM-score.
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Yang Zhang

Information


Unique identifier OMICS_16759
Name TM-Score
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data The template/model structure, the experimental structure.
Input format .PDB
Output data The TM-score.
Operating system Unix/Linux
Programming languages Fortran, Java
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Yang Zhang

Publications for TM-Score

TM-Score citations

 (171)
library_books

Large scale computational drug repositioning to find treatments for rare diseases

2018
NPJ Syst Biol Appl
PMCID: 5847522
PMID: 29560273
DOI: 10.1038/s41540-018-0050-7

[…] eonine-protein kinase Pim-1, was built based on the structure of the murine AMP-activated protein kinase (PDB-ID: 5ufu, chain A, 31.3% sequence identity to Pim-1). This model has a Template Modeling (TM)-score of 0.86 and a Cα-root-mean-square deviation (RMSD) of 5.47 Å against the crystal structure of Pim-1 (PDB-ID: 1yhs, chain A), with a Matthews correlation coefficient (MCC) between predicted a […]

library_books

In silico structural and functional prediction of African swine fever virus protein B263R reveals features of a TATA binding protein

2018
PeerJ
PMCID: 5825884
PMID: 29492339
DOI: 10.7717/peerj.4396

[…] ave the same fold family assignment in either Structural Classification of Proteins (SCOPe) () or Class, Architecture, Topology, and Homology (CATH) () structural classification databases for a given TM score (). For pB263R model 1a, the top eight of 10 experimentally solved TBP structures identified by TM-align had >97.5% posterior probability of sharing a similar fold with pB263R model 1a in bot […]

call_split

Heat activation is intrinsic to the pore domain of TRPV1

2017
Proc Natl Acad Sci U S A
PMCID: 5777071
PMID: 29279388
DOI: 10.1073/pnas.1717192115
call_split See protocol

[…] s of Kv and TRPV1 channels. Atomic coordinates for the pore domain (including S5, pore helix, and S6) of the Kv channel (R322–N410) and the TRPV1 channel (R575–N687) were superimposed and Cα rmsd and TM score calculated using TM align (). TM scores range from 0 to 1 and unlike rmsd are not dependent on the size of the region being compared, with values above 0.5 indicating a high degree of structu […]

library_books

Leishmania infantum 5’ Methylthioadenosine Phosphorylase presents relevant structural divergence to constitute a potential drug target

2017
BMC Struct Biol
PMCID: 5738077
PMID: 29258562
DOI: 10.1186/s12900-017-0079-7

[…] aining models (see Additional file : Table S2). Thus, model 1 was considered as the best one in both cases, and was retained for this study. The 3D model of LiMTAP had a C-score of 1.17, an estimated TM-score of 0.87 ± 0.07 and an estimated root-mean-square deviation RMSD of 3.8 ± 2.6 Ǻ. The 3D model of TbMTAP had a C-score of 0.96, an estimated TM-score of 0.84 ± 0.08 and an estimated RMSD of 4.3 […]

library_books

First insights into a type II toxin antitoxin system from the clinical isolate Mycobacterium sp. MHSD3, similar to epsilon/zeta systems

2017
PLoS One
PMCID: 5728571
PMID: 29236773
DOI: 10.1371/journal.pone.0189459

[…] hown in . The toxin was predicted to be composed of 7 α-helix and 5 β-layers, while the H.P. was predicted to be composed of 5 α-helices.The best model for the H.P. exhibited a C-score of -3.85 and a TM-score of 0.30±0.10; the best model for the zeta-toxin exhibited a C-score of -0.59 and a TM-score of 0.64±0.13. From the available structures, the most suitable structural analogue identified by I- […]

library_books

DeepSF: deep convolutional neural network for mapping protein sequences to folds

2017
Bioinformatics
PMCID: 5905591
PMID: 29228193
DOI: 10.1093/bioinformatics/btx780

[…] TMscore among all the models generated by top templates is selected for comparison. The quality of best predicted models from DeepSF and HHSearch is evaluated against the native structure in terms of TM-score and RMSD ().Here, we mainly evaluated template ranking and protein structure prediction on the 95 template-free CASP targets assuming that our method is more useful for detecting structural s […]


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TM-Score institution(s)
Center of Excellence in Bioinformatics, University at Buffalo, Buffalo, New York, NY, USA; Department of Medical School, Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Department of Molecular Biosciences, Center for Bioinformatics, University of Kansas, Lawrence, KS, USA
TM-Score funding source(s)
This work was supported in part by NIH grant GM-48835 of the Division of General Medical Sciences.

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