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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

 (93)
library_books

Large scale computational drug repositioning to find treatments for rare diseases

2018
PMCID: 5847522
PMID: 29560273
DOI: 10.1038/s41540-018-0050-7

[…] (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 and staurosporine-binding residues of 0.67. the tm-score and cα-rmsd are described in the supplementary text s3. the model of synapsin ia constructed based on a remote template α-aminoadipate-lysw ligase lysx (pdb-id: 3vpd, chain a, 22.8% sequence […]

library_books

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

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

[…] [–]. the features, best model and best structural analogs were selected by the c-score, which ranged between -5 and 2 (higher values indicate a higher confidence in the model obtained), and the tm-score, which measures the structural similarity between two proteins, with values ranging between 0 and 1, with 1 indicating a perfect structural match []. i-tasser uses the structures available […]

library_books

Diverse effects of distance cutoff and residue interval on the performance of distance dependent atom pair potential in protein structure prediction

2017
PMCID: 5723101
PMID: 29221443
DOI: 10.1186/s12859-017-1983-3

[…] less than 2% of potentials.fig. 6 fig. 7 , as shown in additional file : figure s4, short distance cutoffs are never good choices for potentials to achieve more significant pccs between energies and tm-score, which is a general observation on all six groups of decoy sets. but the effects of the residue interval vary significantly with different decoy sets (see additional file : figure s5). […]

library_books

A fragment based method for modeling of protein segments into cryo EM density maps

2017
PMCID: 5683378
PMID: 29132296
DOI: 10.1186/s12859-017-1904-5

[…] of the corresponding termini and stem atoms., to provide a measure of similarity independent from the number of compared atoms, that is, of fragment length [], the template modeling score (tm-score) was employed to assess the ‘topological similarity’ of two proteins (formula 2a) []. the method is described in detail in ref. []. shortly summarized, the tm-score employs the length (‘l’) […]

library_books

Molecular details of secretory phospholipase A2 from flax (Linum usitatissimum L.) provide insight into its structure and function

2017
PMCID: 5593939
PMID: 28894144
DOI: 10.1038/s41598-017-10969-9

[…] correct folding. the c-score values of 0.75 and 0.83 obtained for luspla2i and luspla2ii respectively indicate that both the protein models are of good quality and correct folding., similarly, the tm-score > 0.5 indicates a model of correct topology and a tm-score < 0.17 means random similarity. the desired tm score of 0.81 ± 0.09 and 0.83 ± 0.08 for luspla2i and luspla2ii respectively […]

library_books

The AraC Negative Regulator family modulates the activity of histone like proteins in pathogenic bacteria

2017
PMCID: 5570504
PMID: 28806780
DOI: 10.1371/journal.ppat.1006545

[…] regulator) and orf2058 (transcriptional activator flhd) were slightly able to interact with aar in this assay ()., the molecular interaction between h-ns and aar was also modeled and assembled by tm-score (tm-score 0.2793 and 0.3555) [], rasmol [] and the ucsf chimera package []. the second α-helix of aar was predicted to interact with the oligomerization domain of h-ns ()., if interaction […]


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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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