TM-Score protocols

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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 in pipelines

 (9)
2017
PMCID: 5539115
PMID: 28765603
DOI: 10.1038/s41598-017-07156-1

[…] within predicted loop regions (c), medium-level of flexibility in sheets (e) and low flexibility within helices (h) provided highest cumulative and mean rs values calculated on the dataset., tm-score is a robust, length-independent protein structural similarity metric. it is routinely used in many structure prediction problems. the higher the tm-score is (on the scale of 0 to 1), […]

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

[…] <e decoy> and δare respectively the average and the standard deviation of energy scores of structural decoys cthe average pearson’s correlation coefficient between the energy score and tm-score of all structures in each decoy set, including the native structure dthe potential based on the averaging reference state with both distance cutoff and residue interval to be 6 ethe […]

2017
PMCID: 5739537
PMID: 29199956
DOI: 10.7554/eLife.29023.046

[…] sequence identity templates (<80% to the target) followed by side chain energy minimization using tinker as described above. the quality of the ab models was extremely accurate (), both overall (tm-score: 0.95) and for cdrs (<2 å for cdr-h3 and sub-angstrom for others), consistent with a report on cdr-h3 modeling quality ()., ag targets were either crystal structures from the bound […]

2016
PMCID: 5860252
PMID: 28171606
DOI: 10.1093/bioinformatics/btw618

[…] evenly spread (one correctly predicted contact every 12 residues) ()., we have assessed whether the proportion of satisfied predicted contacts can be used to discriminate between correct (tm-score > 0.5) and incorrect models. for this analysis, we used the 10 000 decoys generated using saint2 and metapsicov stage 1 for each of the 41 protein in our pdb-representative dataset. […]

2015
PMCID: 4580646
PMID: 26398185
DOI: 10.1371/journal.pntd.0004099

[…] function database. the trypanosoma rangeli trans-sialidase (pdb id: 1wcs) was used as an additional restraint template to generate the model. the best model generated had a template modelling score (tm-score) of 0.50±0.15. for reference, a tm-score >0.5 indicates a model of correct topology (independent of protein length) and a tm-score <0.17 means a random similarity []., the dna encoding […]


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TM-Score in publications

 (93)
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 […]

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 […]

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). […]

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’) […]

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 […]


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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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