TM-Score pipeline

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

 (5)
2017
PMCID: 5399370

[…] in molecular docking analysis, as discussed below. despite the low sequence identity among c. gigas and mammalian ilbps, 3d models obtained by threading-homology modeling showed high quality models (tm-score higher then 0.7). all members display a conserved fabp structural fold with 2 α-helices and 10 β-strands, except for cgilbp1b, which exhibits a shorter n-terminal region, and α-helix 2 […]

2015
PMCID: 4642563

[…] of a model’s hydrogen-bonding network. the model quality evaluation automatically calculated by i-tasser indicated that the resulting model had a high confidence (c-score = −0.78, estimated tm score = 0.61 ± 0.14). visualization and analysis of the modelled structure was performed with pymol., how to cite this article: zhang, w. et al. identification of residues important for substrate […]

2015
PMCID: 4694711

[…] reoccurring structural features such as secondary structure elements., fig 2 reveals that predictions for two converged targets, namely 5p21 and 1bdo, resulted in models with an rmsd > 10 å. the tm-score is however above 0.5 in both cases, i.e. 0.65 and 0.58, respectively, showing that the majority of the protein structure was predicted correctly. the good accordance between the top-scoring […]

2012
PMCID: 3598710

[…] for example, in the case of cyp74a modelling (additional file 8), i-tasser utilized a special force field to refine the models. however, it performed even worse than muster in terms of rmsd and tm-score [48]. we found that many models, following energy minimization, were worse than the initial bmcd models, as evaluated by the profile-3d ratio. therefore, we only refined the residues around […]

2007
PMCID: 1878469

[…] however, as strong distance and contact restraints have been implemented in the second-round simulation, the topology improvement of the models is modest. for the 200 test proteins, the average tm-score [22] increases from 0.5734 to 0.5801 (1.2%) and cα-rmsd to native decreases from 6.67å to 6.52å compared with the cluster centroid of the first round. another option of removing the steric […]

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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