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ProTherm specifications


Unique identifier OMICS_07149
Name ProTherm
Restrictions to use None
Maintained No

Publications for ProTherm

ProTherm citations


Identification and in silico analysis of functional SNPs of human TAGAP protein: A comprehensive study

PLoS One
PMCID: 5766082
PMID: 29329296
DOI: 10.1371/journal.pone.0188143

[…] et protein, I-Mutant 2.0 was used which is a support vector machine based web server that helps in predicting any change in stability of protein after getting mutated. The tool uses data derived from ProTherm which is currently the most comprehensive database of experimental data on protein mutations. It predicts reliability index (RI) of the results ranging from 0–10, where 10 being the highest r […]


Mapping genetic variations to three dimensional protein structures to enhance variant interpretation: a proposed framework

Genome Med
PMCID: 5735928
PMID: 29254494
DOI: 10.1186/s13073-017-0509-y

[…] n–protein [, –], protein–nucleic acid [], and protein–ligand complexes []. These methods have been trained on data from wild-type and mutant protein pairs, often using protein stability data from the ProTherm database [], protein–protein binding affinities from SKEMPI [], protein–nucleic acid binding affinities from ProNIT [], and protein–ligand binding affinities from Platinum [].A second set of […]


Global computational mutagenesis provides a critical stability framework in protein structures

PLoS One
PMCID: 5720693
PMID: 29216252
DOI: 10.1371/journal.pone.0189064

[…] tation screen to evaluate the severity of a single mutation to show an agreement of predicted values (~78%) with phenotypes from retinal disease and changes of protein stability for proteins from the ProTherm database []. The most severe mutations cause a protein instability, which has the potential to lead to a complete loss of protein function. These severe mutations make up the critical stabili […]


Computing disease linked SOD1 mutations: deciphering protein stability and patient phenotype relations

Sci Rep
PMCID: 5498623
PMID: 28680046
DOI: 10.1038/s41598-017-04950-9

[…] Topham et al.. I-Mutant 2.0 and I-Mutant 3.0 are based on support vector machines that consider mainly amino acid substitution and structural environment, trained on experimental data points from the Protherm data base. mCSM method is based on graph-based signatures using the atom distances to construct environments that are subsequently been trained on the experimental data. BeatMusic (http://bab […]


Sequence statistics of tertiary structural motifs reflect protein stability

PLoS One
PMCID: 5446159
PMID: 28552940
DOI: 10.1371/journal.pone.0178272

[…] istics as a novel quantitative metric, which although not devoid of biases, should nevertheless be useful in practice with broad applicability.Methods for ΔΔGm prediction have generally relied on the ProTherm database for training/testing. An invaluable large compendium of protein thermodynamic data, the database nevertheless represents a biased set of mutations, strongly skewed towards those more […]


Computational predictors fail to identify amino acid substitution effects at rheostat positions

Sci Rep
PMCID: 5278360
PMID: 28134345
DOI: 10.1038/srep41329

[…] ng data are extracted from Swiss-Prot (disease vs. polymorphism variants) and enriched with OMIM annotations.iMutant3 offers different SVMs to predict (i) stability changes, using SVMs trained on the ProTherm database, from sequence only or from structural information, and (ii) disease associated variants from sequence only using the PhD-SNP prediction pipeline.nsSNPAnalyzer uses a random forest c […]


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ProTherm institution(s)
Department of Bioscience and Bioinformatics, Kyushu Institute of Technology (KIT), Japan

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