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References from Limitations and challenges in protein stability prediction upon genome variations: towards future applications in precision medicine. Local targets link to admitted publications; unresolved targets remain external evidence.
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Large scale analysis of protein stability in OMIM disease related human protein variants
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A review study: computational techniques for expecting the impact of non-synonymous single nucleotide variants in human diseases
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Quantification of biases in predictions of protein stability changes upon mutations
10.1093/bioinformatics/bty348 · 2018 · External reference
A critical review of five machine learning-based algorithms for predicting protein stability changes upon mutation
2019 · External reference
Stability curve prediction of homologous proteins using temperature-dependent statistical potentials
10.1371/journal.pcbi.1003689 · 2014 · External reference
Variation benchmark datasets: update, criteria, quality and applications
10.1093/database/baz117 · 2020 · External reference
ProTherm and ProNIT: thermodynamic databases for proteins and protein-nucleic acid interactions
10.1093/nar/gkj103 · 2006 · External reference
Computational tools help improve protein stability but with a solubility tradeoff
10.1074/jbc.m117.784165 · 2017 · External reference
DeepDDG: predicting the stability change of protein point mutations using neural networks
10.1021/acs.jcim.8b00697 · 2019 · External reference
10.1016/s0022-2836(02)00442-4
10.1016/s0022-2836(02)00442-4 · External reference
Towards a “Golden Standard” for computing globin stability: Stability and structure sensitivity of myoglobin mutants
2015 · External reference
10.1093/bioinformatics/btt691
10.1093/bioinformatics/btt691 · External reference
DDGun: an untrained method for the prediction of protein stability changes upon single and multiple point variations
10.1186/s12859-019-2923-1 · 2019 · External reference
10.1093/bioinformatics/btw361
10.1093/bioinformatics/btw361 · External reference
A neural-network-based method for predicting protein stability changes upon single point mutations
10.1093/bioinformatics/bth928 · 2004 · External reference
EASE-MM: sequence-based prediction of mutation-induced stability changes with feature-based multiple models
10.1016/j.jmb.2016.01.012 · 2016 · External reference
iPTREE-STAB: interpretable decision tree based method for predicting protein stability changes upon mutations
10.1093/bioinformatics/btm100 · 2007 · External reference
I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure
10.1093/nar/gki375 · 2005 · External reference
10.1093/protein/gzp030
10.1093/protein/gzp030 · External reference
PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality
10.1186/1471-2105-12-151 · 2011 · External reference
Predicting changes in protein thermostability brought about by single- or multi-site mutations
10.1186/1471-2105-11-370 · 2010 · External reference
iStable 2.0: Predicting protein thermal stability changes by integrating various characteristic modules. Comput Struct
2020 · External reference
VariBench: a benchmark database for variations
10.1002/humu.22204 · 2013 · External reference
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10.1002/1097-0134(20001115)41:3<385::aid-prot100>3.0.co;2-r · External reference
CUPSAT: prediction of protein stability upon point mutations
10.1093/nar/gkl190 · 2006 · External reference
Predicting binding free energy change caused by point mutations with knowledge-modified MM/PBSA method
10.1371/journal.pcbi.1004276 · 2015 · External reference
10.1021/acs.chemrev.9b00055
10.1021/acs.chemrev.9b00055 · External reference
SAAFEC: predicting the effect of single point mutations on protein folding free energy using a knowledge-modified MM/PBSA approach
10.3390/ijms17040512 · 2016 · External reference
A three-state prediction of single point mutations on protein stability changes
10.1186/1471-2105-9-s2-s6 · 2008 · External reference
10.1093/nar/gku411
10.1093/nar/gku411 · External reference
10.1002/humu.21242
10.1002/humu.21242 · External reference
INPS: predicting the impact of non-synonymous variations on protein stability from sequence
10.1093/bioinformatics/btv291 · 2015 · External reference
Protein design is NP-hard
10.1093/protein/15.10.779 · 2002 · External reference
The SAAPdb web resource: a large-scale structural analysis of mutant proteins
10.1002/humu.20898 · 2009 · External reference
SDM: a server for predicting effects of mutations on protein stability
10.1093/nar/gkx439 · 2017 · External reference
PROTS-RF: a robust model for predicting mutation-induced protein stability changes
10.1371/journal.pone.0047247 · 2012 · External reference
10.1093/bioinformatics/bty340
10.1093/bioinformatics/bty340 · External reference
Predicting protein thermostability changes from sequence upon multiple mutations
10.1093/bioinformatics/btn166 · 2008 · External reference
10.1093/bioinformatics/btp370
10.1093/bioinformatics/btp370 · External reference
10.1002/prot.20810
10.1002/prot.20810 · External reference
Protein stability: a single recorded mutation aids in predicting the effects of other mutations in the same amino acid site
10.1093/bioinformatics/btr576 · 2011 · External reference
iStable: off-the-shelf predictor integration for predicting protein stability changes
10.1186/1471-2105-14-s2-s5 · 2013 · External reference
NeEMO: a method using residue interaction networks to improve prediction of protein stability upon mutation
10.1186/1471-2164-15-s4-s7 · 2014 · External reference
INPS-MD: a web server to predict stability of protein variants from sequence and structure
10.1093/bioinformatics/btw192 · 2016 · External reference
10.1093/bioinformatics/btw031
10.1093/bioinformatics/btw031 · External reference
MAESTRO–multi agent stability prediction upon point mutations
10.1186/s12859-015-0548-6 · 2015 · External reference
Analysis and prediction of protein folding energy changes upon mutation by element specific persistent homology
2017 · External reference
DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability
10.1093/nar/gky300 · 2018 · External reference
ProTstab – predictor for cellular protein stability
10.1186/s12864-019-6138-7 · 2019 · External reference
On the biases in predictions of protein stability changes upon variations: the INPS test case
10.1093/bioinformatics/bty979 · 2019 · External reference
On the upper bounds of the real-valued predictions
10.1177/1177932219871263 · 2019 · External reference
10.1093/bioinformatics/btl461
10.1093/bioinformatics/btl461 · External reference
10.1186/s12864-019-6413-7
10.1186/s12864-019-6413-7 · External reference
On the critical review of five machine learning-based algorithms for predicting protein stability changes upon mutation
2019 · External reference
Reports from the fifth edition of CAGI: the critical assessment of genome interpretation
10.1002/humu.23876 · 2019 · External reference
10.1002/humu.23789
10.1002/humu.23789 · External reference
Evaluating the predictions of the protein stability change upon single amino acid substitutions for the FXN CAGI5 challenge
10.1002/humu.23843 · 2019 · External reference
10.1093/bioinformatics/16.5.412
10.1093/bioinformatics/16.5.412 · External reference
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10.1002/humu.21555 · External reference
Understanding the impacts of missense mutations on structures and functions of human cancer-related genes: a preliminary computational analysis of the COSMIC Cancer Gene Census
10.1371/journal.pone.0219935 · 2019 · External reference
Synthesis and Structure-Activity relationship of 1-(5-isoquinolinesulfonyl)piperazine analogues as inhibitors of Mycobacterium tuberculosis IMPDH
10.1016/j.ejmech.2019.04.027 · 2019 · External reference
Identification and characterization of genetic determinants of isoniazid and rifampicin resistance in mycobacterium tuberculosis in Southern India
10.1038/s41598-019-46756-x · 2019 · External reference
10.1016/j.csbj.2019.03.004
10.1016/j.csbj.2019.03.004 · External reference
Mapping genetic variations to three-dimensional protein structures to enhance variant interpretation: a proposed framework
10.1186/s13073-017-0509-y · 2017 · External reference
10.1002/humu.22145
10.1002/humu.22145 · External reference
Structural analysis of disease-related TDP-43 D169G mutation: linking enhanced stability and caspase cleavage efficiency to protein accumulation
10.1038/srep21581 · 2016 · External reference
10.1016/j.cell.2012.02.063
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Pan-specific prediction of peptide-MHC class I complex stability, a correlate of T cell immunogenicity
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