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Predicting folding free energy changes upon single point mutations
2012
Computer applications in the biosciences : CABIOS
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In both cases, it is desirable to predict the change of the folding free energy upon single point mutations in order to either provide insights of the molecular mechanism of the change or to design new ...
Results: We report an approach that predicts the free energy change upon single point mutation by utilizing the 3D structure of the wild-type protein. ...
Folding free energy calculation The folding free energy changes upon single point mutations were calculated as described in our previous works (Witham et al., 2011; Zhang et al., 2011; Zhang et al., 2010 ...
doi:10.1093/bioinformatics/bts005
pmid:22238268
pmcid:PMC3289912
fatcat:g2f5gt5yo5gwhlvffblngvusyu
Predicting the Viability of Beta-Lactamase: How Folding and Binding Free Energies Correlate with Beta-Lactamase Fitness
[article]
2020
bioRxiv
pre-print
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folding free energies can meaningfully, although not perfectly, predict the experimental folding free energies of single mutants. ...
free energies will be to the large data sets of multiply-mutated proteins forthcoming. ...
resources were provided by the Brown Center for Computation and Visualization (CCV) and the high-performance computing center at Idaho National Laboratory, which is supported by the Office of Nuclear Energy ...
doi:10.1101/2020.04.15.043661
fatcat:cxren3sq3feuxkzt3yyciycaq4
Predicting the viability of beta-lactamase: How folding and binding free energies correlate with beta-lactamase fitness
2020
PLoS ONE
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as FoldX and PyRosetta can meaningfully, although not perfectly, predict the experimental folding free energies of single mutants. ...
Based upon a set of 21 β-lactamase single and double mutants expressly designed to influence protein folding, we first demonstrate that modeling software designed to compute folding free energies such ...
resources were provided by the Brown Center for Computation and Visualization (CCV) and the high-performance computing center at Idaho National Laboratory, which is supported by the Office of Nuclear Energy ...
doi:10.1371/journal.pone.0233509
pmid:32470971
fatcat:mojihcc47vbc7e3xgjmptojwtu
PROTS-RF: A Robust Model for Predicting Mutation-Induced Protein Stability Changes
2012
PLoS ONE
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Contrary to previous suggestions, our results clearly demonstrate that a robust predictive model trained for predicting single point mutation induced thermostability changes can be capable of predicting ...
In this report we present PROTS-RF, a robust model based on the Random Forest algorithm capable of predicting thermostability changes induced by not only single-, but also double- or multiple-point mutations ...
of experimental data for free energy changes upon mutations of this enzyme [46] . ...
doi:10.1371/journal.pone.0047247
pmid:23077576
pmcid:PMC3471942
fatcat:poqnn3jzwjbhdo4u3573y4hm4e
Proteins Evolution Upon Point Mutations
[article]
2021
arXiv
pre-print
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The preliminary results -- without considering epistasis effects explicitly -- indicate that the protein marginal-stability change upon point mutations provides the necessary and sufficient information ...
This finding is of paramount importance because it illustrates the impact of point mutations on both the protein marginal-stability and the ensemble of folded conformations coexisting with the native state ...
Before we proceed, let us remember: firstly, that G ~ GU will provide us with the Gibbs free energy change in the protein's marginal stability upon point mutation; secondly, the amide HX protection ...
arXiv:2111.04199v2
fatcat:fyhc2uswjfc5lhpdh63ngipaxm
SIMPLE estimate of the free energy change due to aliphatic mutations: Superior predictions based on first principles
2007
Proteins: Structure, Function, and Bioinformatics
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point mutations predicts 20-30% less false positives and yields more accurate predictions than any published empirical energy function. ...
Our first principle analysis strongly suggests that both the solute-solute van der Waals interactions in the folded state and the electrostatics free energy change of exposed aliphatic mutations are almost ...
A simplified version of this problem is predicting changes in structure and stability induced by single point-mutations. ...
doi:10.1002/prot.21453
pmid:17523191
fatcat:hjr25ppg4nd43hli7aoqlm2die
SAAFEC-SEQ: A Sequence-Based Method for Predicting the Effect of Single Point Mutations on Protein Thermodynamic Stability
2021
International Journal of Molecular Sciences
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Here, we report a new development of the SAAFEC method, the SAAFEC-SEQ, which is a gradient boosting decision tree machine learning method to predict the change of the folding free energy caused by amino ...
Modeling the effect of mutations on protein thermodynamics stability is useful for protein engineering and understanding molecular mechanisms of disease-causing variants. ...
the change of folding free energy resulting from a single amino acid mutation. ...
doi:10.3390/ijms22020606
pmid:33435356
fatcat:oksdyq2uuvffdapxhjqpnhk3ea
Using DelPhi capabilities to mimic protein's conformational reorganization with amino acid specific dielectric constants
2013
Communications in Computational Physics
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The predicted energy changes are benchmarked against experimentally measured changes of the folding energy on a set of 257 single mutations. ...
Here we report a large scale investigation of modeling the changes of the folding energy due to single mutations involving charged group. ...
upon single point mutations involving charged amino acid. ...
pmid:24683422
pmcid:PMC3966310
fatcat:xds7mfycrrhuraebgvvjgmx6vm
Predictive shifts in free energy couple mutations to their phenotypic consequences
2019
Proceedings of the National Academy of Sciences of the United States of America
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Finally, we show that the induction profiles and resulting free energies associated with pairwise double mutants can be predicted with quantitative accuracy given knowledge of the single mutants, providing ...
Changing these subsets of parameters tunes the free energy of the system in a way that is concordant with theoretical expectations. ...
To determine the free energy for a given set of fold-change measurements (for 1 unique strain at a single inducer concentration), we modeled the observed fold-change measurements as being drawn from a ...
doi:10.1073/pnas.1907869116
pmid:31451655
pmcid:PMC6744869
fatcat:mkinwoovoneoxeq4x3362m7kni
On the physics of thermal-stability changes upon mutations of a protein
2015
Journal of Chemical Physics
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It is of great interest from both scientific and practical viewpoints to theoretically predict the thermal-stability changes upon mutations of a protein. ...
Our approach is compared with one of the most popular approaches, FOLD-X, in terms of the prediction performance not only for single mutations but also for double, triple, and higher-fold (up to sevenfold ...
The free-energy function of FOLD-X is parameterized using only the experimental data for single mutations. ...
doi:10.1063/1.4931814
pmid:26429043
fatcat:b27w6v3qj5fhjlorarguj4yize
DynaMut: predicting the impact of mutations on protein conformation, flexibility and stability
2018
Nucleic Acids Research
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upon static structures. ...
DynaMut integrates our graph-based signatures along with normal mode dynamics to generate a consensus prediction of the impact of a mutation on protein stability. ...
The change in folding free energy is a thermodynamic state function, and it has been proposed that the change in folding free energy of a mutation from a wild-type protein to its mutant ( G WT→MT ) should ...
doi:10.1093/nar/gky300
pmid:29718330
pmcid:PMC6031064
fatcat:q6mxi3iz5fhn5mf4r3yd4cnnke
Prediction of protein thermostability with a direction- and distance-dependent knowledge-based potential
2005
Protein Science
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A total of 76% of the mutations could be predicted correctly as being either stabilizing or destabilizing. The results for the test set are r = 0.74 (747 data points) and 72%, respectively. ...
The increasing use of enzymes in industrial processes and the importance of understanding protein folding and stability have led to several attempts to predict and quantify the effect of every possible ...
Predicting protein stability changes upon mutation ...
doi:10.1110/ps.04940705
pmid:16155198
pmcid:PMC2253293
fatcat:albymq675fh4hne5ymemhzrhh4
I-Mutant2.0: predicting stability changes upon mutation from the protein sequence or structure
2005
Nucleic Acids Research
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I-Mutant2.0 is a support vector machine (SVM)-based tool for the automatic prediction of protein stability changes upon single point mutations. ...
I-Mutant2.0 can be used both as a classifier for predicting the sign of the protein stability change upon mutation and as a regression estimator for predicting the related DDG values. ...
I-Mutant2.0 was also trained/tested to predict the value of the free energy stability change upon single point mutation, starting from the protein structure or sequence. ...
doi:10.1093/nar/gki375
pmid:15980478
pmcid:PMC1160136
fatcat:rhp4qihyizasnijx5yaqusm33u
Using DelPhi Capabilities to Mimic Protein's Conformational Reorganization with Amino Acid Specific Dielectric Constants
2013
Communications in Computational Physics
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The predicted energy changes are benchmarked against experimentally measured changes of the folding energy on a set of 257 single mutations. ...
Here we report a large scale investigation of modeling the changes of the folding energy due to single mutations involving charged group. ...
The compiled folding energy changes, the corresponding structures and in silico made mutant structures, along with calculated energies are available from http://compbio. clemson.edu/delphi.php and clicking ...
doi:10.4208/cicp.300611.120911s
fatcat:pzikfyizgberjky5irovopednq
Biophysical ambiguities prevent accurate genetic prediction
2020
Nature Communications
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This apparent paradox arises because mutations can have different biophysical effects to cause the same change in a phenotype and the outcome in a double mutant depends upon what these hidden biophysical ...
changes actually are. ...
of changes in the free energy of folding (ΔΔG F ) and DNA binding (ΔΔG B ). ...
doi:10.1038/s41467-020-18694-0
pmid:33004824
fatcat:lttls7z3xfcbjnsx42rv5gk6rm
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