ArticleCommunications in computational physics2013
Using DelPhi capabilities to mimic protein's conformational reorganization with amino acid specific dielectric constants.
Article in Communications in computational physics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- NanoShaper-VMD interface: computing and visualizing surfaces, pockets and channels in molecular systems.Bioinformatics (Oxford, England) · 2019Article
- Reproducing the Ensemble Average Polar Solvation Energy of a Protein from a Single Structure: Gaussian-Based Smooth Dielectric Function for Macromolecular Modeling.Journal of chemical theory and computation · 2018Article
- Electrostatic component of binding energy: Interpreting predictions from poisson-boltzmann equation and modeling protocols.Journal of computational chemistry · 2016Article
- Electrostatic effects on the folding stability of FKBP12.Protein engineering, design & selection : PEDS · 2016Article
- SAAFEC: Predicting the Effect of Single Point Mutations on Protein Folding Free Energy Using a Knowledge-Modified MM/PBSA Approach.International journal of molecular sciences · 2016Article
- pKa predictions for proteins, RNAs, and DNAs with the Gaussian dielectric function using DelPhi pKa.Proteins · 2015Article
- Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method.PLoS computational biology · 2015Article
- On the energy components governing molecular recognition in the framework of continuum approaches.Frontiers in molecular biosciences · 2015Review
- Modeling the electrostatic potential of asymmetric lipopolysaccharide membranes: the MEMPOT algorithm implemented in DelPhi.Journal of computational chemistry · 2014Article
- On the Modeling of Polar Component of Solvation Energy using Smooth Gaussian-Based Dielectric Function.Journal of theoretical & computational chemistry · 2014Article
- On the Dielectric "Constant" of Proteins: Smooth Dielectric Function for Macromolecular Modeling and Its Implementation in DelPhi.Journal of chemical theory and computation · 2013Article
- Progress in developing Poisson-Boltzmann equation solvers.Molecular based mathematical biology · 2013Article
- DelPhi: a comprehensive suite for DelPhi software and associated resources.BMC biophysics · 2012Article
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Authors and funding
4 authors.
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Abstract
Many molecular events are associated with small or large conformational changes occurring in the corresponding proteins. Modeling such changes is a challenge and requires significant amount of computing time. From point of view of electrostatics, these changes can be viewed as a reorganization of local charges and dipoles in response to the changes of the electrostatic field, if the cause is insertion or deletion of a charged amino acid. Here we report a large scale investigation of modeling the changes of the folding energy due to single mutations involving charged group. This allows the changes of the folding energy to be considered mostly electrostatics in origin and to be calculated with DelPhi assigning residue-specific value of the internal dielectric constant of protein. The predicted energy changes are benchmarked against experimentally measured changes of the folding energy on a set of 257 single mutations. The best fit between experimental values and predicted changes is used to find out the effective value of the internal dielectric constant for each type of amino acid. The predicted folding free energy changes with the optimal, amino acid specific, dielectric constants are within RMSD=0.86 kcal/mol from experimentally measured changes.
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