Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method
Published 2015 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method
Authors
Keywords
Free energy, Point mutation, Dielectrics, Mutation databases, Hydrogen bonding, Substitution mutation, Algorithms, Molecular dynamics
Journal
PLoS Computational Biology
Volume 11, Issue 7, Pages e1004276
Publisher
Public Library of Science (PLoS)
Online
2015-07-07
DOI
10.1371/journal.pcbi.1004276
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Using DelPhi Capabilities to Mimic Protein’s Conformational Reorganization with Amino Acid Specific Dielectric Constants
- (2016) Lin Wang et al. Communications in Computational Physics
- Protein–protein binding affinity prediction from amino acid sequence
- (2014) K. Yugandhar et al. BIOINFORMATICS
- Predicting the Impact of Missense Mutations on Protein–Protein Binding Affinity
- (2014) Minghui Li et al. Journal of Chemical Theory and Computation
- Combining Structural Modeling with Ensemble Machine Learning to Accurately Predict Protein Fold Stability and Binding Affinity Effects upon Mutation
- (2014) Niklas Berliner et al. PLoS One
- Molecular origins of binding affinity: seeking the Archimedean point
- (2013) Panagiotis L Kastritis et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- BeAtMuSiC: prediction of changes in protein–protein binding affinity on mutations
- (2013) Yves Dehouck et al. NUCLEIC ACIDS RESEARCH
- Applying Physics-Based Scoring to Calculate Free Energies of Binding for Single Amino Acid Mutations in Protein-Protein Complexes
- (2013) Hege Beard et al. PLoS One
- Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions
- (2013) Rocco Moretti et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- pH-selective mutagenesis of protein-protein interfaces:In silicodesign of therapeutic antibodies with prolonged half-life
- (2013) Velin Z. Spassov et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
- Protonation and pK changes in protein–ligand binding
- (2013) Alexey V. Onufriev et al. QUARTERLY REVIEWS OF BIOPHYSICS
- SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models
- (2012) Iain H. Moal et al. BIOINFORMATICS
- On the binding affinity of macromolecular interactions: daring to ask why proteins interact
- (2012) P. L. Kastritis et al. Journal of the Royal Society Interface
- Protein-binding dynamics imaged in a living cell
- (2012) Y. Phillip et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- DelPhi: a comprehensive suite for DelPhi software and associated resources
- (2012) Lin Li et al. BMC Biophysics
- Alchemical free energy methods for drug discovery: progress and challenges
- (2011) John D Chodera et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Applications of isothermal titration calorimetry in pure and applied research-survey of the literature from 2010
- (2011) Rajesh Ghai et al. JOURNAL OF MOLECULAR RECOGNITION
- A Smoothed Backbone-Dependent Rotamer Library for Proteins Derived from Adaptive Kernel Density Estimates and Regressions
- (2011) Maxim V. Shapovalov et al. STRUCTURE
- Statistics and Physical Origins of pK and Ionization State Changes upon Protein-Ligand Binding
- (2010) Boris Aguilar et al. BIOPHYSICAL JOURNAL
- Protein binding specificity versus promiscuity
- (2010) Gideon Schreiber et al. CURRENT OPINION IN STRUCTURAL BIOLOGY
- Assessing the performance of the molecular mechanics/Poisson Boltzmann surface area and molecular mechanics/generalized Born surface area methods. II. The accuracy of ranking poses generated from docking
- (2010) Tingjun Hou et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Prediction of protein–ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations
- (2010) Julien Michel et al. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN
- A Simple Definition of Structural Regions in Proteins and Its Use in Analyzing Interface Evolution
- (2010) Emmanuel D. Levy JOURNAL OF MOLECULAR BIOLOGY
- Small molecules of different origins have distinct distributions of structural complexity that correlate with protein-binding profiles
- (2010) P. A. Clemons et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The Structural Basis of Peptide-Protein Binding Strategies
- (2010) Nir London et al. STRUCTURE
- Energetic determinants of protein binding specificity: Insights into protein interaction networks
- (2009) Pablo Carbonell et al. PROTEOMICS
- Predicting free energy changes using structural ensembles
- (2008) Alexander Benedix et al. NATURE METHODS
Add your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload NowBecome a Peeref-certified reviewer
The Peeref Institute provides free reviewer training that teaches the core competencies of the academic peer review process.
Get Started