The impact of interior dielectric constant and entropic change on HIV-1 complex binding free energy prediction
出版年份 2018 全文链接
标题
The impact of interior dielectric constant and entropic change on HIV-1 complex binding free energy prediction
作者
关键词
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出版物
Structural Dynamics
Volume 5, Issue 6, Pages 064101
出版商
AIP Publishing
发表日期
2018-12-15
DOI
10.1063/1.5058172
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注意:仅列出部分参考文献,下载原文获取全部文献信息。- Determination of absolute configuration and binding efficacy of benzimidazole-based FabI inhibitors through the support of electronic circular dichroism and MM-GBSA techniques
- (2018) Jinhong Ren et al. BIOORGANIC & MEDICINAL CHEMISTRY LETTERS
- Computational Alanine Scanning with Interaction Entropy for Protein–Ligand Binding Free Energies
- (2018) Xiao Liu et al. Journal of Chemical Theory and Computation
- Assessing the performance of MM/PBSA and MM/GBSA methods. 7. Entropy effects on the performance of end-point binding free energy calculation approaches
- (2018) Huiyong Sun et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Statistical Analysis on the Performance of Molecular Mechanics Poisson–Boltzmann Surface Area versus Absolute Binding Free Energy Calculations: Bromodomains as a Case Study
- (2017) Matteo Aldeghi et al. Journal of Chemical Information and Modeling
- Efficient Approximation of Ligand Rotational and Translational Entropy Changes upon Binding for Use in MM-PBSA Calculations
- (2017) Ido Y. Ben-Shalom et al. Journal of Chemical Information and Modeling
- Interaction Entropy for Computational Alanine Scanning
- (2017) Yuna Yan et al. Journal of Chemical Information and Modeling
- Interaction entropy for protein-protein binding
- (2017) Zhaoxi Sun et al. JOURNAL OF CHEMICAL PHYSICS
- Protocol for fast screening of multi-target drug candidates: Application to Alzheimer’s disease
- (2017) Nguyen Quoc Thai et al. JOURNAL OF MOLECULAR GRAPHICS & MODELLING
- Orcein-Related Small Molecule O4 Destabilizes hIAPP Protofibrils by Interacting Mostly with the Amyloidogenic Core Region
- (2017) Yu Zou et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Effect of electrostatic polarization and bridging water on CDK2–ligand binding affinities calculated using a highly efficient interaction entropy method
- (2017) Lili Duan et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- An efficient method for computing excess free energy of liquid
- (2017) Jianing Song et al. Science China-Chemistry
- Interaction entropy for computational alanine scanning in protein-protein binding
- (2017) Linqiong Qiu et al. Wiley Interdisciplinary Reviews-Computational Molecular Science
- Effect of polarization on HIV-1protease and fluoro-substituted inhibitors binding energies by large scale molecular dynamics simulations
- (2017) Li L. Duan et al. Scientific Reports
- Trypsin-Ligand binding affinities calculated using an effective interaction entropy method under polarized force field
- (2017) Yalong Cong et al. Scientific Reports
- New Parameters for Higher Accuracy in the Computation of Binding Free Energy Differences upon Alanine Scanning Mutagenesis on Protein–Protein Interfaces
- (2016) Inês C. M. Simões et al. Journal of Chemical Information and Modeling
- Calculating protein-ligand binding affinities with MMPBSA: Method and error analysis
- (2016) Changhao Wang et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein–Ligand Binding Free Energy
- (2016) Lili Duan et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Assessing the performance of the MM/PBSA and MM/GBSA methods. 6. Capability to predict protein–protein binding free energies and re-rank binding poses generated by protein–protein docking
- (2016) Fu Chen et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Large-scale molecular dynamics simulation: Effect of polarization on thrombin-ligand binding energy
- (2016) Li L. Duan et al. Scientific Reports
- Some Practical Approaches to Treating Electrostatic Polarization of Proteins
- (2014) Changge Ji et al. ACCOUNTS OF CHEMICAL RESEARCH
- Comparative Assessment of Scoring Functions on an Updated Benchmark: 2. Evaluation Methods and General Results
- (2014) Yan Li et al. Journal of Chemical Information and Modeling
- Computing Clinically Relevant Binding Free Energies of HIV-1 Protease Inhibitors
- (2014) David W. Wright et al. Journal of Chemical Theory and Computation
- Protein's native structure is dynamically stabilized by electronic polarization
- (2014) Li L. Duan et al. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY
- Assessing the performance of MM/PBSA and MM/GBSA methods. 4. Accuracies of MM/PBSA and MM/GBSA methodologies evaluated by various simulation protocols using PDBbind data set
- (2014) Huiyong Sun et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Assessing the performance of MM/PBSA and MM/GBSA methods. 5. Improved docking performance using high solute dielectric constant MM/GBSA and MM/PBSA rescoring
- (2014) Huiyong Sun et al. PHYSICAL CHEMISTRY CHEMICAL PHYSICS
- Energetics of protein backbone hydrogen bonds and their local electrostatic environment
- (2014) Li L. Duan et al. Science China-Chemistry
- Computational Alanine Scanning Mutagenesis: MM-PBSA vs TI
- (2013) Sílvia A. Martins et al. Journal of Chemical Theory and Computation
- Assessing the Performance of MM/PBSA and MM/GBSA Methods. 3. The Impact of Force Fields and Ligand Charge Models
- (2013) Lei Xu et al. JOURNAL OF PHYSICAL CHEMISTRY B
- A numerically stable restrained electrostatic potential charge fitting method
- (2012) Juan Zeng et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Effect of atomic charge, solvation, entropy, and ligand protonation state on MM-PB(GB)SA binding energies of HIV protease
- (2012) Daniel P. Oehme et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Origin of Decrease in Potency of Darunavir and Two Related Antiviral Inhibitors against HIV-2 Compared to HIV-1 Protease
- (2012) Parimal Kar et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Folding of a Helix Is Critically Stabilized by Polarization of Backbone Hydrogen Bonds: Study in Explicit Water
- (2012) Li L. Duan et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Improving MM-GB/SA Scoring through the Application of the Variable Dielectric Model
- (2011) Krishna Ravindranathan et al. Journal of Chemical Theory and Computation
- A Direct Comparison of the MM-GB/SA Scoring Procedure and Free-Energy Perturbation Calculations Using Carbonic Anhydrase as a Test Case: Strengths and Pitfalls of Each Approach
- (2011) Cristiano R. W. Guimarães Journal of Chemical Theory and Computation
- Fast and accurate computation schemes for evaluating vibrational entropy of proteins
- (2011) Beisi Xu et al. JOURNAL OF COMPUTATIONAL CHEMISTRY
- Quantifying the Stabilizing Energy of the Intraprotein Hydrogen Bond Due to Local Mutation
- (2011) Chang G. Ji et al. JOURNAL OF PHYSICAL CHEMISTRY B
- Addressing Limitations with the MM-GB/SA Scoring Procedure using the WaterMap Method and Free Energy Perturbation Calculations
- (2010) Cristiano R. W. Guimarães et al. Journal of Chemical Information and Modeling
- Accurate Ensemble Molecular Dynamics Binding Free Energy Ranking of Multidrug-Resistant HIV-1 Proteases
- (2010) S. Kashif Sadiq et al. Journal of Chemical Information and Modeling
- Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations
- (2010) Tingjun Hou et al. Journal of Chemical Information and Modeling
- Electrostatic Polarization Makes a Substantial Contribution to the Free Energy of Avidin−Biotin Binding
- (2010) Yan Tong et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Folding of a Helix at Room Temperature Is Critically Aided by Electrostatic Polarization of Intraprotein Hydrogen Bonds
- (2010) Li L. Duan et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Detecting and understanding combinatorial mutation patterns responsible for HIV drug resistance
- (2010) J. Zhang et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Intra-protein hydrogen bonding is dynamically stabilized by electronic polarization
- (2009) Li L. Duan et al. JOURNAL OF CHEMICAL PHYSICS
- Simulation of NMR Data Reveals That Proteins’ Local Structures Are Stabilized by Electronic Polarization
- (2009) Yan Tong et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Developing Polarized Protein-Specific Charges for Protein Dynamics: MD Free Energy Calculation of pKa Shifts for Asp26/Asp20 in Thioredoxin
- (2008) Changge Ji et al. BIOPHYSICAL JOURNAL
- Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria
- (2008) William L. Jorgensen et al. Journal of Chemical Theory and Computation
- Protein Polarization Is Critical to Stabilizing AF-2 and Helix-2′ Domains in Ligand Binding to PPAR-γ
- (2008) C. G. Ji et al. JOURNAL OF THE AMERICAN CHEMICAL SOCIETY
- Predicting drug resistance of the HIV-1 protease using molecular interaction energy components
- (2008) Tingjun Hou et al. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS
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