Relative Binding Affinity Prediction of Charge-Changing Sequence Mutations with FEP in Protein–Protein Interfaces

[1]  Robert Abel,et al.  Accurate Calculation of Relative Binding Free Energies between Ligands with Different Net Charges. , 2018, Journal of chemical theory and computation.

[2]  Robert Abel,et al.  Modeling the value of predictive affinity scoring in preclinical drug discovery. , 2018, Current opinion in structural biology.

[3]  C. Oostenbrink,et al.  Free energy calculations on the stability of the 14-3-3ζ protein. , 2018, Biochimica et biophysica acta. Proteins and proteomics.

[4]  Robert Abel,et al.  A Critical Review of Validation, Blind Testing, and Real- World Use of Alchemical Protein-Ligand Binding Free Energy Calculations. , 2017, Current topics in medicinal chemistry.

[5]  Melissa Coates Ford,et al.  Examining the Feasibility of Using Free Energy Perturbation (FEP+) in Predicting Protein Stability , 2017, J. Chem. Inf. Model..

[6]  Tongqing Zhou,et al.  Free Energy Perturbation Calculation of Relative Binding Free Energy between Broadly Neutralizing Antibodies and the gp120 Glycoprotein of HIV-1 , 2017, Journal of molecular biology.

[7]  D. Moustakas,et al.  The Necessary Nitrogen Atom: A Versatile High-Impact Design Element for Multiparameter Optimization. , 2017, Journal of medicinal chemistry.

[8]  Dan Li,et al.  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, Physical chemistry chemical physics : PCCP.

[9]  Anna R. Panchenko,et al.  MutaBind estimates and interprets the effects of sequence variants on protein–protein interactions , 2016, Nucleic Acids Res..

[10]  Jennifer L. Knight,et al.  OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins. , 2016, Journal of chemical theory and computation.

[11]  B. Roux,et al.  Constant-pH Hybrid Nonequilibrium Molecular Dynamics–Monte Carlo Simulation Method , 2015, Journal of chemical theory and computation.

[12]  A. Roitberg,et al.  pH-REMD simulations indicate that the catalytic aspartates of HIV-1 protease exist primarily in a monoprotonated state. , 2014, The journal of physical chemistry. B.

[13]  Thomas Simonson,et al.  An Overview of Electrostatic Free Energy Computations for Solutions and Proteins. , 2014, Journal of chemical theory and computation.

[14]  A. Panchenko,et al.  Predicting the Impact of Missense Mutations on Protein–Protein Binding Affinity , 2014, Journal of chemical theory and computation.

[15]  B. Korber,et al.  Prevalence of broadly neutralizing antibody responses during chronic HIV-1 infection , 2014, AIDS.

[16]  Hege S. Beard,et al.  Applying Physics-Based Scoring to Calculate Free Energies of Binding for Single Amino Acid Mutations in Protein-Protein Complexes , 2013, PloS one.

[17]  Chris Oostenbrink,et al.  Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation , 2013, J. Comput. Chem..

[18]  David L Mobley,et al.  Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects. , 2013, The Journal of chemical physics.

[19]  Wei Chen,et al.  Introducing titratable water to all-atom molecular dynamics at constant pH. , 2013, Biophysical journal.

[20]  Marianne Rooman,et al.  BeAtMuSiC: prediction of changes in protein–protein binding affinity on mutations , 2013, Nucleic Acids Res..

[21]  Austin G. Meyer,et al.  Maximum Allowed Solvent Accessibilites of Residues in Proteins , 2012, PloS one.

[22]  Jana K. Shen,et al.  Charge-leveling and proper treatment of long-range electrostatics in all-atom molecular dynamics at constant pH. , 2012, The Journal of chemical physics.

[23]  Juan Fernández-Recio,et al.  SKEMPI: a Structural Kinetic and Energetic database of Mutant Protein Interactions and its use in empirical models , 2012, Bioinform..

[24]  B. Honig,et al.  Thinking outside the cell: how cadherins drive adhesion. , 2012, Trends in cell biology.

[25]  R. Friesner,et al.  The VSGB 2.0 model: A next generation energy model for high resolution protein structure modeling , 2011, Proteins.

[26]  Hwangseo Park,et al.  Free energy perturbation approach for the rational engineering of the antibody for human hepatitis B virus. , 2011, Journal of molecular graphics & modelling.

[27]  Tingjun Hou,et al.  Assessing the Performance of the MM/PBSA and MM/GBSA Methods. 1. The Accuracy of Binding Free Energy Calculations Based on Molecular Dynamics Simulations , 2011, J. Chem. Inf. Model..

[28]  Lynn Morris,et al.  Neutralizing antibodies generated during natural HIV-1 infection: good news for an HIV-1 vaccine? , 2009, Nature Medicine.

[29]  S. Rasmussen,et al.  The structure and function of G-protein-coupled receptors , 2009, Nature.

[30]  Xuesong Yu,et al.  Factors Associated with the Development of Cross-Reactive Neutralizing Antibodies during Human Immunodeficiency Virus Type 1 Infection , 2008, Journal of Virology.

[31]  Mark Connors,et al.  Broad HIV-1 neutralization mediated by CD4-binding site antibodies , 2007, Nature Medicine.

[32]  Gerhard Klebe,et al.  Atypical Protonation States in the Active Site of HIV-1 Protease: A Computational Study , 2007, J. Chem. Inf. Model..

[33]  B. Honig,et al.  A hierarchical approach to all‐atom protein loop prediction , 2004, Proteins.

[34]  T. Pawson,et al.  Assembly of Cell Regulatory Systems Through Protein Interaction Domains , 2003, Science.

[35]  L. Serrano,et al.  Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. , 2002, Journal of molecular biology.

[36]  R. Zwanzig High‐Temperature Equation of State by a Perturbation Method. I. Nonpolar Gases , 1954 .

[37]  Ky-Youb Nam,et al.  Investigation of the Protonated State of HIV-1 Protease Active Site , 2003 .

[38]  Youngdo Won,et al.  The pKa Shift of the Catalytic Aspartyl Dyad in the HIV-1 Protease Complexed with Hydroxyethylene Inhibitors , 2002 .