Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?

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Items 101–200 of 342

1. Comparison of Receptor–Ligand Restraint Schemes for Alchemical Absolute Binding Free Energy Calculations
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2. Hybrid Steered Molecular Dynamics Approach to Computing Absolute Binding Free Energy of Ligand–Protein Complexes: A Brute Force Approach That Is Fast and Accurate
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3. Absolute Free Energy of Binding Calculations for Macrophage Migration Inhibitory Factor in Complex with a Druglike Inhibitor
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4. I. Dissociation free energies of drug–receptor systems via non-equilibrium alchemical simulations: a theoretical framework
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5. Method Evaluations for Adsorption Free Energy Calculations at the Solid/Water Interface through Metadynamics, Umbrella Sampling, and Jarzynski's Equality
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6. The role of solvation in the binding selectivity of the L-type calcium channel
   Dezső Boda, Douglas J. Henderson, Dirk Gillespie · 2013 · The Journal of Chemical Physics
7. Computation of Standard Binding Free Energies of Polar and Charged Ligands to the Glutamate Receptor GluA2
   Germano Heinzelmann, Po‐Chia Chen, Serdar Kuyucak · 2014 · The Journal of Physical Chemistry B
8. An Alternative to Conventional λ-Intermediate States in Alchemical Free Energy Calculations: λ-Enveloping Distribution Sampling
   Gerhard König, Nina Glaser, Benjamin Ries, Alžbeta Kubincová, Philippe H. Hünenberger, Sereina Riniker · 2020 · Journal of Chemical Information and Modeling
9. FEPrepare: A Web-Based Tool for Automating the Setup of Relative Binding Free Energy Calculations
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10. Molecular dynamics simulations of nucleotide release from the circadian clock protein KaiC reveal atomic-resolution functional insights
    Lu Hong, Bodhi P. Vani, Erik H. Thiede, Michael J. Rust, Aaron R. Dinner · 2018 · Proceedings of the National Academy of Sciences
11. Influence of Chirality of Crizotinib on Its MTH1 Protein Inhibitory Activity: Insight from Molecular Dynamics Simulations and Binding Free Energy Calculations
    Yuzhen Niu, Dabo Pan, Danfeng Shi, Qifeng Bai, Huanxiang Liu, Xiaojun Yao · 2015 · PLoS ONE
12. Validation of Free Energy Methods in AMBER
    Hsu‐Chun Tsai, Yujun Tao, Tai‐Sung Lee, Kenneth M. Merz, Darrin M. York · 2020 · Journal of Chemical Information and Modeling
13. Hazardous Shortcuts in Standard Binding Free Energy Calculations
    Blazhynska, Marharyta, Goulard Coderc de Lacam, Emma, Chen, Haochuan, Roux, Benoît, Chipot, Christophe · 2022 · The Journal of Physical Chemistry Letters
14. Chasing collective variables using temporal data-driven strategies
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15. Selectivity and Ranking of Tight-Binding JAK-STAT Inhibitors Using Markovian Milestoning with Voronoi Tessellations
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16. Cooperative DNA Recognition Modulated by an Interplay between Protein-Protein Interactions and DNA-Mediated Allostery
    Felipe Merino, Benjamin Bouvier, Vlad Cojocaru · 2015 · PLoS Computational Biology
17. Recent Advances in Computational Models for the Study of Protein–Peptide Interactions
    Denise Kilburg, Emilio Gallicchio · 2016 · Advances in protein chemistry and structural biology
18. A claudin5-binding peptide enhances the permeability of the blood-brain barrier in vitro
    Martina Trevisani, Alessandro Berselli, Giulio Alberini, Eleonora Centonze, Silvia Vercellino, Veronica Cartocci, Enrico Millo, Dinu Zinovie Ciobanu, Clarissa Braccia, Andrea Armirotti et al. · 2025 · Science Advances
19. DeepCV: A Deep Learning Framework for Blind Search of Collective Variables in Expanded Configurational Space
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20. Free Energy Calculations for the Peripheral Binding of Proteins/Peptides to an Anionic Membrane. 1. Implicit Membrane Models
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21. Investigation of the Drug Resistance Mechanism of M2-S31N Channel Blockers through Biomolecular Simulations and Viral Passage Experiments
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22. Confronting pitfalls of AI-augmented molecular dynamics using statistical physics
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23. Accuracy of Alternate Nonpolarizable Force Fields for the Determination of Protein–Ligand Binding Affinities Dominated by Cation−π Interactions
    Han Liu, Haohao Fu, Christophe J. Chipot, Xueguang Shao, Wensheng Cai · 2021 · Journal of Chemical Theory and Computation
24. Molecular Dynamics Simulation Investigation of the Binding and Interaction of the EphA6–Odin Protein Complex
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25. Computational design of a cyclic peptide that inhibits the CTLA4 immune checkpoint
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26. Lambda-ABF: Simplified, Portable, Accurate, and Cost-Effective Alchemical Free-Energy Computation
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27. Estimating glycosaminoglycan–protein interaction affinity: water dominates the specific antithrombin–heparin interaction
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28. Entropic effect and residue specific entropic contribution to the cooperativity in streptavidin–biotin binding
    Yalong Cong, Kaifang Huang, Yuchen Li, Susu Zhong, John Z. H. Zhang, Lili Duan · 2020 · Nanoscale
29. Adaptive Biasing Combined with Hamiltonian Replica Exchange to Improve Umbrella Sampling Free Energy Simulations
    Fabian Zeller, Martin Zacharias · 2013 · Journal of Chemical Theory and Computation
30. Cyclodextrin-Mediated Recruitment and Delivery of Amphotericin B
    Jia He, Christophe J. Chipot, Xueguang Shao, Wensheng Cai · 2013 · The Journal of Physical Chemistry C
31. Methodology for the Simulation of Molecular Motors at Different Scales
    Abhishek Singharoy, Christophe J. Chipot · 2016 · The Journal of Physical Chemistry B
32. Charge-Changing Perturbations and Path Sampling via Classical Molecular Dynamic Simulations of Simple Guest–Host Systems
    Christoph Öhlknecht, Jan Walther Perthold, Bettina Lier, Chris Oostenbrink · 2020 · Journal of Chemical Theory and Computation
33. A Rigorous Framework for Calculating Protein–Protein Binding Affinities in Membranes
    Blazhynska, Marharyta, Gumbart, James C., Chen, Haochuan, Tajkhorshid, Emad, Roux, Benoît, Chipot, Christophe · 2023 · Journal of Chemical Theory and Computation
34. All-Atom Simulations of Human ACE2-Spike Protein RBD Complexes for SARS-CoV-2 and Some of its Variants: Nature of Interactions and Free Energy Diagrams for Dissociation of the Protein Complexes
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35. Steered molecular dynamics study of inhibitor binding in the internal binding site in dehaloperoxidase-hemoglobin
    Zhisen Zhang, Andrew P. Santos, Qing Zhou, Lijun Liang, Qi Wang, Tao Wu, Stefan Franzen · 2016 · Biophysical Chemistry
36. Harnessing complexity in molecular self-assembly using computer simulations
    Xiangze Zeng, Lizhe Zhu, Xiaoyan Zheng, Marco Cecchini, Xuhui Huang · 2018 · Physical Chemistry Chemical Physics
37. Computational Approaches to the Chemical Equilibrium Constant in Protein‐ligand Binding
    Joel José Montalvo‐Acosta, Marco Cecchini · 2016 · Molecular Informatics
38. Assessment of a Single Decoupling Alchemical Approach for the Calculation of the Absolute Binding Free Energies of Protein-Peptide Complexes
    Denise Kilburg, Emilio Gallicchio · 2018 · Frontiers in Molecular Biosciences
39. 3D-RISM-AI: A Machine Learning Approach to Predict Protein–Ligand Binding Affinity Using 3D-RISM
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40. Delineating Protein–Protein Curvilinear Dissociation Pathways and Energetics with Naïve Multiple‐Walker Umbrella Sampling Simulations
    Dhananjay C. Joshi, Jung‐Hsin Lin · 2019 · Journal of Computational Chemistry
41. On Computing Equilibrium Binding Constants for Protein–Protein Association in Membranes
    Ayan Majumder, Seulki Kwon, John E. Straub · 2022 · Journal of Chemical Theory and Computation
42. A computationally designed ACE2 decoy has broad efficacy against SARS-CoV-2 omicron variants and related viruses in vitro and in vivo
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43. Computational Studies of Molecular Permeation through Connexin26 Channels
    Yun Luo, Angelo R. Rossi, Andrew L. Harris · 2016 · Biophysical Journal
44. Efficient calculation of relative binding free energies by umbrella sampling perturbation
    Fabian Zeller, Martin Zacharias · 2014 · Journal of Computational Chemistry
45. Bringing Clarity to the Prediction of Protein–Ligand Binding Free Energies via “Blurring”
    Melek Nihan Ucisik, Zheng Zheng, John C. Faver, Kenneth M. Merz · 2014 · Journal of Chemical Theory and Computation
46. Robust, Efficient and Automated Methods for Accurate Prediction of Protein-Ligand Binding Affinities in AMBER Drug Discovery Boost
    Tai‐Sung Lee, Hsu‐Chun Tsai, Abir Ganguly, Timothy J. Giese, Darrin M. York · 2021 · ACS symposium series
47. Computing the binding affinity of a ligand buried deep inside a protein with the hybrid steered molecular dynamics
    Oscar David Villarreal, Lili Yu, R. Rodríguez, Liao Yuan Chen · 2016 · Biochemical and Biophysical Research Communications
48. Free Energy Calculations of Microcin J25 Variants Binding to the FhuA Receptor
    Pin‐Kuang Lai, Yiannis N. Kaznessis · 2017 · Journal of Chemical Theory and Computation
49. The Role of the Active Site Flap in Streptavidin/Biotin Complex Formation
    Nupur Bansal, Zheng Zheng, Lin Frank Song, Jun Pei, Kenneth M. Merz · 2018 · Journal of the American Chemical Society
50. Prediction of Binding Energy of Keap1 Interaction Motifs in the Nrf2 Antioxidant Pathway and Design of Potential High-Affinity Peptides
    Mikko Karttunen, Wing‐Yiu Choy, Elio A. Cino · 2018 · The Journal of Physical Chemistry B
51. Crystal structure of the deglycating enzyme Amadoriase I in its free form and substrate‐bound complex
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52. Evaluation of Generalized Born Model Accuracy for Absolute Binding Free Energy Calculations
    Fabian Zeller, Martin Zacharias · 2014 · The Journal of Physical Chemistry B
53. Standard Binding Free-Energy Calculations: How Far Are We from Automation?
    Haohao Fu, Christophe J. Chipot, Xueguang Shao, Wensheng Cai · 2023 · The Journal of Physical Chemistry B
54. Understanding the non-catalytic behavior of human butyrylcholinesterase silent variants: Comparison of wild-type enzyme, catalytically active Ala328Cys mutant, and silent Ala328Asp variant
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55. Molecular Simulations of Disulfide-Rich Venom Peptides with Ion Channels and Membranes
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56. Protamine Binding Site on DNA: Molecular Dynamics Simulations and Free Energy Calculations with Full Atomistic Details
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57. Computational Assessment of Protein–Protein Binding Specificity within a Family of Synaptic Surface Receptors
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58. On Free Energy Calculations in Drug Discovery
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59. CL-FEP: An End-State Free Energy Perturbation Approach
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60. Consistent Picture of Phosphate–Divalent Cation Binding from Models with Implicit and Explicit Electronic Polarization
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61. Nonspecific vs. specific DNA binding free energetics of a transcription factor domain protein
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62. Binding Thermodynamics of Fourth-Generation EGFR Inhibitors Revealed by Absolute Binding Free Energy Calculations
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63. Calculation of binding affinities for linear alcohols to α -cyclodextrin by twin-system enveloping distribution sampling simulations
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64. Targeting G-quadruplexes with Organic Dyes: Chelerythrine–DNA Binding Elucidated by Combining Molecular Modeling and Optical Spectroscopy
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65. Computational Modeling of Claudin Structure and Function
    Shadi Fuladi, Ridaka Wal Jannat, Le Shen, Christopher R. Weber, Fatemeh Khalili‐Araghi · 2020 · International Journal of Molecular Sciences
66. Molecular basis of the activation and dissociation of dimeric PYL2 receptor in abscisic acid signaling
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67. Accurate Host–Guest Binding Free Energies Using the AMOEBA Polarizable Force Field
    Moses K. J. Chung, Ryan J. Miller, Borna Novak, Zhi Wang, Jay W. Ponder · 2023 · Journal of Chemical Information and Modeling
68. Systematic mutagenesis of oncocin reveals enhanced activity and insights into the mechanisms of antimicrobial activity
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69. Analyzing machupo virus-receptor binding by molecular dynamics simulations
    Austin G. Meyer, Sara L. Sawyer, Andrew D. Ellington, Claus O. Wilke · 2014 · PeerJ
70. Theoretical Study of the Initial Stages of Self-Assembly of a Carboxysome’s Facet
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71. In Silico Analysis of the Effect of Alkyl Tail Length on Antiagglomerant Adsorption to Natural Gas Hydrates in Brine
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72. Binding free energy predictions in host-guest systems using Autodock4. A retrospective analysis on SAMPL6, SAMPL7 and SAMPL8 challenges
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73. Absolute binding free energies for octa-acids and guests in SAMPL5
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74. Binding Free Energies of Host–Guest Systems by Nonequilibrium Alchemical Simulations with Constrained Dynamics: Theoretical Framework
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75. On Restraints in End‐Point Protein–Ligand Binding Free Energy Calculations
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76. PELE-MSM: A Monte Carlo Based Protocol for the Estimation of Absolute Binding Free Energies
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77. The cis conformation of proline leads to weaker binding of a p53 peptide to MDM2 compared to trans
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78. Role of Electrostatic Interactions in Binding of Peptides and Intrinsically Disordered Proteins to Their Folded Targets: 2. The Model of Encounter Complex Involving the Double Mutant of the c-Crk N-SH3 Domain and Peptide Sos
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79. New Insights into the Opening of the Occluded Ligand-Binding Pocket of Sigma1 Receptor: Binding of a Novel Bivalent RC-33 Derivative
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80. New Strategies for Integrative Dynamic Modeling of Macromolecular Assembly
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81. Binding Free Energies of Host–Guest Systems by Nonequilibrium Alchemical Simulations with Constrained Dynamics: Illustrative Calculations and Numerical Validation
    Edoardo Giovannelli, Matteo Cioni, Piero Procacci, Gianni Cardini, Marco Pagliai, Victor V. Volkov, Riccardo Chelli · 2017 · Journal of Chemical Theory and Computation
82. Alchemical free energy calculations via metadynamics: Application to the theophylline‐RNA aptamer complex
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83. Distinct binding of cetirizine enantiomers to human serum albumin and the human histamine receptor H1
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84. Inside and Out of the Pore: Comparing Interactions and Molecular Dynamics of Influenza A M2 Viroporin Complexes in Standard Lipid Bilayers
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85. Uncovering the Mechanism of Drug Resistance Caused by the T790M Mutation in EGFR Kinase From Absolute Binding Free Energy Calculations
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86. Molecular Mechanism of Processive 3′ to 5′ RNA Translocation in the Active Subunit of the RNA Exosome Complex
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87. Beta-1,3 Oligoglucans Specifically Bind to Immune Receptor CD28 and May Enhance T Cell Activation
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88. Uncovering Molecular Bases Underlying Bone Morphogenetic Protein Receptor Inhibitor Selectivity
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89. Anion–π interactions in complexes of proteins and halogen-containing amino acids
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90. Location and Character of Volatile General Anesthetics Binding Sites in the Transmembrane Domain of TRPV1
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91. Elimination of Finite-Size Effects on Binding Free Energies via the Warp-Drive Method
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92. Cooperative Recruitment of Amphotericin B Mediated by a Cyclodextrin Dimer
    Jia He, Christophe J. Chipot, Xueguang Shao, Wensheng Cai · 2014 · The Journal of Physical Chemistry C
93. Standard Binding Free Energy of a SIM–SUMO Complex
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94. Computation of Drug‐Binding Thermodynamics
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95. 1-(3-Tert-Butylphenyl)-2,2,2-Trifluoroethanone as a Potent Transition-State Analogue Slow-Binding Inhibitor of Human Acetylcholinesterase: Kinetic, MD and QM/MM Studies
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96. Standard Binding Free Energy and Membrane Desorption Mechanism for a Phospholipase C
    Emmanuel E. Moutoussamy, Hanif Muhammad Khan, Mary Fedarko Roberts, Anne Gershenson, Christophe J. Chipot, Nathalie Reuter · 2022 · Journal of Chemical Information and Modeling
97. A Consistent Thermodynamic Characterization of the Adsorption Process through the Calculation of Free Energy Contributions
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98. Conformational dynamics and free energy of BHRF1 binding to Bim BH3
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99. Boosting Enzyme Activity in Biomass Conversion by Modulating the Hydrolysis Process of Cellobiohydrolases
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100. Applying Absolute Free Energy Perturbation Molecular Dynamics to Diffusively Binding Ligands
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