Predicting Absolute Ligand Binding Free Energies to a Simple Model Site

Cited by (272)

Items 101–200 of 272

1. Protein–Ligand Electrostatic Binding Free Energies from Explicit and Implicit Solvation
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2. Best practices in free energy calculations for drug design.
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3. Molecular Simulation Workflows as Parallel Algorithms: The Execution Engine of Copernicus, a Distributed High-Performance Computing Platform
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4. Exploring the conformational changes of the ATP binding site of gyrase B from Escherichia coli complexed with different established inhibitors by using molecular dynamics simulation
   Liane Saı́z-Urra, Miguel Ángel Cabrera‐Pérez, Matheus Froeyen · 2010 · Journal of Molecular Graphics and Modelling
5. Application of a polarizable force field to calculations of relative protein–ligand binding affinities
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6. Accurate Prediction of Complex Structure and Affinity for a Flexible Protein Receptor and Its Inhibitor
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7. Unorthodox uses of Bennett's acceptance ratio method
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8. Density functional theory calculations on entire proteins for free energies of binding: Application to a model polar binding site
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9. Separated topologies--a method for relative binding free energy calculations using orientational restraints.
   G. Rocklin, D. Mobley, K. Dill · 2013 · Journal of Chemical Physics
10. An overview of the SAMPL8 host–guest binding challenge
    Martin Amezcua, Jeffry Setiadi, Yunhui Ge, David L. Mobley · 2022 · Journal of Computer-Aided Molecular Design
11. Convolutional neural network scoring and minimization in the D3R 2017 community challenge
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12. Improved Binding Free Energy Predictions from Single-Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange
    I. Khavrutskii, A. Wallqvist · 2011 · Journal of Chemical Theory and Computation
13. Design of protein-ligand binding based on the molecular-mechanics energy model.
    F. Boas, P. Harbury · 2008 · Journal of Molecular Biology
14. Comparing the Performance of Different AMBER Protein Forcefields, Partial Charge Assignments, and Water Models for Absolute Binding Free Energy Calculations.
    D. Huggins · 2022 · Journal of Chemical Theory and Computation
15. 3D-RISM-Dock: A New Fragment-Based Drug Design Protocol.
    Dragan Nikolić, Nikolay Blinov, D. Wishart, A. Kovalenko · 2012 · Journal of Chemical Theory and Computation
16. Absolute Alchemical Free Energy Calculations for Ligand Binding: A Beginner's Guide.
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17. Optimal Measurement Network of Pairwise Differences
    Huafeng Xu · 2019 · Journal of Chemical Information and Modeling
18. The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling
    Lily Wang, Pavan Kumar Behara, Matthew W. Thompson, Trevor Gokey, Yuanqing Wang, Jeffrey Wagner, Daniel J. Cole, Michael K. Gilson, Michael R. Shirts, David L. Mobley · 2024 · The Journal of Physical Chemistry B
19. Enhanced Monte Carlo Methods for Modeling Proteins Including Computation of Absolute Free Energies of Binding
    Israel Cabeza de Vaca, Yue Qian, Jonah Z. Vilseck, J. Tirado-Rives, W. L. Jorgensen · 2018 · Journal of Chemical Theory and Computation
20. Resolving the Ligand-Binding Specificity in c-MYC G-Quadruplex DNA: Absolute Binding Free Energy Calculations and SPR Experiment
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21. II. Dissociation free energies in drug–receptor systems via nonequilibrium alchemical simulations: application to the FK506-related immunophilin ligands
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22. Absolute Free Energy of Binding of Avidin/Biotin, Revisited
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23. Using Free Energy of Binding Calculations to Improve the Accuracy of Virtual Screening Predictions
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24. The effect of different electrostatic potentials on docking accuracy: a case study using DOCK5.4.
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25. Site Identification by Ligand Competitive Saturation (SILCS) Simulations for Fragment-Based Drug Design
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26. Meta-Analysis Reveals That Absolute Binding Free-Energy Calculations Approach Chemical Accuracy
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27. Absolute Binding Free Energies between T4 Lysozyme and 141 Small Molecules: Calculations Based on Multiple Rigid Receptor Configurations
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28. Uncoupling the Structure–Activity Relationships of β2 Adrenergic Receptor Ligands from Membrane Binding
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29. Insights from free-energy calculations: protein conformational equilibrium, driving forces, and ligand-binding modes.
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30. The adsorption of DNA bases on neutral and charged (8, 8) carbon-nanotubes
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31. Modeling molecular and ionic absolute solvation free energies with quasichemical theory bounds.
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32. Molecular insights of protein contour recognition with ligand pharmacophoric sites through combinatorial library design and MD simulation in validating HTLV-1 PR inhibitors.
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33. Statistically Optimal Continuous Free Energy Surfaces from Biased Simulations and Multistate Reweighting
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34. Perturbation potentials to overcome order/disorder transitions in alchemical binding free energy calculations
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35. Calculating the sensitivity and robustness of binding free energy calculations to force field parameters
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36. Bayesian estimation of free energies from equilibrium simulations.
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37. Using thermodynamic integration MD simulation to compute relative protein–ligand binding free energy of a GSK3β kinase inhibitor and its analogs
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38. Avoiding the van der Waals endpoint problem using serial atomic insertion
    Stefan Boresch, Stefan Brückner · 2011 · Journal of Computational Chemistry
39. Energy Penalties Enhance Flexible Receptor Docking in a Model Cavity
    Kamenik, Anna S., Singh, Isha, Lak, Parnian, Balius, Trent E., Liedl, Klaus R., Shoichet, Brian K. · 2021
40. Temperature artifacts in protein structures bias ligand-binding predictions
    S.Y.C. Bradford, Léa El Khoury, Yunhui Ge, Meghan Osato, David L. Mobley, Marcus M. Fischer · 2021 · Chemical Science
41. The Effect of Conformational Flexibility on Binding Free Energy Estimation between Kinases and Their Inhibitors
    M. Araki, N. Kamiya, Miwa Sato, M. Nakatsui, T. Hirokawa, Y. Okuno · 2016 · Journal of Chemical Information and Modeling
42. Predicting binding affinities of host-guest systems in the SAMPL3 blind challenge
    G. König, B. Brooks · 2011 · Journal of Computer-Aided Molecular Design
43. 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
44. The thermodynamics of charge transfer in DNA photolyase: using thermodynamic integration calculations to analyse the kinetics of electron transfer reactions
    Sebastian Krapf, Thorsten Koslowski, Thomas B. Steinbrecher · 2010 · Physical Chemistry Chemical Physics
45. Optimizing drug design by merging generative AI with a physics-based active learning framework
    Isaac Filella-Mercè, Alexis Molina, Lucía Díaz, Marek Orzechowski, Yamina A. Berchiche, Yang Ming Zhu, Júlia Vilalta-Mor, Laura Malo, Ajay S. Yekkirala, Soumya S. Ray et al. · 2025 · Communications Chemistry
46. Flexible CDOCKER: Hybrid Searching Algorithm and Scoring Function with Side Chain Conformational Entropy
    Yujin Wu, Charles L. Brooks · 2021 · Journal of Chemical Information and Modeling
47. Enhancing Side Chain Rotamer Sampling Using Nonequilibrium Candidate Monte Carlo
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48. Identification of protein binding surfaces using surface triplet propensities
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49. Accelerated Molecular Dynamics in Computational Drug Design
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50. Open Force Field Consortium: Escaping atom types using direct chemical perception with SMIRNOFF v0.1
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51. Quantitative Assessment of the Energetics of Dopamine Translocation by Human Dopamine Transporter
    Mary Hongying Cheng, Cihan Kaya, İvet Bahar · 2017 · The Journal of Physical Chemistry B
52. Computation of relative binding free energy for an inhibitor and its analogs binding with Erk kinase using thermodynamic integration MD simulation
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53. Quantifying Water-Mediated Protein–Ligand Interactions in a Glutamate Receptor: A DFT Study
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54. Accurate prediction of protein–ligand interactions by combining physical energy functions and graph-neural networks
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55. Lysozyme and Human Serum Albumin Proteins as Potential Nitric Oxide Cardiovascular Drug Carriers: Theoretical and Experimental Investigation
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56. Mechanisms for Benzene Dissociation through the Excited State of T4 Lysozyme L99A Mutant.
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57. 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.
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58. Computation of protein–ligand binding free energies using quantum mechanical bespoke force fields
    Daniel J. Cole, Israel Cabeza de Vaca, William L. Jorgensen · 2019 · MedChemComm
59. Using the fast fourier transform in binding free energy calculations
    Trung Hai Nguyen, Huan‐Xiang Zhou, David D. L. Minh · 2017 · Journal of Computational Chemistry
60. Alchemical Grid Dock (AlGDock): Binding Free Energy Calculations between Flexible Ligands and Rigid Receptors
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61. Scoring Multipole Electrostatics in Condensed-Phase Atomistic Simulations
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62. Recent Advances in Computational Models for the Study of Protein–Peptide Interactions
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63. Automated Absolute Binding Free Energy Calculation Workflow for Drug Discovery
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64. Harnessing Deep Learning for Optimization of Lennard-Jones Parameters for the Polarizable Classical Drude Oscillator Force Field
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65. Robust FEP Protocols for Creating Molecules in Solution
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66. Accurate calculation of mutational effects on the thermodynamics of inhibitor binding to p38α MAP kinase: a combined computational and experimental study
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67. Using docking and alchemical free energy approach to determine the binding mechanism of eEF2K inhibitors and prioritizing the compound synthesis
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68. Enhanced Sampling in Free Energy Calculations: Combining SGLD with the Bennett’s Acceptance Ratio and Enveloping Distribution Sampling Methods
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69. The errors of our ways: taking account of error in computer-aided drug design to build confidence intervals for our next 25 years
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70. Absolute Binding Free Energy Calculations for Highly Flexible Protein MDM2 and Its Inhibitors
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71. Bringing Clarity to the Prediction of Protein–Ligand Binding Free Energies via “Blurring”
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72. Effects of Biomolecular Flexibility on Alchemical Calculations of Absolute Binding Free Energies
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73. Comparison of the umbrella sampling and the double decoupling method in binding free energy predictions for SAMPL6 octa-acid host-guest challenges
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74. Ligand-Receptor Affinities Computed by an Adapted Linear Interaction Model for Continuum Electrostatics and by Protein Conformational Averaging
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75. Structure-based in silico approaches for drug discovery against Mycobacterium tuberculosis
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76. A Benchmark of Electrostatic Method Performance in Relative Binding Free Energy Calculations
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77. Modeling loop backbone flexibility in receptor‐ligand docking simulations
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78. A Physics-Guided Neural Network for Predicting Protein–Ligand Binding Free Energy: From Host–Guest Systems to the PDBbind Database
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79. Investigating the Accuracy of Water Models through the Van Hove Correlation Function.
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80. Absolute protein binding free energy simulations for ligands with multiple poses, a thermodynamic path which avoids exhaustive enumeration of the poses
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81. Insights into Ligand–Protein Binding from Local Mechanical Response
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82. No free energy lunch
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83. Accurate Host–Guest Binding Free Energies Using the AMOEBA Polarizable Force Field
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84. Computing Ligands Bound to Proteins Using MELD-Accelerated MD
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85. Optimizing Electrostatic Field Calculations with the Adaptive Poisson–Boltzmann Solver to Predict Electric Fields at Protein–Protein Interfaces. I. Sampling and Focusing
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86. PopShift: A Thermodynamically Sound Approach to Estimate Binding Free Energies by Accounting for Ligand-Induced Population Shifts from a Ligand-Free Markov State Model
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87. Optimizing Electrostatic Field Calculations with the Adaptive Poisson–Boltzmann Solver to Predict Electric Fields at Protein–Protein Interfaces II: Explicit Near-Probe and Hydrogen-Bonding Water Molecules
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88. Protein-ligand binding free energies from exhaustive docking.
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89. QM/MM Refinement and Analysis of Protein Bound Retinoic Acid
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90. Multiscale Monte Carlo Sampling of Protein Sidechains: Application to Binding Pocket Flexibility.
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91. Machine Learning-Enhanced Calculation of Quantum-Classical Binding Free Energies
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92. Equilibrium and Nonequilibrium Ensemble Methods for Accurate, Precise and Reproducible Absolute Binding Free Energy Calculations
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93. The slow but steady rise of binding free energy calculations in drug discovery
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94. Computationally-Guided Optimization of Small-Molecule Inhibitors of the Aurora A Kinase – TPX2 Protein-Protein Interaction
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95. Absolute binding free energies for octa-acids and guests in SAMPL5
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96. The measured and calculated affinity of methyl‐ and methoxy‐substituted benzoquinones for the QAsite of bacterial reaction centers
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97. Host–Guest Binding Free Energies à la Carte: An Automated OneOPES Protocol
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98. Theoretical understanding of the thermodynamics and interactions in transcriptional regulator TtgR-ligand binding.
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99. Accelerating Convergence of Free Energy Computations with Hamiltonian Simulated Annealing of Solvent (HSAS)
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100. Assessing the effect of forcefield parameter sets on the accuracy of relative binding free energy calculations
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