Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations

Cited by (177)

Items 101–177 of 177

1. Relative Binding Free Energy between Chemically Distant Compounds Using a Bidirectional Nonequilibrium Approach
   Piero Procacci · 2022 · Journal of Chemical Theory and Computation
2. Designing BH3-Mimetic Peptide Inhibitors for the Viral Bcl-2 Homologues A179L and BHRF1: Importance of Long-Range Electrostatic Interactions
   C. Narendra Reddy, Ramasubbu Sankararamakrishnan · 2021 · ACS Omega
3. Structure-Based Development of Isoform-Selective Inhibitors of Casein Kinase 1ε vs Casein Kinase 1δ
   Jun Yong Choi, Yoshihiko Noguchi, James M. Alburger, Simon Bayle, Eugene Chung, Wayne M. Grant, A. Chaikuad, Stefan Knapp, Derek R. Duckett, William R. Roush · 2023 · Journal of Medicinal Chemistry
4. Proton Control of Transitions in an Amino Acid Transporter
   Zhiyi Wu, Irfan Alibay, Simon L. Newstead, Philip Charles Biggin · 2019 · Biophysical Journal
5. The slow but steady rise of binding free energy calculations in drug discovery
   Huafeng Xu · 2022 · Journal of Computer-Aided Molecular Design
6. An efficient computational chemistry approach to generating negative data for drug discovery pipeline validation
   Stefan M. Ivanov · 2026 · Frontiers in Bioinformatics
7. Machine Learning-Enhanced Calculation of Quantum-Classical Binding Free Energies
   Moritz Bensberg, M. Eckhoff, F. E. Thomasen, William Bro-Jo̷rgensen, Matthew S. Teynor, Valentina Sora, Thomas Weymuth, Raphael T. Husistein, Frederik E. Knudsen, Anders Krogh et al. · 2025 · Journal of Chemical Theory and Computation
8. Accelerating and Automating the Free Energy Perturbation Absolute Binding Free Energy Calculation with the RED-E Function
   Runduo Liu, Wenchao Li, Yufen Yao, Yinuo Wu, Hai‐Bin Luo, Zhe Li · 2023 · Journal of Chemical Information and Modeling
9. Computational screening of FDA approved drugs of fungal origin that may interfere with SARS-CoV-2 spike protein activation, viral RNA replication, and post‐translational modification: a multiple target approach
   Rajveer Singh, Anupam Gautam, Shivani Chandel, Vipul Sharma, Arijit Ghosh, Dhritiman Dey, Syamal Roy, V. Ravichandiran, Dipanjan Ghosh · 2021 · In Silico Pharmacology
10. Theoretical exploration of the binding selectivity of inhibitors to BRD7 and BRD9 with multiple short molecular dynamics simulations
    Lifei Wang, Yan Wang, Juan Zhao, Y.X. Yu, Nian-Qian Kang, Zhiyong Yang · 2022 · RSC Advances
11. Calculations of Absolute Free Energies, Enthalpies, and Entropies for Drug Binding
    Christopher M. Summa, Dillon P. Langford, Sam H. Dinshaw, Jennifer Webb, Steven W. Rick · 2024 · Journal of Chemical Theory and Computation
12. Accurate calculation of absolute free energy of binding for SHP2 allosteric inhibitors using free energy perturbation
    Li Liang, Haichun Liu, Guomeng Xing, Chenglong Deng, Yi Hua, Rui Gu, Tao Lu, Yadong Chen, Yanmin Zhang · 2022 · Physical Chemistry Chemical Physics
13. Discovery of Highly Potent CRBN Ligands and Insight into Their Binding Mode through Molecular Docking and Molecular Dynamics Simulations
    Jian Wei Yan, Zhibing Zheng · 2023 · ChemMedChem
14. Selective mechanism of inhibitors to two bromodomains of BRD4 revealed by multiple replica molecular dynamics simulations and free energy analyses
    Meng Li, Xinguo Liu, Shaolong Zhang, Jiahao Sun, Qinggang Zhang, Jianzhong Chen · 2023 · Chinese Journal of Chemical Physics
15. Accurate calculation of absolute protein-ligand binding free energies
    Wei Chen, Di Cui, Robert Abel, Richard A. Friesner, Lingle Wang · 2022 · ChemRxiv
16. Computational Analysis of Heat Capacity Effects in Protein–Ligand Binding
    Lucien Koenekoop, Johan Åqvist · 2024 · Journal of Chemical Theory and Computation
17. Predicting Resistance to Small Molecule Kinase Inhibitors
    Anu Nagarajan, Katherine Amberg-Johnson, Evan Paull, Kunling Huang, Phani Ghanakota, Asela Chandrasinghe, Jackson Chief Elk, Jared M. Sampson, Lingle Wang, Robert Abel et al. · 2025 · Journal of Chemical Information and Modeling
18. Surface Binding Energy Landscapes Affect Phosphodiesterase Isoform-Specific Inhibitor Selectivity
    Qing Liu, Andreas Herrmann, Qiang Huang · 2018 · Computational and Structural Biotechnology Journal
19. Estimating the binding energetics of reversible covalent inhibitors of the SARS-CoV-2 main protease: an in silico study
    Ernest Awoonor‐Williams · 2022 · Physical Chemistry Chemical Physics
20. Tuning Potential Functions to Host–Guest Binding Data
    Jeffry Setiadi, Simon Boothroyd, David R. Slochower, David Dotson, Matthew W. Thompson, Jeffrey Wagner, Lee‐Ping Wang, Michael K. Gilson · 2023 · Journal of Chemical Theory and Computation
21. Unveiling the Selectivity Mechanism of Type-I LRRK2 Inhibitors by Computational Methods: Insights from Binding Thermodynamics and Kinetics Simulation
    Shuoyan Tan, Jun Wang, Peng Gao, Guotong Xie, Qianqian Zhang, Huanxiang Liu, Xiaojun Yao · 2023 · ACS Chemical Neuroscience
22. Non-bonding energy directed designing of HDAC2 inhibitors through molecular dynamics simulation
    Varun Dewaker, Pratik Narain Srivastava, Saroj Kumar Verma, Ajay Kumar Srivastava, Yenamandra S. Prabhakar · 2021 · Journal of Biomolecular Structure and Dynamics
23. Alchemical Absolute Protein-Ligand Binding Free Energies for Drug Design
    Yuriy Khalak, Gary Tresadern, Matteo Aldeghi, Hannah Magdalena Baumann, David L. Mobley, Bert L. de Groot, Vytautas Gapsys · 2021
24. Correction Schemes for Absolute Binding Free Energies Involving Lipid Bilayers
    Zhiyi Wu, Philip Charles Biggin · 2022 · Journal of Chemical Theory and Computation
25. Current advances on the development of BET inhibitors: insights from computational methods
    Fernando Daniel Prieto-Martínez, José L. Medina‐Franco · 2020 · Advances in protein chemistry and structural biology
26. Challenges encountered applying equilibrium and non-equilibrium binding free energy calculations
    Hannah Baumann, Vytautas Gapsys, B. L. de Groot, D. Mobley · 2020 · Journal of Physical Chemistry B
27. Comparative Assessment of Free Energy Computational Methods for Revealing the Interactions Driving PARP1 Selective Inhibition
    Alejandro Feito, Natàlia DeMoya‐Valenzuela, Cristian Privat, Andrés R. Tejedor, Marco DelValle-Carrillo, Sara Cembellín, Lucía Paniagua‐Herranz, Adiran Garaizar, J. Oller-Iscar, Alberto Ocana et al. · 2026 · Journal of Chemical Information and Modeling
28. Analysis of Glycan Recognition by Concanavalin A Using Absolute Binding Free Energy Calculations
    Sondos Musleh, Irfan Alibay, P. Biggin, Richard A. Bryce · 2024 · Journal of Chemical Information and Modeling
29. Evaluation of the ABCG2 Charge Model in Protein–Ligand Binding Free-Energy Calculations
    Sudarshan Behera, Vytautas Gapsys, Bert L. de Groot · 2025 · Journal of Chemical Information and Modeling
30. Binding Selectivity of Inhibitors toward Bromodomains BAZ2A and BAZ2B Uncovered by Multiple Short Molecular Dynamics Simulations and MM-GBSA Calculations
    Lifei Wang, Yan Wang, Zhiyong Yang, Shuobo Xu, Hongyun Li · 2021 · ACS Omega
31. Applied Biophysics for Bromodomain Drug Discovery
    William C. K. Pomerantz, Jorden A. Johnson, Peter D. Ycas · 2019 · Topics in medicinal chemistry
32. Exploring the binding mechanism of positive allosteric modulators in human metabotropic glutamate receptor 2 using molecular dynamics simulations
    Panpan Wang, Xiaonan Gao, Ke Zhang, Qinglan Pei, Xiaobo Xu, Fengmei Yan, Jianghong Dong, Chenxi Jing · 2021 · Physical Chemistry Chemical Physics
33. Synergetic enhancement: Imprinted magnetic microspheres based on the thiol-ene-amine conjugation and metal coordination for selective recognition of BSA
    Mingqi Wang, Jingjing Zhou, Shixin Fa, Qiuyu Zhang · 2023 · Colloids and Surfaces A Physicochemical and Engineering Aspects
34. Exploring Reactive Conformations of Coenzyme A during Binding and Unbinding to Pyruvate Formate–Lyase
    Marko Hanževački, Radha D. Banhatti, Karmen Čondić‐Jurkić, Ana‐Sunčana Smith, David M. Smith · 2019 · The Journal of Physical Chemistry A
35. Challenges of Absolute Binding Free Energies for Membrane Exposed Binding Pockets
    Charlie Cook, Irfan Alibay, Nithishwer Mouroug Anand, Ewa I. Chudyk, Ronald M. A. Knegtel, Philip Charles Biggin · 2024 · ChemRxiv
36. In Silico Design of a Peptide Receptor for Dopamine Recognition
    Luna Rodriguez-Salazar, James O. Guevara‐Pulido, A. Cifuentes · 2020 · Molecules
37. Insights into the Microscopic Structure of RNF4-SIM-SUMO Complexes from MD Simulations
    Alex Kötter, Henning D. Mootz, Andreas Heuer · 2020 · Biophysical Journal
38. Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints
    Notari, Evangelia, Wood, Christopher W., Michel, Julien · 2025 · Journal of Chemical Theory and Computation
39. Identification of novel dihydroorotate dehydrogenase (DHODH) inhibitors for cancer: computational drug repurposing strategy
    Rahamathtunnisa Rajamohamed, Shanthi Veerappapillai · 2025 · BMC Pharmacology and Toxicology
40. Targeted Coacervates Enabled by Polyphenol–Peptide Networks for Therapeutic Delivery
    Lu Jiang, Qiantao Song, Zhixing Lin, Hai Liu, Jingqu Chen, Xiangchun Zhang, Hui Li, Christina Cortez‐Jugo, Jiajing Zhou, Lu Liu et al. · 2026 · Journal of the American Chemical Society
41. Computed Protein–Protein Enthalpy Signatures as a Tool for Identifying Conformation Sampling Problems
    Süleyman Selim Çınaroğlu, Philip Charles Biggin · 2023 · Journal of Chemical Information and Modeling
42. Thermodynamic integration combined with molecular dynamic simulations to explore the cross‐resistance mechanism of isoniazid and ethionamide
    Qianqian Zhang, Yuwei Yang, Xiaoqing Gong, Nannan Zhao, Yang Zhang, Huanxiang Liu · 2022 · Proteins Structure Function and Bioinformatics
43. Binding selectivity analysis of AURKs inhibitors through molecular dynamics simulation studies
    Rima D. Alharthy, Ghulam Fatima, Numan Yousaf, Muhammad Shaheen Iqbal, Sadia Sattar, Abdullah R. Alanzi, Ijaz Ali, Muhammad Muddassar · 2023 · PLoS ONE
44. Extracting binding energies and binding modes from biomolecular simulations of fragment binding to endothiapepsin
    Birte Schmitz, B. Frieg, Nadine Homeyer, G. Jessen, Holger Gohlke · 2024 · Archiv der Pharmazie
45. Accurate calculation of absolute protein-ligand binding free energies
    Wei Chen, Di Cui, Robert Abel, Richard A. Friesner, Lingle Wang · 2022 · ChemRxiv
46. Automated Adaptive Absolute Binding FreeEnergy Calculations
    Finlay Clark, Graeme R. Robb, Daniel J. Cole, Julien Michel · 2024 · ChemRxiv
47. BindFlow: A Free, User-Friendly Pipeline for Absolute Binding Free Energy Calculations Using Free Energy Perturbation or MM(PB/GB)SA
    Alejandro Martínez León, Lucas Andersen, Jochen S. Hub · 2026 · Journal of Chemical Theory and Computation
48. Binding Networks Identify Targetable Protein Pockets for Mechanism-Based Drug Design
    Mónika Bálint, Balázs Zoltán Zsidó, David van der Spoel, Csaba Hetényi · 2022 · International Journal of Molecular Sciences
49. Investigating the Solvent Effects on Binding Affinity of PAHs-ExBox4+ Complexes: An Alchemical Approach.
    Fabio E. S. Souza, Germano Heinzelmann, G. Caramori · 2023 · Journal of Physical Chemistry B
50. Leveraging the Thermodynamics of Protein Conformations in Drug Discovery
    Bin W. Zhang, Mikolai Fajer, Wei Chen, Francesca Moraca, Lingle Wang · 2024 · Journal of Chemical Information and Modeling
51. RED-E-Function-Based Equilibrium Parameter Finder: Finding the Best Restraint Parameters in Absolute Binding Free Energy Calculations
    Wanyi Huang, Runduo Liu, Yufen Yao, Yijun Lai, Hai‐Bin Luo, Zhe Li · 2024 · The Journal of Physical Chemistry Letters
52. Assessment of Flexible Shape Complementarity: New Opportunities to Explain and Induce Selectivity in Ligands of Protein Tyrosine Phosphatase 1B
    Alexandra Naß, David Schaller, Gerhard Wolber · 2019 · Molecular Informatics
53. Evaluating the use of absolute binding free energy in the fragment optimization process.
    Irfan Alibay, Aniket Magarkar, Daniel Seeliger, Philip Charles Biggin · 2022 · ChemRxiv
54. Calculating the Full Free Energy Profile for Covalent Modification of a Druggable Cysteine in Bruton’s Tyrosine Kinase
    Ernest Awoonor‐Williams, Christopher N. Rowley · 2020 · ChemRxiv
55. Core Flipping in Lead Optimization: Rank Ordering Using λ‑Dynamics
    Parveen Gartan, Charles L. Brooks, Nathalie Reuter · 2025 · Journal of Chemical Information and Modeling
56. Calculations of the Absolute Free Energy, Enthalpy, and Entropy of Drug Binding Using Different Potential Models.
    S. Rick, Christopher M. Summa · 2025 · Journal of Physical Chemistry B
57. Synergistic design of ionic liquid monomers and MOF–cellulose scaffolds for selective protein recognition in molecularly imprinted materials
    Yi Yang, Sufeng Zhang, Lijing Zhang, Nan Zhang, Liwei Qian, Wenqi Song · 2026 · Carbohydrate Polymers
58. Accurate Estimation of Protein-ligand Binding Free Energies Based on Geometric Restraints
    Haohao Fu, Haochuan Chen, Hong Zhang, Xueguang Shao, Wensheng Cai · 2021 · 化学学报
59. Predictive Modelling of the Primary and Secondary Pharmacology of Compounds in Drug Discovery
    Kathryn A. Giblin · 2019 · Apollo (University of Cambridge)
60. Endless Data for Drug Discovery Pipeline Validation for Free – Computational Chemistry’s Gift
    Stefan M. Ivanov · 2025 · Research Square
61. From bench to bedside, via desktop. Recent advances in the application of cutting-edge in silico tools in the research of drugs targeting bromodomain modules
    Vassilios Myrianthopoulos, Emmanuel Mikros · 2018 · Biochemical Pharmacology
62. Insight into the Binding Energetics of Targeted Reversible Covalent Inhibitors of the SARS-CoV-2 Main Protease
    Ernest Awoonor‐Williams · 2021 · ChemRxiv
63. Evaluating the use of absolute binding free energy in the fragment optimization process.
    Irfan Alibay, Aniket Magarkar, Daniel Seeliger, Philip Charles Biggin · 2022 · ChemRxiv
64. Alchemical Absolute Protein-Ligand Binding Free Energies for Drug Design
    Yuriy Khalak, Gary Tresadern, Matteo Aldeghi, Hannah Magdalena Baumann, David L. Mobley, Bert L. de Groot, Vytautas Gapsys · 2021
65. Targeting the Acetylation Reader Family: Bromodomain Proteins
    Martin P. Schwalm, Atoosa Karimi Babaahmadi, Suzanne Z. Ackloo, Stefan Knapp · 2024 · Royal Society of Chemistry eBooks
66. Drug Discovery for Chromatin Readers, Writers, Erasers, Remodelers and Epitranscriptomic Targets
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67. Assessment of the Topology and OligomerisationStates of Coiled Coils Using Metadynamics withConformational Restraints
    Evangelia Notari, Christopher W. Wood, Julien Michel · 2024 · ChemRxiv
68. Benchmarking Free Energy Computational Methods for Revealing the Interactions Driving PARP1 Selective Inhibition
    Alejandro Feito, Natàlia DeMoya‐Valenzuela, Cristian Privat, Andrés R. Tejedor, Marco DelValle-Carrillo, Sara Cembellín, Lucía Paniagua‐Herranz, Adiran Garaizar, J. Oller-Iscar, Alberto Ocana et al. · 2025 · bioRxiv (Cold Spring Harbor Laboratory)
69. A Non-Alchemical Absolute Binding Free Energy Framework for Small Molecule Drugs
    Yu Shi, Jianing Li · 2026 · bioRxiv (Cold Spring Harbor Laboratory)
70. D-MBIS Nonbonded Force Field Parameters Improve Specificity and Selectivity Prediction in Bromodomains
    Luis Macaya, Esteban Vöhringer‐Martinez · 2026 · The Journal of Physical Chemistry B
71. Caractérisation de complexes d'inhibiteurs à visée thérapeutique avec des métalloprotéines : cas de l'intégrase du VIH-1
    Perla El Darazi · 2021
72. A Binding-Depth-Dependent Continuum of ADAM17/TACE Inhibition Revealed by Punicalagin-Derived Polyphenols
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73. A binding-depth-dependent continuum of ADAM17/TACE inhibition revealed by punicalagin-derived polyphenols
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74. Evaluation of Physics-Based Pose Prediction and the Role of Receptor Flexibility in a Community Antiviral Blind Challenge
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75. Advances in multi-scale computational approaches for kinase selectivity profiling
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76. What Can Molecular Dynamics Legitimately Claim in Pharmaceutical Research? A Critical Review of Sampling, Validation, and Mechanistic Interpretation
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77. BindingDB Entry 50019722: Structure-Based Development of Isoform-Selective Inhibitors of Casein Kinase 1ε vs Casein Kinase 1δ.
    BindingDB · 2024 · UC San Diego