Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models

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1. Molecular Mechanism of the Inhibition of EGCG on the Alzheimer Aβ1–42Dimer
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2. Steered Molecular Dynamics Simulation in Rational Drug Design
   Phuc-Chau Do, Eric H. Lee, Ly Le · 2018 · Journal of Chemical Information and Modeling
3. Synthesis, Anti-Inflammatory Activity, and in Vitro Antitumor Effect of a Novel Class of Cyclooxygenase Inhibitors: 4-(Aryloyl)phenyl Methyl Sulfones
   Youssef Harrak, Giovanni Casula, Joan Basset, Glòria Rosell, Salvatore Plescia, Demetrio Raffa, Maria Grazia Cusimano, R. Pouplana, María Dolors Pujol · 2010 · Journal of Medicinal Chemistry
4. Virtual screening using molecular simulations
   Tianyi Yang, Johnny C. Wu, Chunli Yan, Yuanfeng Wang, Ray Luo, Michael B. Gonzales, Kevin N. Dalby, Pengyu Y. Ren · 2011 · Proteins Structure Function and Bioinformatics
5. Crystal Structure and Molecular Modeling of 17-DMAG in Complex with Human Hsp90
   Joseph M. Jez, Julian C.‐H. Chen, Giulio Rastelli, Robert Michael Stroud, Daniel V. Santi · 2003 · Chemistry & Biology
6. Protocol for MM/PBSA Molecular Dynamics Simulations of Proteins
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7. Inhibition of Aggregation of Amyloid Peptides by Beta-Sheet Breaker Peptides and Their Binding Affinity
   Viet Hoang Man, Sơn Tùng Ngô, Nguyen Sy Lam, Mai Suan Li · 2011 · The Journal of Physical Chemistry B
8. Unveiling the Full Potential of Flexible Receptor Docking Using Multiple Crystallographic Structures
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9. Solvation Thermodynamics of Organic Molecules by the Molecular Integral Equation Theory: Approaching Chemical Accuracy
   Ekaterina L. Ratkova, David Scott Palmer, Maxim V. Fedorov · 2015 · Chemical Reviews
10. Rigorous Free Energy Simulations in Virtual Screening
    Z. Cournia, Bryce K. Allen, T. Beuming, D. Pearlman, B. Radak, W. Sherman · 2020 · Journal of Chemical Information and Modeling
11. Evaluating the Molecular Mechanics Poisson−Boltzmann Surface Area Free Energy Method Using a Congeneric Series of Ligands to p38 MAP Kinase
    David A. Pearlman · 2005 · Journal of Medicinal Chemistry
12. A generalized Born formalism for heterogeneous dielectric environments: application to the implicit modeling of biological membranes.
    S. Tanizaki, M. Feig · 2005 · Journal of Chemical Physics
13. Twenty‐five years of nucleic acid simulations
    Thomas E. Cheatham, David Andrew Case · 2013 · Biopolymers
14. Characterization of Domain–Peptide Interaction Interface: A Case Study on the Amphiphysin-1 SH3 Domain
    Tingjun Hou, Wei Zhang, David Andrew Case, Wei Wang · 2008 · Journal of Molecular Biology
15. A Comprehensive Docking and MM/GBSA Rescoring Study of Ligand Recognition upon Binding Antithrombin
    Xiaohua Zhang, Horacio Pérez‐Sánchez, Felice C. Lightstone · 2017 · Current Topics in Medicinal Chemistry
16. Exploring the Stability of Ligand Binding Modes to Proteins by Molecular Dynamics Simulations: A Cross-docking Study
    Kai Liu, Hironori Kokubo · 2017 · Journal of Chemical Information and Modeling
17. Interaction of antibacterial compounds with RND efflux pumps in Pseudomonas aeruginosa
    Jürg Dreier, Paolo Ruggerone · 2015 · Frontiers in Microbiology
18. High-Performance Drug Discovery: Computational Screening by Combining Docking and Molecular Dynamics Simulations
    Noriaki Okimoto, Noriyuki Futatsugi, Hideyoshi Fuji, Atsushi Suenaga, Gentaro Morimoto, Ryoko Yanai, Yousuke Ohno, Tetsu Narumi, Makoto Taiji · 2009 · PLoS Computational Biology
19. Recent Development and Application of Virtual Screening in Drug Discovery: An Overview
    Tingjun Hou, Xiaojie Xu · 2004 · Current Pharmaceutical Design
20. Long-chain carboxychromanols, metabolites of vitamin E, are potent inhibitors of cyclooxygenases
    Qing Jiang, Xinmin Yin, Markus A. Lill, Matthew L. Danielson, Helene Freiser, Jianjie Huang · 2008 · Proceedings of the National Academy of Sciences
21. Biomolecular electrostatics and solvation: a computational perspective
    Pengyu Y. Ren, Jaehun Chun, Dennis Thomas, Michael J. Schnieders, Marcelo Marucho, Jiajing Zhang, Nathan Baker · 2012 · Quarterly Reviews of Biophysics
22. CaFE: a tool for binding affinity prediction using end-point free energy methods
    Hui Liu, Tingjun Hou · 2016 · Bioinformatics
23. Biomolecular diffusional association
    Razif R. Gabdoulline, Rebecca C. Wade · 2002 · Current Opinion in Structural Biology
24. Coarse-Grained Model of Proteins Incorporating Atomistic Detail of the Active Site
    Marilisa Neri, Claudio Anselmi, Michele Cascella, Amos Maritan, Paolo Carloni · 2005 · Physical Review Letters
25. Fast Boundary Element Method for the Linear Poisson−Boltzmann Equation
    Alexander H. Boschitsch, Márcia O. Fenley, Huan‐Xiang Zhou · 2002 · The Journal of Physical Chemistry B
26. Estimation of Absolute Free Energies of Hydration Using Continuum Methods: Accuracy of Partial Charge Models and Optimization of Nonpolar Contributions
    Robert C. Rizzo, Tiba Aynechi, David Andrew Case, Irwin D. Kuntz · 2005 · Journal of Chemical Theory and Computation
27. Groove Binding Mechanism of Ionic Liquids: A Key Factor in Long-Term Stability of DNA in Hydrated Ionic Liquids?
    Aneesh Chandran, Debostuti Ghoshdastidar, Sanjib Senapati · 2012 · Journal of the American Chemical Society
28. Molecular Mechanism of MBX2319 Inhibition of Escherichia coli AcrB Multidrug Efflux Pump and Comparison with Other Inhibitors
    Attilio Vittorio Vargiu, Paolo Ruggerone, Timothy J. Opperman, Son T. Nguyen, Hiroshi Nikaido · 2014 · Antimicrobial Agents and Chemotherapy
29. Integration of element specific persistent homology and machine learning for protein‐ligand binding affinity prediction
    Cang, Zixuan, Wei, Guo‐Wei · 2018 · International Journal for Numerical Methods in Biomedical Engineering
30. Dual Binding Modes of Congo Red to Amyloid Protofibril Surface Observed in Molecular Dynamics Simulations
    Chun Fu Wu, Zhixiang Wang, Hongxing Lei, Wei Zhang, Yong Duan · 2007 · Journal of the American Chemical Society
31. Ligand binding free-energy calculations with funnel metadynamics
    Stefano Raniolo, Vittorio Limongelli · 2020 · Nature Protocols
32. The relaxed complex method: Accommodating receptor flexibility for drug design with an improved scoring scheme
    Jung‐Hsin Lin, Alexander L. Perryman, Julie R. Schames, James Andrew McCammon · 2002 · Biopolymers
33. A Poisson–Boltzmann dynamics method with nonperiodic boundary condition
    Qiang Lü, Ray Luo · 2003 · The Journal of Chemical Physics
34. Small Molecule Affinity Fingerprinting
    Doron C. Greenbaum, William David Arnold, Felice Lu, Linda Hayrapetian, Amos Baruch, Jennifer R. Krumrine, Samuel Toba, Kareem A. H. Chehade, Dieter Brömme, Irwin D. Kuntz et al. · 2002 · Chemistry & Biology
35. Docking-based inverse virtual screening: methods, applications, and challenges
    Xianjin Xu, Marshal Huang, Xiaoqin Zou · 2018 · Biophysics Reports
36. Ligand binding free energy and kinetics calculation in 2020
    V. Limongelli · 2020 · Wiley Interdisciplinary Reviews Computational Molecular Science
37. Statistical mechanics and molecular dynamics in evaluating thermodynamic properties of biomolecular recognition
    Jeff Wereszczynski, J. McCammon · 2011 · Quarterly Reviews of Biophysics (print)
38. The FHA and BRCT domains recognize ADP-ribosylation during DNA damage response
    Li Mo, Lin‐Yu Lu, Chao‐Yie Yang, Shaomeng Wang, Xiaochun Yu · 2013 · Genes & Development
39. Molecular Dynamics and Free Energy Analyses of Cathepsin D−Inhibitor Interactions: Insight into Structure-Based Ligand Design
    Shuanghong Huo, Junmei Wang, Piotr Cieplak, Peter A. Kollman, Irwin D. Kuntz · 2002 · Journal of Medicinal Chemistry
40. Drug Discovery Using Chemical Systems Biology: Weak Inhibition of Multiple Kinases May Contribute to the Anti-Cancer Effect of Nelfinavir
    Li Xie, Thomas Evangelidis, Lei Xie, Philip E. Bourne · 2011 · PLoS Computational Biology
41. Computational Analysis and Prediction of the Binding Motif and Protein Interacting Partners of the Abl SH3 Domain
    Tingjun Hou, Ken Chen, William A. McLaughlin, Benzhuo Lu, Wei Wang · 2006 · PLoS Computational Biology
42. Analyzing Effects of Naturally Occurring Missense Mutations
    Zhe Zhang, Maria A. Miteva, Lin Wang, Emil G Alexov · 2012 · Computational and Mathematical Methods in Medicine
43. Protein flexibility in docking and surface mapping
    Katrina W. Lexa, Heather A. Carlson · 2012 · Quarterly Reviews of Biophysics
44. Rational engineering of L-asparaginase reveals importance of dual activity for cancer cell toxicity
    Marc N. Offman, Marcin Król, Naina R. Patel, Shekhar Krishnan, JiZhong Liu, Vaskar Saha, Paul A. Bates · 2010 · Blood
45. Molecular Dynamics—Solvated Interaction Energy Studies of Protein–Protein Interactions: The MP1–p14 Scaffolding Complex
    Cui, Qizhi, Sulea, Traian, Schrag, Joseph D., Munger, Christine, Hung, Ming-Ni, Naïm, Marwen, Cygler, Miroslaw, Purisima, Enrico O. · 2008 · Journal of Molecular Biology
46. An accurate free energy estimator: based on MM/PBSA combined with interaction entropy for protein–ligand binding affinity
    Kaifang Huang, Song Luo, Yalong Cong, Susu Zhong, John Z. H. Zhang, Lili Duan · 2020 · Nanoscale
47. Analytical electrostatics for biomolecules: Beyond the generalized Born approximation
    Grigori Sigalov, Andrew T. Fenley, Alexey V. Onufriev · 2006 · The Journal of Chemical Physics
48. Binding Energy Distribution Analysis Method (BEDAM) for Estimation of Protein−Ligand Binding Affinities
    Emilio Gallicchio, Mauro Lapelosa, Ronald M. Levy · 2010 · Journal of Chemical Theory and Computation
49. Accurate prediction of stability changes in protein mutants by combining machine learning with structure based computational mutagenesis
    Majid Masso, Iosif I. Vaisman · 2008 · Bioinformatics
50. Structure⧸Function Correlations of Proteins using MM, QM⧸MM, and Related Approaches: Methods, Concepts, Pitfalls, and Current Progress
    Avital Shurki, Arieh Warshel · 2003 · Advances in protein chemistry
51. Modeling Backbone Flexibility Improves Protein Stability Estimation
    Shuangye Yin, Feng Ding, Nikolay V. Dokholyan · 2007 · Structure
52. Treatment of charge singularities in implicit solvent models
    Weihua Geng, Sining Yu, Guo‐Wei Wei · 2007 · The Journal of Chemical Physics
53. Comparison of MM/GBSA calculations based on explicit and implicit solvent simulations
    Frithjof Godschalk, Samuel Genheden, Pär Söderhjelm, Ulf Ryde · 2013 · Physical Chemistry Chemical Physics
54. Molecular Dynamics Simulations and Thermodynamics Analysis of DNA−Drug Complexes. Minor Groove Binding between 4‘,6-Diamidino-2-phenylindole and DNA Duplexes in Solution
    Nad’a Špačková, Thomas E. Cheatham, Filip Ryjáček, Filip Lankaš, Luc Van Meervelt, Pavel Hobza, Jiřı́ Šponer · 2003 · Journal of the American Chemical Society
55. Towards accurate free energy calculations in ligand protein-binding studies.
    T. Steinbrecher, A. Labahn · 2010 · Current Medicinal Chemistry
56. Hierarchical virtual screening approaches in small molecule drug discovery
    Ashutosh Kumar, Kam Y. J. Zhang · 2014 · Methods
57. Evaluation of DOCK 6 as a pose generation and database enrichment tool
    Scott R. Brozell, Sudipto Mukherjee, Trent E. Balius, Daniel R. Roe, David Andrew Case, Robert C. Rizzo · 2012 · Journal of Computer-Aided Molecular Design
58. Assessing the performance of MM/PBSA and MM/GBSA methods. 9. Prediction reliability of binding affinities and binding poses for protein–peptide complexes
    Gaoqi Weng, Ercheng Wang, Fu Chen, Huiyong Sun, Zhe Wang, Tingjun Hou · 2019 · Physical Chemistry Chemical Physics
59. Limitations and challenges in protein stability prediction upon genome variations: towards future applications in precision medicine
    Tiziana Sanavia, Giovanni Birolo, Ludovica Montanucci, Paola Turina, Emidio Capriotti, Piero Fariselli · 2020 · Computational and Structural Biotechnology Journal
60. Recent Developments in Free Energy Calculations for Drug Discovery
    Edward King, Eric W. Aitchison, Han Li, Ray Luo · 2021 · Frontiers in Molecular Biosciences
61. Navigating the landscape of enzyme design: from molecular simulations to machine learning
    Jiahui Zhou, Meilan Huang · 2024 · Chemical Society Reviews
62. Computational Determination of Potential Inhibitors of SARS-CoV‑2 Main Protease
    Sơn Tùng Ngô, Ngoc Quynh Anh Pham, Ly Le, Duc-Hung Pham, Van V. Vu · 2020 · Journal of Chemical Information and Modeling
63. Proton-coupled sugar transport in the prototypical major facilitator superfamily protein XylE
    Goragot Wisedchaisri, Min-Sun Park, Matthew G. Iadanza, Hongjin Zheng, Tamir Gonen · 2014 · Nature Communications
64. Mutations at protein-protein interfaces: Small changes over big surfaces have large impacts on human health
    Harry C. Jubb, Arun Prasad Pandurangan, Meghan A. Turner, Bernardo Ochoa‐Montaño, Tom L. Blundell, David Benjamin Ascher · 2016 · Progress in Biophysics and Molecular Biology
65. Fragment‐based drug discovery—the importance of high‐quality molecule libraries
    Marta Bon, Alan E Bilsland, Justin F. Bower, Kirsten McAulay · 2022 · Molecular Oncology
66. Bioinformatics approaches to discovering food-derived bioactive peptides: Reviews and perspectives
    Zhenjiao Du, Jeffrey R. Comer, Yonghui Li · 2023 · TrAC Trends in Analytical Chemistry
67. A Combination of Docking, QM/MM Methods, and MD Simulation for Binding Affinity Estimation of Metalloprotein Ligands
    Akash Khandelwal, Viera Lukáčová, Doğan Çömez, Daniel M. Kroll, Soumyendu Raha, Štefan Baláž · 2005 · Journal of Medicinal Chemistry
68. Structure-based systems biology for analyzing off-target binding
    Lei Xie, Li Xie, Philip E. Bourne · 2011 · Current Opinion in Structural Biology
69. Rapid, accurate, precise and reproducible ligand–protein binding free energy prediction
    Shunzhou Wan, Agastya P. Bhati, Stefan J. Zasada, Peter V. Coveney · 2020 · Interface Focus
70. Consequences of chirality on the dynamics of a water-soluble supramolecular polymer
    Matthew Brandon Baker, Lorenzo Albertazzi, Ilja Karina Voets, Christianus M. A. Leenders, Anja R. A. Palmans, Giovanni Maria Pavan, Egbert W. Meijer · 2015 · Nature Communications
71. Structure-Based Identification of Potential Drugs Against FmtA of Staphylococcus aureus: Virtual Screening, Molecular Dynamics, MM-GBSA, and QM/MM
    Vikram Dalal, Poonam Dhankhar, Vishakha Singh, Vishakha Singh, Gaddy Rakhaminov, Dasantila Golemi, Pravindra Kumar · 2021 · The Protein Journal
72. Rapid and Accurate Prediction of Binding Free Energies for Saquinavir-Bound HIV-1 Proteases
    Ileana Stoica, S. Kashif Sadiq, Peter V. Coveney · 2008 · Journal of the American Chemical Society
73. Scaffold-based discovery of indeglitazar, a PPAR pan-active anti-diabetic agent
    Dean R. Artis, Jack J. Lin, Chao Zhang, Weiru Wang, Upasana Mehra, Mylène Perreault, David V. Erbe, Heike I. Krupka, Bruce P. England, James Arnold et al. · 2008 · Proceedings of the National Academy of Sciences
74. Computational identification of the binding mechanism of a triple reuptake inhibitor amitifadine for the treatment of major depressive disorder
    Weiwei Xue, Panpan Wang, Gao Tu, Fengyuan Yang, Guoxun Zheng, Xiaofeng Li, Xiaoxu Li, Yu Chen, Xiaojun Yao, Feng Zhu · 2018 · Physical Chemistry Chemical Physics
75. Molecular dynamics simulations of biological membranes and membrane proteins using enhanced conformational sampling algorithms
    Takaharu Mori, Naoyuki Miyashita, Wonpil Im, Michael Feig, Yuji Sugita · 2016 · Biochimica et Biophysica Acta (BBA) - Biomembranes
76. Statistical Analysis on the Performance of Molecular Mechanics Poisson–Boltzmann Surface Area versus Absolute Binding Free Energy Calculations: Bromodomains as a Case Study
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77. Is the Rigidity of SARS-CoV-2 Spike Receptor-Binding Motif the Hallmark for Its Enhanced Infectivity? Insights from All-Atom Simulations
    Angelo Spinello, Andrea Saltalamacchia, Alessandra Magistrato · 2020 · The Journal of Physical Chemistry Letters
78. An MM/3D-RISM Approach for Ligand Binding Affinities
    Samuel Genheden, Tyler Luchko, Sergey Gusarov, Andriy Kovalenko, Ulf Ryde · 2010 · The Journal of Physical Chemistry B
79. Predicting Relative Protein Affinity of Novel Per- and Polyfluoroalkyl Substances (PFASs) by An Efficient Molecular Dynamics Approach
    Cheng, Weixiao, Ng, Carla A. · 2018 · Environmental Science & Technology
80. An improved method to predict the entropy term with the MM/PBSA approach
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81. Targeting Self-Binding Peptides as a Novel Strategy To Regulate Protein Activity and Function: A Case Study on the Proto-oncogene Tyrosine Protein Kinase c-Src
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82. Plant-derived natural polyphenols as potential antiviral drugs against SARS-CoV-2 via RNA‐dependent RNA polymerase (RdRp) inhibition: an in-silico analysis
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83. Current developments of computer-aided drug design
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84. Molecular dynamics in the endgame of protein structure prediction
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85. Ethidium bromide interactions with DNA: an exploration of a classic DNA–ligand complex with unbiased molecular dynamics simulations
    Rodrigo Galindo‐Murillo, Thomas E. Cheatham · 2021 · Nucleic Acids Research
86. Molecular Insight into Conformational Transition of Amyloid β-Peptide 42 Inhibited by (−)-Epigallocatechin-3-gallate Probed by Molecular Simulations
    Fufeng Liu, Xiaoyan Dong, Lizhong He, Anton P. J. Middelberg, Yan Ping Sun · 2011 · The Journal of Physical Chemistry B
87. Structural and Mechanistic Insights into LEOPARD Syndrome-Associated SHP2 Mutations
    Zhi-Hong Yu, Jie Xu, Chad D. Walls, Lan Chen, Sheng Zhang, Ruoyu Zhang, Li Wu, Lina Wang, Sijiu Liu, Zhong‐Yin Zhang · 2013 · Journal of Biological Chemistry
88. The Binding of Thioflavin T and Its Neutral Analog BTA-1 to Protofibrils of the Alzheimer’s Disease Aβ16–22 Peptide Probed by Molecular Dynamics Simulations
    Chun Fu Wu, Zhixiang Wang, Hongxing Lei, Yong Duan, Michael T. Bowers, Joan‐Emma Shea · 2008 · Journal of Molecular Biology
89. Rapid, Accurate, Precise, and Reliable Relative Free Energy Prediction Using Ensemble Based Thermodynamic Integration
    Agastya P. Bhati, Shunzhou Wan, David W. Wright, Peter V. Coveney · 2016 · Journal of Chemical Theory and Computation
90. Computing Clinically Relevant Binding Free Energies of HIV-1 Protease Inhibitors
    David W. Wright, Benjamin A. Hall, Owain A. Kenway, Shantenu Jha, Peter V. Coveney · 2014 · Journal of Chemical Theory and Computation
91. An Effective MM/GBSA Protocol for Absolute Binding Free Energy Calculations: A Case Study on SARS-CoV-2 Spike Protein and the Human ACE2 Receptor
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92. Repurposing approved drugs as inhibitors of SARS-CoV-2 S-protein from molecular modeling and virtual screening
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93. Poisson–Nernst–Planck Theory Approach to the Calculation of Current Through Biological Ion Channels
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94. Binding Modes of Thioflavin-T to the Single-Layer β-Sheet of the Peptide Self-Assembly Mimics
    Chun Fu Wu, Matthew Biancalana, Shohei Koide, Joan‐Emma Shea · 2009 · Journal of Molecular Biology
95. Characterizing Loop Dynamics and Ligand Recognition in Human- and Avian-Type Influenza Neuraminidases via Generalized Born Molecular Dynamics and End-Point Free Energy Calculations
    Rommie E. Amaro, Xiaolin Cheng, Ivaylo N. Ivanov, Dong Xu, James Andrew McCammon · 2009 · Journal of the American Chemical Society
96. An Analysis of the Interactions between the Sem−5 SH3 Domain and Its Ligands Using Molecular Dynamics, Free Energy Calculations, and Sequence Analysis
    Wei Wang, Wendell A. Lim, Araz Jakalian, Jian Wang, Junmei Wang, Ray Luo, Christopher I. Bayly, Peter A. Kollman · 2001 · Journal of the American Chemical Society
97. Complete aggregation pathway of amyloid β (1-40) and (1-42) resolved on an atomically clean interface
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98. Formation Pathways of a Guanine-Quadruplex DNA Revealed by Molecular Dynamics and Thermodynamic Analysis of the Substates
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99. Thermodynamic Basis for Promiscuity and Selectivity in Protein−Protein Interactions: PDZ Domains, a Case Study
    Nathalie Basdevant, Harel Weinstein, Marco A. Ceruso · 2006 · Journal of the American Chemical Society
100. Prospective Evaluation of Free Energy Calculations for the Prioritization of Cathepsin L Inhibitors
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