Note: In lieu of an abstract, this is the article's first page.
Cited By
This article is cited by 1767 publications.
- Margarita Stampelou, Graham Ladds, Antonios Kolocouris. Computational Workflow for Refining AlphaFold Models in Drug Design Using Kinetic and Thermodynamic Binding Calculations: A Case Study for the Unresolved Inactive Human Adenosine A3 Receptor. The Journal of Physical Chemistry B 2024, 128 (4) , 914-936. https://doi.org/10.1021/acs.jpcb.3c05986
- Zhaorui Xin, Yue Zhang, Dongshuai Hou, Huiwen Sun, Zhiheng Ding, Pan Wang, Muhan Wang, Xinpeng Wang, Qingqing Xu, Jing Guan, Jiayi Yang, Yingchun Liu, Liran Zhang. Atomic Insights into the Relationship between Molecular Structure and Dispersion Performance of Phenyl Polymer on Graphene Oxide. Langmuir 2024, 40 (1) , 413-425. https://doi.org/10.1021/acs.langmuir.3c02648
- Kwangho Nam, Abdul Raafik Arattu Thodika, Christin Grundström, Uwe H. Sauer, Magnus Wolf-Watz. Elucidating Dynamics of Adenylate Kinase from Enzyme Opening to Ligand Release. Journal of Chemical Information and Modeling 2024, 64 (1) , 150-163. https://doi.org/10.1021/acs.jcim.3c01618
- Andreia Fortuna, Paulo J. Costa. Assessment of Halogen Off-Center Point-Charge Models Using Explicit Solvent Simulations. Journal of Chemical Information and Modeling 2023, 63 (23) , 7464-7475. https://doi.org/10.1021/acs.jcim.3c01561
- Muhan Wang, Huiwen Sun, Xiangming Zhou, Pan Wang, Zongjin Li, Dongshuai Hou. Surface Engineering of Migratory Corrosion Inhibitors: Controlling the Wettability of Calcium Silicate Hydrate in the Nanoscale. Langmuir 2023, 39 (48) , 17110-17121. https://doi.org/10.1021/acs.langmuir.3c01953
- David A. Case, Hasan Metin Aktulga, Kellon Belfon, David S. Cerutti, G. Andrés Cisneros, Vinícius Wilian D. Cruzeiro, Negin Forouzesh, Timothy J. Giese, Andreas W. Götz, Holger Gohlke, Saeed Izadi, Koushik Kasavajhala, Mehmet C. Kaymak, Edward King, Tom Kurtzman, Tai-Sung Lee, Pengfei Li, Jian Liu, Tyler Luchko, Ray Luo, Madushanka Manathunga, Matias R. Machado, Hai Minh Nguyen, Kurt A. O’Hearn, Alexey V. Onufriev, Feng Pan, Sergio Pantano, Ruxi Qi, Ali Rahnamoun, Ali Risheh, Stephan Schott-Verdugo, Akhil Shajan, Jason Swails, Junmei Wang, Haixin Wei, Xiongwu Wu, Yongxian Wu, Shi Zhang, Shiji Zhao, Qiang Zhu, Thomas E. Cheatham, III, Daniel R. Roe, Adrian Roitberg, Carlos Simmerling, Darrin M. York, Maria C. Nagan, Kenneth M. Merz, Jr.. AmberTools. Journal of Chemical Information and Modeling 2023, 63 (20) , 6183-6191. https://doi.org/10.1021/acs.jcim.3c01153
- César de Oliveira, Karl Leswing, Shulu Feng, René Kanters, Robert Abel, Sathesh Bhat. FEP Protocol Builder: Optimization of Free Energy Perturbation Protocols Using Active Learning. Journal of Chemical Information and Modeling 2023, 63 (17) , 5592-5603. https://doi.org/10.1021/acs.jcim.3c00681
- Miyi Li, Liqiang Lv, Tao Fang, Long Hao, Shenhui Li, Shoulong Dong, Yufeng Wu, Xiao Dong, Helei Liu. Self-Consistent Implementation of a Solvation Free Energy Framework to Predict the Salt Solubilities of Six Alkali Halides. Journal of Chemical Theory and Computation 2023, 19 (16) , 5586-5601. https://doi.org/10.1021/acs.jctc.3c00083
- Johannes C. B. Dietschreit, Dennis J. Diestler, Rafael Gómez-Bombarelli. Entropy and Energy Profiles of Chemical Reactions. Journal of Chemical Theory and Computation 2023, 19 (16) , 5369-5379. https://doi.org/10.1021/acs.jctc.3c00448
- Bastien Belzunces, Sophie Hoyau, Jérôme Cuny, Fabienne Bessac. Desorption Mechanism of a Pesticide from a Hydrated Calcium Montmorillonite Unraveled by Molecular Dynamics Simulations. The Journal of Physical Chemistry C 2023, 127 (27) , 12953-12966. https://doi.org/10.1021/acs.jpcc.3c01006
- Kwangho Nam, Yunwen Tao, Victor Ovchinnikov. Molecular Simulations of Conformational Transitions within the Insulin Receptor Kinase Reveal Consensus Features in a Multistep Activation Pathway. The Journal of Physical Chemistry B 2023, 127 (26) , 5789-5798. https://doi.org/10.1021/acs.jpcb.3c01804
- Vinayak Bhat, Connor P. Callaway, Chad Risko. Computational Approaches for Organic Semiconductors: From Chemical and Physical Understanding to Predicting New Materials. Chemical Reviews 2023, 123 (12) , 7498-7547. https://doi.org/10.1021/acs.chemrev.2c00704
- Sudip Das, Umberto Raucci, Rui P. P. Neves, Maria J. Ramos, Michele Parrinello. How and When Does an Enzyme React? Unraveling α-Amylase Catalytic Activity with Enhanced Sampling Techniques. ACS Catalysis 2023, 13 (12) , 8092-8098. https://doi.org/10.1021/acscatal.3c01473
- Joseph Clayton, Vinícius Martins de Oliveira, Mohamed Fouad Ibrahim, Xinyuanyuan Sun, Paween Mahinthichaichan, Mingzhe Shen, Rolf Hilgenfeld, Jana Shen. Integrative Approach to Dissect the Drug Resistance Mechanism of the H172Y Mutation of SARS-CoV-2 Main Protease. Journal of Chemical Information and Modeling 2023, 63 (11) , 3521-3533. https://doi.org/10.1021/acs.jcim.3c00344
- Shan Sun, Makoto Fushimi, Thomas Rossetti, Navpreet Kaur, Jacob Ferreira, Michael Miller, Jonathan Quast, Joop van den Heuvel, Clemens Steegborn, Lonny R. Levin, Jochen Buck, Robert W. Myers, Stacia Kargman, Nigel Liverton, Peter T. Meinke, David J. Huggins. Scaffold Hopping and Optimization of Small Molecule Soluble Adenyl Cyclase Inhibitors Led by Free Energy Perturbation. Journal of Chemical Information and Modeling 2023, 63 (9) , 2828-2841. https://doi.org/10.1021/acs.jcim.2c01577
- Farzad Molani, Simon Webb, Art E. Cho. Combining QM/MM Calculations with Classical Mining Minima to Predict Protein–Ligand Binding Free Energy. Journal of Chemical Information and Modeling 2023, 63 (9) , 2728-2734. https://doi.org/10.1021/acs.jcim.2c01637
- Izaz Monir Kamal, Saikat Chakrabarti. MetaDOCK: A Combinatorial Molecular Docking Approach. ACS Omega 2023, 8 (6) , 5850-5860. https://doi.org/10.1021/acsomega.2c07619
- Tai-Sung Lee, Hsu-Chun Tsai, Abir Ganguly, Darrin M. York. ACES: Optimized Alchemically Enhanced Sampling. Journal of Chemical Theory and Computation 2023, 19 (2) , 472-487. https://doi.org/10.1021/acs.jctc.2c00697
- Madelyn Smith, Pengfei Li. Molecular Insights into the Calcium Binding in Troponin C through a Molecular Dynamics Study. Journal of Chemical Information and Modeling 2023, 63 (1) , 354-361. https://doi.org/10.1021/acs.jcim.2c01411
- Pengfei Pei, Long Chen, Ruru Fan, Xi-Rui Zhou, Shan Feng, Hangrui Liu, Quanqiang Guo, Huiwei Yin, Qiang Zhang, Fude Sun, Liang Peng, Peng Wei, Chengzhi He, Renzhong Qiao, Zai Wang, Shi-Zhong Luo. Computer-Aided Design of Lasso-like Self-Assembling Anticancer Peptides with Multiple Functions for Targeted Self-Delivery and Cancer Treatments. ACS Nano 2022, 16 (9) , 13783-13799. https://doi.org/10.1021/acsnano.2c01014
- Ali Mehdizadeh Rahimi, Safa Jamali, Jaydeep P. Bardhan, Steven R. Lustig. Solvation Thermodynamics of Solutes in Water and Ionic Liquids Using the Multiscale Solvation-Layer Interface Condition Continuum Model. Journal of Chemical Theory and Computation 2022, 18 (9) , 5539-5558. https://doi.org/10.1021/acs.jctc.2c00248
- Mikhail Volkov, Joseph-André Turk, Nicolas Drizard, Nicolas Martin, Brice Hoffmann, Yann Gaston-Mathé, Didier Rognan. On the Frustration to Predict Binding Affinities from Protein–Ligand Structures with Deep Neural Networks. Journal of Medicinal Chemistry 2022, 65 (11) , 7946-7958. https://doi.org/10.1021/acs.jmedchem.2c00487
- Diego Moreno Martinez, Dominique Guillaumont, Philippe Guilbaud. Force Field Parameterization of Actinyl Molecular Cations Using the 12-6-4 Model. Journal of Chemical Information and Modeling 2022, 62 (10) , 2432-2445. https://doi.org/10.1021/acs.jcim.2c00153
- Sebastian Spicher, Christoph Plett, Philipp Pracht, Andreas Hansen, Stefan Grimme. Automated Molecular Cluster Growing for Explicit Solvation by Efficient Force Field and Tight Binding Methods. Journal of Chemical Theory and Computation 2022, 18 (5) , 3174-3189. https://doi.org/10.1021/acs.jctc.2c00239
- Thomas Mangin, Rachel Schurhammer, Georges Wipff. Liquid–Liquid Extraction of the Eu(III) Cation by BTP Ligands into Ionic Liquids: Interfacial Features and Extraction Mechanisms Investigated by MD Simulations. The Journal of Physical Chemistry B 2022, 126 (15) , 2876-2890. https://doi.org/10.1021/acs.jpcb.2c00488
- Mina Ebrahimi, Jérôme Hénin. Symmetry-Adapted Restraints for Binding Free Energy Calculations. Journal of Chemical Theory and Computation 2022, 18 (4) , 2494-2502. https://doi.org/10.1021/acs.jctc.1c01235
- Payal Chatterjee, Mert Y. Sengul, Anmol Kumar, Alexander D. MacKerell, Jr.. Harnessing Deep Learning for Optimization of Lennard-Jones Parameters for the Polarizable Classical Drude Oscillator Force Field. Journal of Chemical Theory and Computation 2022, 18 (4) , 2388-2407. https://doi.org/10.1021/acs.jctc.2c00115
- Shailesh Kumar Panday, Emil Alexov. Protein–Protein Binding Free Energy Predictions with the MM/PBSA Approach Complemented with the Gaussian-Based Method for Entropy Estimation. ACS Omega 2022, 7 (13) , 11057-11067. https://doi.org/10.1021/acsomega.1c07037
- Yu-Xin Zhu, Yan-Jing Sheng, Yu-Qiang Ma, Hong-Ming Ding. Assessing the Performance of Screening MM/PBSA in Protein–Ligand Interactions. The Journal of Physical Chemistry B 2022, 126 (8) , 1700-1708. https://doi.org/10.1021/acs.jpcb.1c09424
- Jun Zhang, Zhang Xie, Shaoqian Hao, Zheng Li, Jun Yao, Jianlong Kou. Heterogeneous Effect of Organic Matter on Accumulation Behaviors of Shale Gas in Water. Energy & Fuels 2022, 36 (3) , 1507-1514. https://doi.org/10.1021/acs.energyfuels.1c03967
- Callum J Dickson, Viktor Hornak, Jose S Duca. Relative Binding Free-Energy Calculations at Lipid-Exposed Sites: Deciphering Hot Spots. Journal of Chemical Information and Modeling 2021, 61 (12) , 5923-5930. https://doi.org/10.1021/acs.jcim.1c01147
- Ann E. Cleves, Stephen R. Johnson, Ajay N. Jain. Synergy and Complementarity between Focused Machine Learning and Physics-Based Simulation in Affinity Prediction. Journal of Chemical Information and Modeling 2021, 61 (12) , 5948-5966. https://doi.org/10.1021/acs.jcim.1c01382
- Zoe Cournia Christophe Chipot Benoît Roux Darrin M. York Woody Sherman . Free Energy Methods in Drug Discovery—Introduction. , 1-38. https://doi.org/10.1021/bk-2021-1397.ch001
- Andrew J. Veenis, Pengfei Li, Alexander V. Soudackov, Sharon Hammes-Schiffer, Philip C. Bevilacqua. Investigation of the pKa of the Nucleophilic O2′ of the Hairpin Ribozyme. The Journal of Physical Chemistry B 2021, 125 (43) , 11869-11883. https://doi.org/10.1021/acs.jpcb.1c06546
- Dmitrii M. Nikolaev, Madushanka Manathunga, Yoelvis Orozco-Gonzalez, Andrey A. Shtyrov, Yansel Omar Guerrero Martínez, Samer Gozem, Mikhail N. Ryazantsev, Kaline Coutinho, Sylvio Canuto, Massimo Olivucci. Free Energy Computation for an Isomerizing Chromophore in a Molecular Cavity via the Average Solvent Electrostatic Configuration Model: Applications in Rhodopsin and Rhodopsin-Mimicking Systems. Journal of Chemical Theory and Computation 2021, 17 (9) , 5885-5895. https://doi.org/10.1021/acs.jctc.1c00221
- Mariana Yoshinaga, Willian R. Rocha. Theoretical Investigation of the 4,5-Dibromorodamine Methyl Ester (TH9402) Photosensitizer Used in Photodynamic Therapy: Photophysics, Reactions in the Excited State, and Interactions with DNA. The Journal of Physical Chemistry B 2021, 125 (31) , 8932-8943. https://doi.org/10.1021/acs.jpcb.1c05463
- Jonah Z. Vilseck, Xinqiang Ding, Ryan L. Hayes, Charles L. Brooks III. Generalizing the Discrete Gibbs Sampler-Based λ-Dynamics Approach for Multisite Sampling of Many Ligands. Journal of Chemical Theory and Computation 2021, 17 (7) , 3895-3907. https://doi.org/10.1021/acs.jctc.1c00176
- Xiaomeng Zhang, Yazhou Wang, Xue Li, Jie Wu, Liwen Zhao, Wei Li, Jian Liu. Dynamics-Based Discovery of Novel, Potent Benzoic Acid Derivatives as Orally Bioavailable Selective Estrogen Receptor Degraders for ERα+ Breast Cancer. Journal of Medicinal Chemistry 2021, 64 (11) , 7575-7595. https://doi.org/10.1021/acs.jmedchem.1c00280
- Son Tung Ngo, Nguyen Minh Tam, Minh Quan Pham, Trung Hai Nguyen. Benchmark of Popular Free Energy Approaches Revealing the Inhibitors Binding to SARS-CoV-2 Mpro. Journal of Chemical Information and Modeling 2021, 61 (5) , 2302-2312. https://doi.org/10.1021/acs.jcim.1c00159
- Florian Leidner, Nese Kurt Yilmaz, Celia A. Schiffer. Deciphering Complex Mechanisms of Resistance and Loss of Potency through Coupled Molecular Dynamics and Machine Learning. Journal of Chemical Theory and Computation 2021, 17 (4) , 2054-2064. https://doi.org/10.1021/acs.jctc.0c01244
- Billy J. Williams-Noonan, Nevena Todorova, Ketav Kulkarni, Marie-Isabel Aguilar, Irene Yarovsky. An Active Site Inhibitor Induces Conformational Penalties for ACE2 Recognition by the Spike Protein of SARS-CoV-2. The Journal of Physical Chemistry B 2021, 125 (10) , 2533-2550. https://doi.org/10.1021/acs.jpcb.0c11321
- Sebastian Spicher, Stefan Grimme. Single-Point Hessian Calculations for Improved Vibrational Frequencies and Rigid-Rotor-Harmonic-Oscillator Thermodynamics. Journal of Chemical Theory and Computation 2021, 17 (3) , 1701-1714. https://doi.org/10.1021/acs.jctc.0c01306
- Viet Hoang Man, Xiongwu Wu, Xibing He, Xiang-Qun Xie, Bernard R. Brooks, Junmei Wang. Determination of van der Waals Parameters Using a Double Exponential Potential for Nonbonded Divalent Metal Cations in TIP3P Solvent. Journal of Chemical Theory and Computation 2021, 17 (2) , 1086-1097. https://doi.org/10.1021/acs.jctc.0c01267
- Peiran Chen, Igor Vorobyov, Benoît Roux, Toby W. Allen. Molecular Dynamics Simulations Based on Polarizable Models Show that Ion Permeation Interconverts between Different Mechanisms as a Function of Membrane Thickness. The Journal of Physical Chemistry B 2021, 125 (4) , 1020-1035. https://doi.org/10.1021/acs.jpcb.0c08613
- Tanotnon Tanawattanasuntorn, Tienthong Thongpanchang, Thanyada Rungrotmongkol, Chonnikan Hanpaibool, Potchanapond Graidist, Varomyalin Tipmanee. (−)-Kusunokinin as a Potential Aldose Reductase Inhibitor: Equivalency Observed via AKR1B1 Dynamics Simulation. ACS Omega 2021, 6 (1) , 606-614. https://doi.org/10.1021/acsomega.0c05102
- Son Tung Ngo, Ngoc Quynh Anh Pham, Ly Thi Le, Duc-Hung Pham, Van V. Vu. Computational Determination of Potential Inhibitors of SARS-CoV-2 Main Protease. Journal of Chemical Information and Modeling 2020, 60 (12) , 5771-5780. https://doi.org/10.1021/acs.jcim.0c00491
- Alessio Bartocci, Natacha Gillet, Tao Jiang, Florence Szczepaniak, Elise Dumont. Molecular Dynamics Approach for Capturing Calixarene–Protein Interactions: The Case of Cytochrome C. The Journal of Physical Chemistry B 2020, 124 (50) , 11371-11378. https://doi.org/10.1021/acs.jpcb.0c08482
- Marina P. Oliveira, Maurice Andrey, Salomé R. Rieder, Leyla Kern, David F. Hahn, Sereina Riniker, Bruno A. C. Horta, Philippe H. Hünenberger. Systematic Optimization of a Fragment-Based Force Field against Experimental Pure-Liquid Properties Considering Large Compound Families: Application to Saturated Haloalkanes. Journal of Chemical Theory and Computation 2020, 16 (12) , 7525-7555. https://doi.org/10.1021/acs.jctc.0c00683
- Ido Y. Ben-Shalom, Zhixiong Lin, Brian K. Radak, Charles Lin, Woody Sherman, Michael K. Gilson. Accounting for the Central Role of Interfacial Water in Protein–Ligand Binding Free Energy Calculations. Journal of Chemical Theory and Computation 2020, 16 (12) , 7883-7894. https://doi.org/10.1021/acs.jctc.0c00785
- Jan Walther Perthold, Dražen Petrov, Chris Oostenbrink. Toward Automated Free Energy Calculation with Accelerated Enveloping Distribution Sampling (A-EDS). Journal of Chemical Information and Modeling 2020, 60 (11) , 5395-5406. https://doi.org/10.1021/acs.jcim.0c00456
- Lin Frank Song, Kenneth M. Merz, Jr.. Evolution of Alchemical Free Energy Methods in Drug Discovery. Journal of Chemical Information and Modeling 2020, 60 (11) , 5308-5318. https://doi.org/10.1021/acs.jcim.0c00547
- Haochuan Chen, Julio D. C. Maia, Brian K. Radak, David J. Hardy, Wensheng Cai, Christophe Chipot, Emad Tajkhorshid. Boosting Free-Energy Perturbation Calculations with GPU-Accelerated NAMD. Journal of Chemical Information and Modeling 2020, 60 (11) , 5301-5307. https://doi.org/10.1021/acs.jcim.0c00745
- Xinqiang Ding, Bin Zhang. Computing Absolute Free Energy with Deep Generative Models. The Journal of Physical Chemistry B 2020, 124 (45) , 10166-10172. https://doi.org/10.1021/acs.jpcb.0c08645
- Liang Xu, Liao Y. Chen. Identification of a New Allosteric Binding Site for Cocaine in Dopamine Transporter. Journal of Chemical Information and Modeling 2020, 60 (8) , 3958-3968. https://doi.org/10.1021/acs.jcim.0c00346
- Yaozong Li, Kwangho Nam. Repulsive Soft-Core Potentials for Efficient Alchemical Free Energy Calculations. Journal of Chemical Theory and Computation 2020, 16 (8) , 4776-4789. https://doi.org/10.1021/acs.jctc.0c00163
- Florian Hofer, Johannes Kraml, Ursula Kahler, Anna S. Kamenik, Klaus R. Liedl. Catalytic Site pKa Values of Aspartic, Cysteine, and Serine Proteases: Constant pH MD Simulations. Journal of Chemical Information and Modeling 2020, 60 (6) , 3030-3042. https://doi.org/10.1021/acs.jcim.0c00190
- Hao Wang, Shuai He, Weilong Deng, Ying Zhang, Guobang Li, Jixue Sun, Wei Zhao, Yu Guo, Zheng Yin, Dongmei Li, Luqing Shang. Comprehensive Insights into the Catalytic Mechanism of Middle East Respiratory Syndrome 3C-Like Protease and Severe Acute Respiratory Syndrome 3C-Like Protease. ACS Catalysis 2020, 10 (10) , 5871-5890. https://doi.org/10.1021/acscatal.0c00110
- Nguyen Thanh Nguyen, Trung Hai Nguyen, T. Ngoc Han Pham, Nguyen Truong Huy, Mai Van Bay, Minh Quan Pham, Pham Cam Nam, Van V. Vu, Son Tung Ngo. Autodock Vina Adopts More Accurate Binding Poses but Autodock4 Forms Better Binding Affinity. Journal of Chemical Information and Modeling 2020, 60 (1) , 204-211. https://doi.org/10.1021/acs.jcim.9b00778
- Kira A. Armacost, Sereina Riniker, Zoe Cournia. Novel Directions in Free Energy Methods and Applications. Journal of Chemical Information and Modeling 2020, 60 (1) , 1-5. https://doi.org/10.1021/acs.jcim.9b01174
- Jixue Sun, Fandi Shi, Na Yang. Exploration of the Substrate Preference of Lysine Methyltransferase SMYD3 by Molecular Dynamics Simulations. ACS Omega 2019, 4 (22) , 19573-19581. https://doi.org/10.1021/acsomega.9b01842
- Nikhil Maroli, Naveen Kumar Kalagatur, Balu Bhasuran, Achuth Jayakrishnan, Renuka Ramalingam Manoharan, Ponmalai Kolandaivel, Jeyakumar Natarajan, Krishna Kadirvelu. Molecular Mechanism of T-2 Toxin-Induced Cerebral Edema by Aquaporin-4 Blocking and Permeation. Journal of Chemical Information and Modeling 2019, 59 (11) , 4942-4958. https://doi.org/10.1021/acs.jcim.9b00711
- Jonah Z. Vilseck, Noor Sohail, Ryan L. Hayes, Charles L. Brooks III. Overcoming Challenging Substituent Perturbations with Multisite λ-Dynamics: A Case Study Targeting β-Secretase 1. The Journal of Physical Chemistry Letters 2019, 10 (17) , 4875-4880. https://doi.org/10.1021/acs.jpclett.9b02004
- Lin Frank Song, Tai-Sung Lee, Chun Zhu, Darrin M. York, Kenneth M. Merz, Jr.. Using AMBER18 for Relative Free Energy Calculations. Journal of Chemical Information and Modeling 2019, 59 (7) , 3128-3135. https://doi.org/10.1021/acs.jcim.9b00105
- Emelie Flood, Céline Boiteux, Bogdan Lev, Igor Vorobyov, Toby W. Allen. Atomistic Simulations of Membrane Ion Channel Conduction, Gating, and Modulation. Chemical Reviews 2019, 119 (13) , 7737-7832. https://doi.org/10.1021/acs.chemrev.8b00630
- Israel Cabeza de Vaca, Ricardo Zarzuela, Julian Tirado-Rives, William L. Jorgensen. Robust Free Energy Perturbation Protocols for Creating Molecules in Solution. Journal of Chemical Theory and Computation 2019, 15 (7) , 3941-3948. https://doi.org/10.1021/acs.jctc.9b00213
- Alexander D. Wade, Andrea Rizzi, Yuanqing Wang, David J. Huggins. Computational Fluorine Scanning Using Free-Energy Perturbation. Journal of Chemical Information and Modeling 2019, 59 (6) , 2776-2784. https://doi.org/10.1021/acs.jcim.9b00228
- Jessica G. Freeze, H. Ray Kelly, Victor S. Batista. Search for Catalysts by Inverse Design: Artificial Intelligence, Mountain Climbers, and Alchemists. Chemical Reviews 2019, 119 (11) , 6595-6612. https://doi.org/10.1021/acs.chemrev.8b00759
- Frédéric Célerse, Louis Lagardère, Etienne Derat, Jean-Philip Piquemal. Massively Parallel Implementation of Steered Molecular Dynamics in Tinker-HP: Comparisons of Polarizable and Non-Polarizable Simulations of Realistic Systems. Journal of Chemical Theory and Computation 2019, 15 (6) , 3694-3709. https://doi.org/10.1021/acs.jctc.9b00199
- Shu-Ching Ou, B. Montgomery Pettitt. Free Energy Calculations Based on Coupling Proximal Distribution Functions and Thermodynamic Cycles. Journal of Chemical Theory and Computation 2019, 15 (4) , 2649-2658. https://doi.org/10.1021/acs.jctc.8b01157
- Katarina Roos, Chuanjie Wu, Wolfgang Damm, Mark Reboul, James M. Stevenson, Chao Lu, Markus K. Dahlgren, Sayan Mondal, Wei Chen, Lingle Wang, Robert Abel, Richard A. Friesner, Edward D. Harder. OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules. Journal of Chemical Theory and Computation 2019, 15 (3) , 1863-1874. https://doi.org/10.1021/acs.jctc.8b01026
- Laura Pérez-Benito, Nil Casajuana-Martin, Mireia Jiménez-Rosés, Herman van Vlijmen, Gary Tresadern. Predicting Activity Cliffs with Free-Energy Perturbation. Journal of Chemical Theory and Computation 2019, 15 (3) , 1884-1895. https://doi.org/10.1021/acs.jctc.8b01290
- Son Tung Ngo, Khanh B. Vu, Le Minh Bui, Van V. Vu. Effective Estimation of Ligand-Binding Affinity Using Biased Sampling Method. ACS Omega 2019, 4 (2) , 3887-3893. https://doi.org/10.1021/acsomega.8b03258
- Xiangyu Jia, Pengfei Li. Solvation Free Energy Calculation Using a Fixed-Charge Model: Implicit and Explicit Treatments of the Polarization Effect. The Journal of Physical Chemistry B 2019, 123 (5) , 1139-1148. https://doi.org/10.1021/acs.jpcb.8b10479
- Alja Prah, Eric Frančišković, Janez Mavri, Jernej Stare. Electrostatics as the Driving Force Behind the Catalytic Function of the Monoamine Oxidase A Enzyme Confirmed by Quantum Computations. ACS Catalysis 2019, 9 (2) , 1231-1240. https://doi.org/10.1021/acscatal.8b04045
- Pan Zhang, Lin Shen, Weitao Yang. Solvation Free Energy Calculations with Quantum Mechanics/Molecular Mechanics and Machine Learning Models. The Journal of Physical Chemistry B 2019, 123 (4) , 901-908. https://doi.org/10.1021/acs.jpcb.8b11905
- Lucianna H. Santos, Birgit J. Waldner, Julian E. Fuchs, Glaécia A. N. Pereira, Klaus R. Liedl, Ernesto R. Caffarena, Rafaela S. Ferreira. Understanding Structure–Activity Relationships for Trypanosomal Cysteine Protease Inhibitors by Simulations and Free Energy Calculations. Journal of Chemical Information and Modeling 2019, 59 (1) , 137-148. https://doi.org/10.1021/acs.jcim.8b00557
- Stefan M. Ivanov, Roland G. Huber, Irfan Alibay, Jim Warwicker, Peter J. Bond. Energetic Fingerprinting of Ligand Binding to Paralogous Proteins: The Case of the Apoptotic Pathway. Journal of Chemical Information and Modeling 2019, 59 (1) , 245-261. https://doi.org/10.1021/acs.jcim.8b00765
- Toru Ekimoto, Tsutomu Yamane, Mitsunori Ikeguchi. Elimination of Finite-Size Effects on Binding Free Energies via the Warp-Drive Method. Journal of Chemical Theory and Computation 2018, 14 (12) , 6544-6559. https://doi.org/10.1021/acs.jctc.8b00280
- Hannes H. Loeffler, Stefano Bosisio, Guilherme Duarte Ramos Matos, Donghyuk Suh, Benoit Roux, David L. Mobley, Julien Michel. Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages. Journal of Chemical Theory and Computation 2018, 14 (11) , 5567-5582. https://doi.org/10.1021/acs.jctc.8b00544
- Maximiliano Riquelme, Alejandro Lara, David L. Mobley, Toon Verstraelen, Adelio R. Matamala, Esteban Vöhringer-Martinez. Hydration Free Energies in the FreeSolv Database Calculated with Polarized Iterative Hirshfeld Charges. Journal of Chemical Information and Modeling 2018, 58 (9) , 1779-1797. https://doi.org/10.1021/acs.jcim.8b00180
- Jonah Z. Vilseck, Kira A. Armacost, Ryan L. Hayes, Garrett B. Goh, Charles L. Brooks, III. Predicting Binding Free Energies in a Large Combinatorial Chemical Space Using Multisite λ Dynamics. The Journal of Physical Chemistry Letters 2018, 9 (12) , 3328-3332. https://doi.org/10.1021/acs.jpclett.8b01284
- Agastya P. Bhati, Shunzhou Wan, Yuan Hu, Brad Sherborne, Peter V. Coveney. Uncertainty Quantification in Alchemical Free Energy Methods. Journal of Chemical Theory and Computation 2018, 14 (6) , 2867-2880. https://doi.org/10.1021/acs.jctc.7b01143
- Samuel C. Gill, Nathan M. Lim, Patrick B. Grinaway, Ariën S. Rustenburg, Josh Fass, Gregory A. Ross, John D. Chodera, David L. Mobley. Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo. The Journal of Physical Chemistry B 2018, 122 (21) , 5579-5598. https://doi.org/10.1021/acs.jpcb.7b11820
- Fang-Yu Lin, Pedro E. M. Lopes, Edward Harder, Benoît Roux, Alexander D. MacKerell, Jr.. Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator. Journal of Chemical Information and Modeling 2018, 58 (5) , 993-1004. https://doi.org/10.1021/acs.jcim.8b00132
- Noriaki Okimoto, Takao Otsuka, Yoshinori Hirano, Makoto Taiji. Use of the Multilayer Fragment Molecular Orbital Method to Predict the Rank Order of Protein–Ligand Binding Affinities: A Case Study Using Tankyrase 2 Inhibitors. ACS Omega 2018, 3 (4) , 4475-4485. https://doi.org/10.1021/acsomega.8b00175
- Jiří Šponer, Giovanni Bussi, Miroslav Krepl, Pavel Banáš, Sandro Bottaro, Richard A. Cunha, Alejandro Gil-Ley, Giovanni Pinamonti, Simón Poblete, Petr Jurečka, Nils G. Walter, Michal Otyepka. RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Chemical Reviews 2018, 118 (8) , 4177-4338. https://doi.org/10.1021/acs.chemrev.7b00427
- Songling Ma, Sungbo Hwang, Sehan Lee, William E. Acree, Jr., Kyoung Tai No. Incorporation of Hydrogen Bond Angle Dependency into the Generalized Solvation Free Energy Density Model. Journal of Chemical Information and Modeling 2018, 58 (4) , 761-772. https://doi.org/10.1021/acs.jcim.7b00410
- Saeed Izadi, Robert C. Harris, Marcia O. Fenley, Alexey V. Onufriev. Accuracy Comparison of Generalized Born Models in the Calculation of Electrostatic Binding Free Energies. Journal of Chemical Theory and Computation 2018, 14 (3) , 1656-1670. https://doi.org/10.1021/acs.jctc.7b00886
- Xiao Liu, Long Peng, Yifan Zhou, Youzhi Zhang, John Z. H. Zhang. Computational Alanine Scanning with Interaction Entropy for Protein–Ligand Binding Free Energies. Journal of Chemical Theory and Computation 2018, 14 (3) , 1772-1780. https://doi.org/10.1021/acs.jctc.7b01295
- Fang-Yu Lin and Alexander D. MacKerell, Jr. . Polarizable Empirical Force Field for Halogen-Containing Compounds Based on the Classical Drude Oscillator. Journal of Chemical Theory and Computation 2018, 14 (2) , 1083-1098. https://doi.org/10.1021/acs.jctc.7b01086
- Billy J. Williams-Noonan, Elizabeth Yuriev, and David K. Chalmers . Free Energy Methods in Drug Design: Prospects of “Alchemical Perturbation” in Medicinal Chemistry. Journal of Medicinal Chemistry 2018, 61 (3) , 638-649. https://doi.org/10.1021/acs.jmedchem.7b00681
- Zoe Cournia, Bryce Allen, and Woody Sherman . Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations. Journal of Chemical Information and Modeling 2017, 57 (12) , 2911-2937. https://doi.org/10.1021/acs.jcim.7b00564
- Payal Chatterjee, Wesley M. Botello-Smith, Han Zhang, Li Qian, Abdelaziz Alsamarah, David Kent, Jerome J. Lacroix, Michel Baudry, and Yun Luo . Can Relative Binding Free Energy Predict Selectivity of Reversible Covalent Inhibitors?. Journal of the American Chemical Society 2017, 139 (49) , 17945-17952. https://doi.org/10.1021/jacs.7b08938
- Christopher Pfleger, Alexander Minges, Markus Boehm, Christopher L. McClendon, Rubben Torella, and Holger Gohlke . Ensemble- and Rigidity Theory-Based Perturbation Approach To Analyze Dynamic Allostery. Journal of Chemical Theory and Computation 2017, 13 (12) , 6343-6357. https://doi.org/10.1021/acs.jctc.7b00529
- Yoelvis Orozco-Gonzalez, Madushanka Manathunga, María del Carmen Marín, Damianos Agathangelou, Kwang-Hwan Jung, Federico Melaccio, Nicolas Ferré, Stefan Haacke, Kaline Coutinho, Sylvio Canuto, and Massimo Olivucci . An Average Solvent Electrostatic Configuration Protocol for QM/MM Free Energy Optimization: Implementation and Application to Rhodopsin Systems. Journal of Chemical Theory and Computation 2017, 13 (12) , 6391-6404. https://doi.org/10.1021/acs.jctc.7b00860
- Yinan Lin, Bo An, Mehran Bagheri, Qianrui Wang, James L. Harden, and David L. Kaplan . Electrochemically Directed Assembly of Designer Coiled-Coil Telechelic Proteins. ACS Biomaterials Science & Engineering 2017, 3 (12) , 3195-3206. https://doi.org/10.1021/acsbiomaterials.7b00599
- Haohao Fu, Wensheng Cai, Jérôme Hénin, Benoît Roux, and Christophe Chipot . New Coarse Variables for the Accurate Determination of Standard Binding Free Energies. Journal of Chemical Theory and Computation 2017, 13 (11) , 5173-5178. https://doi.org/10.1021/acs.jctc.7b00791
- Mauro Lapelosa . Free Energy of Binding and Mechanism of Interaction for the MEEVD-TPR2A Peptide–Protein Complex. Journal of Chemical Theory and Computation 2017, 13 (9) , 4514-4523. https://doi.org/10.1021/acs.jctc.7b00105
- Shijie Sheng, Michael Miller, and Jianzhong Wu . Molecular Theory of Hydration at Different Temperatures. The Journal of Physical Chemistry B 2017, 121 (28) , 6898-6908. https://doi.org/10.1021/acs.jpcb.7b04264
- Robert Abel, Lingle Wang, Edward D. Harder, B. J. Berne, and Richard A. Friesner . Advancing Drug Discovery through Enhanced Free Energy Calculations. Accounts of Chemical Research 2017, 50 (7) , 1625-1632. https://doi.org/10.1021/acs.accounts.7b00083