Daniel R Roe, Thomas E Cheatham. J Chem Theory Comput 2013
Times Cited: 2605
Times Cited: 2605
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ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB.
James A Maier, Carmenza Martinez, Koushik Kasavajhala, Lauren Wickstrom, Kevin E Hauser, Carlos Simmerling. J Chem Theory Comput 2015
James A Maier, Carmenza Martinez, Koushik Kasavajhala, Lauren Wickstrom, Kevin E Hauser, Carlos Simmerling. J Chem Theory Comput 2015
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Development and testing of a general amber force field.
Junmei Wang, Romain M Wolf, James W Caldwell, Peter A Kollman, David A Case. J Comput Chem 2004
Junmei Wang, Romain M Wolf, James W Caldwell, Peter A Kollman, David A Case. J Comput Chem 2004
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UCSF Chimera--a visualization system for exploratory research and analysis.
Eric F Pettersen, Thomas D Goddard, Conrad C Huang, Gregory S Couch, Daniel M Greenblatt, Elaine C Meng, Thomas E Ferrin. J Comput Chem 2004
Eric F Pettersen, Thomas D Goddard, Conrad C Huang, Gregory S Couch, Daniel M Greenblatt, Elaine C Meng, Thomas E Ferrin. J Comput Chem 2004
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Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh Ewald.
Romelia Salomon-Ferrer, Andreas W Götz, Duncan Poole, Scott Le Grand, Ross C Walker. J Chem Theory Comput 2013
Romelia Salomon-Ferrer, Andreas W Götz, Duncan Poole, Scott Le Grand, Ross C Walker. J Chem Theory Comput 2013
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MMPBSA.py: An Efficient Program for End-State Free Energy Calculations.
Bill R Miller, T Dwight McGee, Jason M Swails, Nadine Homeyer, Holger Gohlke, Adrian E Roitberg. J Chem Theory Comput 2012
Bill R Miller, T Dwight McGee, Jason M Swails, Nadine Homeyer, Holger Gohlke, Adrian E Roitberg. J Chem Theory Comput 2012
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Automatic atom type and bond type perception in molecular mechanical calculations.
Junmei Wang, Wei Wang, Peter A Kollman, David A Case. J Mol Graph Model 2006
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The Protein Data Bank.
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Garrett M Morris, Ruth Huey, William Lindstrom, Michel F Sanner, Richard K Belew, David S Goodsell, Arthur J Olson. J Comput Chem 2009
Garrett M Morris, Ruth Huey, William Lindstrom, Michel F Sanner, Richard K Belew, David S Goodsell, Arthur J Olson. J Comput Chem 2009
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The Amber biomolecular simulation programs.
David A Case, Thomas E Cheatham, Tom Darden, Holger Gohlke, Ray Luo, Kenneth M Merz, Alexey Onufriev, Carlos Simmerling, Bing Wang, Robert J Woods. J Comput Chem 2005
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The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities.
Samuel Genheden, Ulf Ryde. Expert Opin Drug Discov 2015
Samuel Genheden, Ulf Ryde. Expert Opin Drug Discov 2015
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Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation.
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Assessing the performance of the MM/PBSA and MM/GBSA methods. 1. The accuracy of binding free energy calculations based on molecular dynamics simulations.
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Tingjun Hou, Junmei Wang, Youyong Li, Wei Wang. J Chem Inf Model 2011
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GLYCAM06: a generalizable biomolecular force field. Carbohydrates.
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Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born.
Andreas W Götz, Mark J Williamson, Dong Xu, Duncan Poole, Scott Le Grand, Ross C Walker. J Chem Theory Comput 2012
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Open Babel: An open chemical toolbox.
Noel M O'Boyle, Michael Banck, Craig A James, Chris Morley, Tim Vandermeersch, Geoffrey R Hutchison. J Cheminform 2011
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SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules.
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AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading.
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Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms.
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PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions.
Mats H M Olsson, Chresten R Søndergaard, Michal Rostkowski, Jan H Jensen. J Chem Theory Comput 2011
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Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum models.
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A modified TIP3P water potential for simulation with Ewald summation.
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Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations.
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Structure of Mpro from SARS-CoV-2 and discovery of its inhibitors.
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H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations.
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CHARMM-GUI: a web-based graphical user interface for CHARMM.
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Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening.
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Langevin dynamics of peptides: the frictional dependence of isomerization rates of N-acetylalanyl-N'-methylamide.
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G Madhavi Sastry, Matvey Adzhigirey, Tyler Day, Ramakrishna Annabhimoju, Woody Sherman. J Comput Aided Mol Des 2013
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GPU-Accelerated Molecular Dynamics and Free Energy Methods in Amber18: Performance Enhancements and New Features.
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Tai-Sung Lee, David S Cerutti, Dan Mermelstein, Charles Lin, Scott LeGrand, Timothy J Giese, Adrian Roitberg, David A Case, Ross C Walker, Darrin M York. J Chem Inf Model 2018
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End-Point Binding Free Energy Calculation with MM/PBSA and MM/GBSA: Strategies and Applications in Drug Design.
Ercheng Wang, Huiyong Sun, Junmei Wang, Zhe Wang, Hui Liu, John Z H Zhang, Tingjun Hou. Chem Rev 2019
Ercheng Wang, Huiyong Sun, Junmei Wang, Zhe Wang, Hui Liu, John Z H Zhang, Tingjun Hou. Chem Rev 2019
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SWISS-MODEL: homology modelling of protein structures and complexes.
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Langevin thermostat for rigid body dynamics.
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Improved Reweighting of Accelerated Molecular Dynamics Simulations for Free Energy Calculation.
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Lipid14: The Amber Lipid Force Field.
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Gaussian Accelerated Molecular Dynamics: Unconstrained Enhanced Sampling and Free Energy Calculation.
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Lead- and drug-like compounds: the rule-of-five revolution.
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Insights into protein-protein binding by binding free energy calculation and free energy decomposition for the Ras-Raf and Ras-RalGDS complexes.
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Nisha A Jonniya, Parimal Kar. J Biomol Struct Dyn 2020
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ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution.
Chuan Tian, Koushik Kasavajhala, Kellon A A Belfon, Lauren Raguette, He Huang, Angela N Migues, John Bickel, Yuzhang Wang, Jorge Pincay, Qin Wu,[...]. J Chem Theory Comput 2020
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Structure, Function, and Antigenicity of the SARS-CoV-2 Spike Glycoprotein.
Alexandra C Walls, Young-Jun Park, M Alejandra Tortorici, Abigail Wall, Andrew T McGuire, David Veesler. Cell 2020
Alexandra C Walls, Young-Jun Park, M Alejandra Tortorici, Abigail Wall, Andrew T McGuire, David Veesler. Cell 2020
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Structure of the SARS-CoV-2 spike receptor-binding domain bound to the ACE2 receptor.
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Crystal structure of SARS-CoV-2 main protease provides a basis for design of improved α-ketoamide inhibitors.
Linlin Zhang, Daizong Lin, Xinyuanyuan Sun, Ute Curth, Christian Drosten, Lucie Sauerhering, Stephan Becker, Katharina Rox, Rolf Hilgenfeld. Science 2020
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Comparison of multiple Amber force fields and development of improved protein backbone parameters.
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