CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed

Hwang, Wonmuk, Austin, Steven L., Blondel, Arnaud, Boittier, Eric D., Boresch, Stefan, Buck, Matthias, Buckner, Joshua, Caflisch, Amedeo +65 more·2024·The Journal of Physical Chemistry B
DOI 10.1021/acs.jpcb.4c04100

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  140. Improved Modeling of Cation‐π and Anion‐Ring Interactions Using the Drude Polarizable Empirical Force Field for Proteins
    Fang‐Yu Lin, Alexander D. MacKerell · 2019 · Journal of Computational Chemistry
  141. Effect of Methylation on Local Mechanics and Hydration Structure of DNA.
    Xiaojing Teng, W. Hwang · 2018 · Biophysical Journal
  142. Hybrid All-Atom/Coarse-Grained Simulations of Proteins by Direct Coupling of CHARMM and PRIMO Force Fields
    P. Kar, M. Feig · 2017 · Journal of Chemical Theory and Computation
  143. Gibbs Sampler Based λ-Dynamics and Rao-Blackwell Estimator for Alchemical Free Energy Calculation
    Xin-Qiang Ding, Jonah Z. Vilseck, Ryan L. Hayes, C. Brooks · 2017 · Journal of Chemical Theory and Computation
  144. Structural Interpretation of Metastable States in Myoglobin-NO.
    Maksym Soloviov, A. K. Das, M. Meuwly · 2016 · Angewandte Chemie
  145. Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields.
    Bin Lin, Pedro E. M. Lopes, B. Roux, Alexander D. MacKerell · 2013 · Journal of Chemical Physics
  146. Structural Determinants of Transmembrane β-Barrels
    Themis Lazaridis · 2005 · Journal of Chemical Theory and Computation
  147. Membrane Curvature Sensing by Amphipathic Helices: Insights from Implicit Membrane Modeling
    Binod Nepal, John M. Leveritt, Themis Lazaridis · 2018 · Biophysical Journal
  148. Generalized Metropolis acceptance criterion for hybrid non-equilibrium molecular dynamics-Monte Carlo simulations.
    Yunjie Chen, B. Roux · 2015 · Journal of Chemical Physics
  149. PhysNet meets CHARMM: A framework for routine machine learning/molecular mechanics simulations.
    Kai-Sheng Song, Silvan Käser, Kai Töpfer, Luis Itza Vazquez-Salazar, M. Meuwly · 2023 · Journal of Chemical Physics
  150. Developing Initial Conditions for Simulations of Asymmetric Membranes: A Practical Recommendation.
    S. Park, W. Im, R. Pastor · 2021 · Biophysical Journal
  151. Polarization Effects in Water-Mediated Selective Cation Transport Across a Narrow Transmembrane Channel
    Van A. Ngo, Hui Li, Alexander D. MacKerell, T. Allen, B. Roux, S. Noskov · 2021 · Journal of Chemical Theory and Computation
  152. Computational scheme for pH‐dependent binding free energy calculation with explicit solvent
    Ju-Yong Lee, Benjamin T. Miller, B. Brooks · 2015 · Protein Science
  153. Transferring the PRIMO Coarse-Grained Force Field to the Membrane Environment: Simulations of Membrane Proteins and Helix–Helix Association
    P. Kar, S. Gopal, Yi-Ming Cheng, Afra Panahi, M. Feig · 2014 · Journal of Chemical Theory and Computation
  154. Role of hydrogen bonding and helix-lipid interactions in transmembrane helix association.
    Jinhyuk Lee, W. Im · 2008 · Journal of the American Chemical Society
  155. Drude Polarizable Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Saturated and Monounsaturated Zwitterionic Lipids
    Yalun Yu, R. Venable, Jonathan Thirman, P. Chatterjee, Anmol Kumar, R. Pastor, Benoı T. Roux, A. MacKerell, Jeffery B. Klauda · 2023 · Journal of Chemical Theory and Computation
  156. Update of the CHARMM36 United Atom Chain Model for Hydrocarbons and Phospholipids.
    Yalun Yu, Jeffery B. Klauda · 2020 · Journal of Physical Chemistry B
  157. Pressure Profile Calculation with Mesh Ewald Methods.
    M. Sega, B. Fábián, P. Jedlovszky · 2016 · Journal of Chemical Theory and Computation
  158. Inclusion of lateral pressure/curvature stress effects in implicit membrane models.
    H. Zhan, T. Lazaridis · 2013 · Biophysical Journal
  159. A Simplified Confinement Method (SCM) for Calculating Absolute Free Energies and Free Energy and Entropy Differences
    V. Ovchinnikov, M. Cecchini, M. Karplus · 2013 · Journal of Physical Chemistry B
  160. Induced Dipole–Dipole Interactions Influence the Unfolding Pathways of Wild-Type and Mutant Amyloid β-Peptides
    Justin A. Lemkul, Jing Huang, Alexander D. MacKerell · 2015 · The Journal of Physical Chemistry B
  161. Extensive free-energy simulations identify water as the base in nucleotide addition by DNA polymerase
    Daniel Roston, Darren Demapan, Q. Cui · 2019 · Proceedings of the National Academy of Sciences of the United States of America
  162. Improved Modeling of Halogenated Ligand-Protein Interactions using the Drude Polarizable and CHARMM Additive Empirical Force Fields
    Fang-Yu Lin, Alexander D. MacKerell · 2018 · Journal of Chemical Information and Modeling
  163. Path-Integral Calculations of Nuclear Quantum Effects in Model Systems, Small Molecules, and Enzymes via Gradient-Based Forward Corrector Algorithms.
    Asaf Azuri, H. Engel, Dvir Doron, D. Major · 2011 · Journal of Chemical Theory and Computation
  164. Application of solid-state NMR restraint potentials in membrane protein modeling.
    Jinhyuk Lee, Jian-Han Chen, C. Brooks, W. Im · 2008 · Journal of magnetic resonance (San Diego, Calif. 1997 : Print)
  165. Implementation and application of helix–helix distance and crossing angle restraint potentials
    Jinhyuk Lee, W. Im · 2007 · Journal of Computational Chemistry
  166. CHARMM-GUI-Based Induced Fit Docking Workflow to Generate Reliable Protein–Ligand Binding Modes
    H. Guterres, W. Im · 2023 · Journal of Chemical Information and Modeling
  167. The Impression of a Nonexisting Catalytic Effect: The Role of CotB2 in Guiding the Complex Biosynthesis of Cyclooctat-9-en-7-ol.
    K. Raz, R. Driller, N. Dimos, Marion Ringel, T. Brück, B. Loll, D. Major · 2020 · Journal of the American Chemical Society
  168. Isomerization and decomposition reactions of acetaldehyde relevant to atmospheric processes from dynamics simulations on neural network-based potential energy surfaces.
    Silvan Käser, O. Unke, M. Meuwly · 2020 · Journal of Chemical Physics
  169. An empirical extrapolation scheme for efficient treatment of induced dipoles.
    Andrew C. Simmonett, Frank C. Pickard, J. Ponder, B. Brooks · 2016 · Journal of Chemical Physics
  170. Towards Accurate Prediction of Protonation Equilibrium of Nucleic Acids
    Garrett B. Goh, Jennifer L. Knight, C. Brooks · 2013 · Journal of Physical Chemistry Letters
  171. Hybrid Quantum and Classical Simulations of the Formate Dehydrogenase Catalyzed Hydride Transfer Reaction on an Accurate Semiempirical Potential Energy Surface.
    Alexandra Vardi-Kilshtain, D. Major, A. Kohen, H. Engel, Dvir Doron · 2012 · Journal of Chemical Theory and Computation
  172. Drude Polarizable Force Field Parametrization of Carboxylate and N-acetyl Amine Carbohydrate Derivatives
    Poonam Pandey, Asaminew H. Aytenfisu, Alexander D. MacKerell, S. Mallajosyula · 2019 · Journal of Chemical Theory and Computation
  173. Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments
    R. Shen, Wei Han, G. Fiorin, Shahidul M. Islam, K. Schulten, B. Roux · 2015 · PLoS Comput. Biol.
  174. Transmembrane helix orientation and dynamics: insights from ensemble dynamics with solid-state NMR observables.
    Sunhwan Jo, W. Im · 2011 · Biophysical Journal
  175. Conformational sampling of influenza fusion peptide in membrane bilayers as a function of termini and protonation states.
    Afra Panahi, M. Feig · 2010 · Journal of Physical Chemistry B
  176. Covalent docking in CDOCKER
    Yujin Wu, Charles L. Brooks · 2022 · Journal of Computer-Aided Molecular Design
  177. An Alternative to Conventional λ-Intermediate States in Alchemical Free Energy Calculations: λ-Enveloping Distribution Sampling
    Gerhard König, Nina Glaser, Benjamin Ries, Alžbeta Kubincová, Philippe H. Hünenberger, Sereina Riniker · 2020 · Journal of Chemical Information and Modeling
  178. Flexible CDOCKER: Hybrid Searching Algorithm and Scoring Function with Side Chain Conformational Entropy
    Yu-jie Wu, C. Brooks · 2021 · Journal of Chemical Information and Modeling
  179. Vibrational Spectroscopy and Proton Transfer Dynamics in Protonated Oxalate.
    Zhen-Hao Xu, M. Meuwly · 2017 · Journal of Physical Chemistry A
  180. Free energy simulations of active-site mutants of dihydrofolate reductase.
    Dvir Doron, V. Stojković, L. Gakhar, Alexandra Vardi-Kilshtain, A. Kohen, D. Major · 2015 · Journal of Physical Chemistry B
  181. Unrestrained Computation of Free Energy along a Path
    B. M. Dickson, He Huang, C. Post · 2012 · Journal of Physical Chemistry B
  182. Exploring the Limits of the Generalized CHARMM and AMBER Force Fields through Predictions of Hydration Free Energy of Small Molecules
    Arghya Chakravorty, Azam Hussain, Luis F. Cervantes, Thanh T. Lai, Charles L. Brooks · 2024 · Journal of Chemical Information and Modeling
  183. Evaluation of Several Two-Step Scoring Functions Based on Linear Interaction Energy, Effective Ligand Size, and Empirical Pair Potentials for Prediction of Protein–Ligand Binding Geometry and Free Energy
    Obaidur Rahaman, Trilce Estrada, Douglas J. Doren, Michela Taufer, Charles L. Brooks, Roger S. Armen · 2011 · Journal of Chemical Information and Modeling
  184. Fast free energy estimates from λ-dynamics with bias-updated Gibbs sampling
    Michael T. Robo, Ryan L. Hayes, Xin-Qiang Ding, Brian Pulawski, Jonah Z. Vilseck · 2023 · Nature Communications
  185. Practical Guidance for Consensus Scoring and Force Field Selection in Protein-Ligand Binding Free Energy Simulations
    Han Zhang, Seonghoon Kim, W. Im · 2022 · Journal of Chemical Information and Modeling
  186. Classical Drude Polarizable Force Field Model for Methyl Phosphate and its Interactions with Mg2+
    Francesco Villa, Alexander D. MacKerell, B. Roux, T. Simonson · 2018 · Journal of Physical Chemistry A
  187. Restraint potential and free energy decomposition formalism for helical tilting
    Jinhyuk Lee, W. Im · 2007
  188. CHARMM‐GUI Enhanced Sampler for various collective variables and enhanced sampling methods
    Donghyuk Suh, Shasha Feng, Hwa-Young Lee, Han Zhang, Sang‐Jun Park, Seonghan Kim, Jumin Lee, Sun Choi, Wonpil Im · 2022 · Protein Science
  189. Overcoming Challenging Substituent Perturbations with Multisite λ-Dynamics: A Case Study Targeting β-Secretase 1
    Jonah Z. Vilseck, Noor Sohail, Ryan L. Hayes, C. Brooks · 2019 · Journal of Physical Chemistry Letters
  190. Role of Protein Dynamics in Allosteric Control of the Catalytic Phosphoryl Transfer of Insulin Receptor Kinase.
    P. Ojeda-May, Yaozong Li, V. Ovchinnikov, Kwangho Nam · 2015 · Journal of the American Chemical Society
  191. Effect of membrane thickness on conformational sampling of phospholamban from computer simulations.
    M. Sayadi, S. Tanizaki, M. Feig · 2010 · Biophysical Journal
  192. Structural refinement of membrane proteins by restrained molecular dynamics and solvent accessibility data.
    P. Sompornpisut, B. Roux, E. Perozo · 2008 · Biophysical Journal
  193. Semiempirical QM/MM potential with simple valence bond (SVB) for enzyme reactions. Application to the nucleophilic addition reaction in haloalkane dehalogenase
    Lakshmi S Devi-Kesavan, M. Garcia‐Viloca, Jia-Li Gao · 2003
  194. The backbone 15N chemical shift tensor of the gramicidin channel. A molecular dynamics and density functional study
    T. Woolf, V. Malkin, O. Malkina, D. Salahub, B. Roux · 1995
  195. Toward Prediction of Electrostatic Parameters for Force Fields That Explicitly Treat Electronic Polarization
    Esther Heid, Markus Fleck, Payal Chatterjee, Christian Schröder, Alexander D. MacKerell · 2019 · Journal of Chemical Theory and Computation
  196. Non-equilibrium reaction and relaxation dynamics in a strongly interacting explicit solvent: F + CD3CN treated with a parallel multi-state EVB model.
    D. Glowacki, A. Orr-Ewing, Jeremy N. Harvey · 2014 · Journal of Chemical Physics
  197. Thermal and Vibrationally Activated Decomposition of the syn-CH3CHOO Criegee Intermediate
    Meenu Upadhyay, M. Meuwly · 2021 · ACS Earth and Space Chemistry
  198. CHRAMM-GUI MDFF/xMDFF Utilizer for Molecular Dynamics Flexible Fitting Simulations in Various Environments
    Yifei Qi, Ju-Min Lee, A. Singharoy, R. McGreevy, K. Schulten, W. Im · 2016 · Journal of Physical Chemistry B
  199. Analysis of multi-domain protein dynamics
    Amitava Roy, Duy P. Hua, C. Post · 2015 · Journal of Chemical Theory and Computation
  200. Efficient hybrid non-equilibrium molecular dynamics--Monte Carlo simulations with symmetric momentum reversal.
    Yunjie Chen, B. Roux · 2014 · Journal of Chemical Physics