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

Journal Article · · Journal of Physical Chemistry. B
ORCiD logo [1];  [2]; ORCiD logo [3];  [4]; ORCiD logo [5];  [6];  [7]; ORCiD logo [8];  [9]; ORCiD logo [10]; ORCiD logo [11]; ORCiD logo [12]; ORCiD logo [13]; ORCiD logo [14]; ORCiD logo [15];  [16]; ORCiD logo [4]; ORCiD logo [17]; ORCiD logo [18]; ORCiD logo [19] more »; ORCiD logo [20]; ORCiD logo [21]; ORCiD logo [6]; ORCiD logo [22]; ORCiD logo [23]; ORCiD logo [24]; ORCiD logo [25];  [26]; ORCiD logo [11]; ORCiD logo [27]; ORCiD logo [28]; ORCiD logo [29]; ORCiD logo [4]; ORCiD logo [2]; ORCiD logo [11]; ORCiD logo [30]; ORCiD logo [31];  [32]; ORCiD logo [33]; ORCiD logo [7]; ORCiD logo [34]; ORCiD logo [35]; ORCiD logo [36]; ORCiD logo [37]; ORCiD logo [38]; ORCiD logo [39]; ORCiD logo [40]; ORCiD logo [41]; ORCiD logo [11]; ORCiD logo [29];  [2]; ORCiD logo [42];  [29]; ORCiD logo [43]; ORCiD logo [44]; ORCiD logo [45]; ORCiD logo [29]; ORCiD logo [46]; ORCiD logo [47]; ORCiD logo [35]; ORCiD logo [29]; ORCiD logo [48]; ORCiD logo [4]; ORCiD logo [4]; ORCiD logo [2]; ORCiD logo [4];  [29]; ORCiD logo [2]; ORCiD logo [2];  [7]; ORCiD logo [7]; ORCiD logo [29];  [49] « less
  1. Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States, Department of Materials Science and Engineering, Texas A&M University, College Station, Texas 77843, United States, Department of Physics and Astronomy, Texas A&M University, College Station, Texas 77843, United States, Center for AI and Natural Sciences, Korea Institute for Advanced Study, Seoul 02455, Republic of Korea
  2. Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
  3. Institut Pasteur, Université Paris Cité, CNRS UMR3825, Structural Bioinformatics Unit, 28 rue du Dr. Roux F-75015 Paris, France
  4. Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
  5. Faculty of Chemistry, Department of Computational Biological Chemistry, University of Vienna, Wahringerstrasse 17, 1090 Vienna, Austria
  6. Department of Physiology and Biophysics, Case Western Reserve University, School of Medicine, Cleveland, Ohio 44106, United States
  7. Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
  8. Department of Biochemistry, University of Zürich, CH-8057 Zürich, Switzerland
  9. Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan, ROC
  10. Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
  11. Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania 18015, United States
  12. Institute of Bioinformatics and Systems Biology, Department of Biological Science and Technology, Institute of Molecular Medicine and Bioengineering, and Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 30010, Taiwan, ROC
  13. Renewable Resources and Enabling Sciences Center, National Renewable Energy Laboratory, Golden, Colorado 80401, United States
  14. Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States, Department of Physics, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States, Department of Biomedical Engineering, Boston University, 44 Cummington Mall, Boston, Massachusetts 02215, United States
  15. Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218, United States, Department of Physics and Astronomy, Johns Hopkins University, Baltimore, Maryland 21218, United States, Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
  16. Shanghai R&D Center, DP Technology, Ltd., Shanghai 201210, China
  17. Department of Chemistry, Tufts University, Medford, Massachusetts 02155, United States
  18. Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, United States
  19. School of Chemical Biology & Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, Guangdong 518055, China, Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen, Guangdong 518055, China, Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
  20. CiTIUS Centro Singular de Investigación en Tecnoloxías Intelixentes da USC, 15705 Santiago de Compostela, Spain
  21. Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States, Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
  22. Schrodinger, Inc., New York, New York 10036, United States
  23. Department of Chemical and Biomolecular Engineering, University of California, Irvine, Irvine, California 92697, United States, Department of Pharmaceutical Sciences, University of California, Irvine, Irvine, California 92697, United States
  24. Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang 310024, China
  25. College of Computer Engineering, Jimei University, Xiamen 361021, China
  26. Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States, Medicine Design, Pfizer Inc., Cambridge, Massachusetts 02139, United States
  27. Department of Chemistry, Delaware State University, Dover, Delaware 19901, United States
  28. Computational Science Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
  29. Laboratory of Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
  30. Department of Chemical and Biomolecular Engineering, Institute for Physical Science and Technology, Biophysics Program, University of Maryland, College Park, Maryland 20742, United States
  31. Department of Chemistry, City College of New York, New York, New York 10031, United States
  32. Disease Target Structure Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 34141, Republic of Korea, Department of Bioinformatics, KRIBB School of Bioscience, University of Science and Technology, Daejeon 34141, Republic of Korea
  33. Department of Biochemistry, Virginia Polytechnic Institute and State University, Blacksburg, Virginia 24061, United States
  34. Department of Biotechnology and Pharmaceutical Sciences, College of Pharmacy, Western University of Health Sciences, Pomona, California 91766, United States
  35. Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, Baltimore, Maryland 21201, United States
  36. Department of Chemistry and Institute for Nanotechnology & Advanced Materials, Bar-Ilan University, Ramat-Gan 52900, Israel
  37. Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland, Department of Chemistry, Brown University, Providence, Rhode Island 02912, United States
  38. Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
  39. Karolinska Institutet, Department of Biosciences and Nutrition, SE-14183 Huddinge, Sweden
  40. Harvard University, Department of Chemistry and Chemical Biology, Cambridge, Massachusetts 02138, United States
  41. Dipartimento di Fisica e Astronomia, Universitá di Bologna, Bologna 40127, Italy
  42. Borch Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
  43. Department of Chemistry and Chemical Biology, Indiana University Indianapolis, Indianapolis, Indiana 46202, United States
  44. School of Pharmacy, Fudan University, Shanghai 201203, China
  45. Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana State, 502284, India
  46. Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
  47. Department of Chemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
  48. Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland 20892, United States
  49. Harvard University, Department of Chemistry and Chemical Biology, Cambridge, Massachusetts 02138, United States, Laboratoire de Chimie Biophysique, ISIS, Université de Strasbourg, 67000 Strasbourg, France
+ Show Author Affiliations

Not Available

Sponsoring Organization:
USDOE
Grant/Contract Number:
AC02-06CH11357
OSTI ID:
2447479
Journal Information:
Journal of Physical Chemistry. B, Journal Name: Journal of Physical Chemistry. B Journal Issue: 41 Vol. 128; ISSN 1520-6106
Publisher:
American Chemical SocietyCopyright Statement
Country of Publication:
United States
Language:
English

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CHARMM-GUI Supports Hydrogen Mass Repartitioning and Different Protonation States of Phosphates in Lipopolysaccharides journal January 2021
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CHARMM-GUI LBS Finder & Refiner for Ligand Binding Site Prediction and Refinement journal July 2021
CHARMM-GUI Free Energy Calculator for Practical Ligand Binding Free Energy Simulations with AMBER journal September 2021
CHARMM-GUI Membrane Builder for Lipid Nanoparticles with Ionizable Cationic Lipids and PEGylated Lipids journal September 2021
Comparative Molecular Dynamics Simulation Studies of Realistic Eukaryotic, Prokaryotic, and Archaeal Membranes journal February 2022
Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale journal November 2022
Attracting Cavities 2.0: Improving the Flexibility and Robustness for Small-Molecule Docking journal June 2023
Is Ring Breaking Feasible in Relative Binding Free Energy Calculations? journal March 2015
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Polarizable Force Field for Molecular Ions Based on the Classical Drude Oscillator journal April 2018
Improved Modeling of Halogenated Ligand–Protein Interactions Using the Drude Polarizable and CHARMM Additive Empirical Force Fields journal November 2018
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Further Optimization and Validation of the Classical Drude Polarizable Protein Force Field journal April 2020
Determining Free-Energy Differences Through Variationally Derived Intermediates journal May 2020
Accelerated CDOCKER with GPUs, Parallel Simulated Annealing, and Fast Fourier Transforms journal May 2020
Both Configuration and QM Region Size Matter: Zinc Stability in QM/MM Models of DNA Methyltransferase journal April 2020
Conformational Free-Energy Differences of Large Solvated Systems with the Focused Confinement Method journal June 2020
Permutationally Invariant, Reproducing Kernel-Based Potential Energy Surfaces for Polyatomic Molecules: From Formaldehyde to Acetone journal July 2020
Automated, Accurate, and Scalable Relative Protein–Ligand Binding Free-Energy Calculations Using Lambda Dynamics journal November 2020
CHARMM-GUI Free Energy Calculator for Absolute and Relative Ligand Solvation and Binding Free Energy Simulations journal October 2020
Polarization Effects in Water-Mediated Selective Cation Transport across a Narrow Transmembrane Channel journal February 2021
Structure, Dynamics, Receptor Binding, and Antibody Binding of the Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein in a Viral Membrane journal March 2021
CHARMM36 Lipid Force Field with Explicit Treatment of Long-Range Dispersion: Parametrization and Validation for Phosphatidylethanolamine, Phosphatidylglycerol, and Ether Lipids journal February 2021
CHARMM-GUI Polymer Builder for Modeling and Simulation of Synthetic Polymers journal April 2021
Generalizing the Discrete Gibbs Sampler-Based λ-Dynamics Approach for Multisite Sampling of Many Ligands journal June 2021
Additive CHARMM36 Force Field for Nonstandard Amino Acids journal May 2021
Efficient Alchemical Intermediate States in Free Energy Calculations Using λ-Enveloping Distribution Sampling journal September 2021
Doubly Polarized QM/MM with Machine Learning Chaperone Polarizability journal November 2021
BLaDE: A Basic Lambda Dynamics Engine for GPU-Accelerated Molecular Dynamics Free Energy Calculations journal October 2021
CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems journal December 2021
Harnessing Deep Learning for Optimization of Lennard-Jones Parameters for the Polarizable Classical Drude Oscillator Force Field journal April 2022
Molecular Dynamics with Conformationally Dependent, Distributed Charges journal November 2022
Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field journal May 2023
Unwrapping NPT Simulations to Calculate Diffusion Coefficients journal May 2023
Constant-pH Hybrid Nonequilibrium Molecular Dynamics–Monte Carlo Simulation Method journal July 2015
Enhanced Sampling of an Atomic Model with Hybrid Nonequilibrium Molecular Dynamics—Monte Carlo Simulations Guided by a Coarse-Grained Model journal July 2015
CHARMM-GUI Martini Maker for Coarse-Grained Simulations with the Martini Force Field journal August 2015
Quantum Effects in Cation Interactions with First and Second Coordination Shell Ligands in Metalloproteins journal October 2015
DFTB3 Parametrization for Copper: The Importance of Orbital Angular Momentum Dependence of Hubbard Parameters journal August 2015
Multiple Time-Step Dual-Hamiltonian Hybrid Molecular Dynamics – Monte Carlo Canonical Propagation Algorithm journal March 2016
Direct-Space Corrections Enable Fast and Accurate Lorentz–Berthelot Combination Rule Lennard-Jones Lattice Summation journal November 2015
Analysis of Multidomain Protein Dynamics journal December 2015
CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field journal December 2015
Extended Adaptive Biasing Force Algorithm. An On-the-Fly Implementation for Accurate Free-Energy Calculations journal July 2016
All-Atom Continuous Constant pH Molecular Dynamics With Particle Mesh Ewald and Titratable Water journal October 2016
Improving the Force Field Description of Tyrosine–Choline Cation−π Interactions: QM Investigation of Phenol–N(Me) 4 + Interactions journal October 2016
Influence of Coupling and Embedding Schemes on QM Size Convergence in QM/MM Approaches for the Example of a Proton Transfer in DNA journal February 2017
Accurate Modeling of Scaffold Hopping Transformations in Drug Discovery journal December 2016
Polarizable Force Field for DNA Based on the Classical Drude Oscillator: II. Microsecond Molecular Dynamics Simulations of Duplex DNA journal April 2017
Gibbs Sampler-Based λ-Dynamics and Rao–Blackwell Estimator for Alchemical Free Energy Calculation journal May 2017
Drude Polarizable Force Field for Molecular Dynamics Simulations of Saturated and Unsaturated Zwitterionic Lipids journal August 2017
Hybrid All-Atom/Coarse-Grained Simulations of Proteins by Direct Coupling of CHARMM and PRIMO Force Fields journal October 2017
Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems journal November 2017
Comparison of Additive and Polarizable Models with Explicit Treatment of Long-Range Lennard-Jones Interactions Using Alkane Simulations journal January 2018
Rapid Convergence of Energy and Free Energy Profiles with Quantum Mechanical Size in Quantum Mechanical–Molecular Mechanical Simulations of Proton Transfer in DNA journal February 2018
Polarizable Empirical Force Field for Halogen-Containing Compounds Based on the Classical Drude Oscillator journal January 2018
Multi-State VALBOND for Atomistic Simulations of Hypervalent Molecules, Metal Complexes, and Reactions journal February 2018
Optimized Lennard-Jones Parameters for Druglike Small Molecules journal April 2018
CHARMM Drude Polarizable Force Field for Glycosidic Linkages Involving Pyranoses and Furanoses journal April 2018
Tinker 8: Software Tools for Molecular Design journal August 2018
Reproducibility of Free Energy Calculations across Different Molecular Simulation Software Packages journal October 2018
CHARMM-GUI Membrane Builder for Complex Biological Membrane Simulations with Glycolipids and Lipoglycans journal November 2018
Toward Prediction of Electrostatic Parameters for Force Fields That Explicitly Treat Electronic Polarization journal February 2019
Quantitative Analysis of QM/MM Boundary Artifacts and Correction in Adaptive QM/MM Simulations journal May 2019
PhysNet: A Neural Network for Predicting Energies, Forces, Dipole Moments, and Partial Charges journal April 2019
Drude Polarizable Force Field Parametrization of Carboxylate and N-Acetyl Amine Carbohydrate Derivatives journal August 2019
String Method for Protein–Protein Binding Free-Energy Calculations journal October 2019
ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in Solution journal November 2019
String Method with Swarms-of-Trajectories, Mean Drifts, Lag Time, and Committor journal August 2021
Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg 2+ journal July 2018
Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane journal June 2020
Biomolecular QM/MM Simulations: What Are Some of the “Burning Issues”? journal January 2021
Competition among Li + , Na + , K + , and Rb + Monovalent Ions for DNA in Molecular Dynamics Simulations Using the Additive CHARMM36 and Drude Polarizable Force Fields journal March 2015
CHARMM Drude Polarizable Force Field for Aldopentofuranoses and Methyl-aldopentofuranosides journal June 2015
Molecular Multipole Potential Energy Functions for Water journal November 2015
Induced Dipole–Dipole Interactions Influence the Unfolding Pathways of Wild-Type and Mutant Amyloid β-Peptides journal December 2015
Exploring the Dependence of QM/MM Calculations of Enzyme Catalysis on the Size of the QM Region journal August 2016
How Large Should the QM Region Be in QM/MM Calculations? The Case of Catechol O -Methyltransferase journal October 2016
Adaptive Landscape Flattening Accelerates Sampling of Alchemical Space in Multisite λ Dynamics journal February 2017
Smoothed Biasing Forces Yield Unbiased Free Energies with the Extended-System Adaptive Biasing Force Method journal December 2016
Do Halogen–Hydrogen Bond Donor Interactions Dominate the Favorable Contribution of Halogens to Ligand–Protein Binding? journal July 2017
Graph–Theoretic Analysis of Monomethyl Phosphate Clustering in Ionic Solutions journal January 2018
Molecular Dynamics Simulations of the c-kit1 Promoter G-Quadruplex: Importance of Electronic Polarization on Stability and Cooperative Ion Binding journal December 2018
Multistate Reactive Molecular Dynamics Simulations of Proton Diffusion in Water Clusters and in the Bulk journal October 2019
BuRNN: Buffer Region Neural Network Approach for Polarizable-Embedding Neural Network/Molecular Mechanics Simulations journal April 2022
Use of Nonequilibrium Work Methods to Compute Free Energy Differences Between Molecular Mechanical and Quantum Mechanical Representations of Molecular Systems journal November 2015
Predicting Catalytic Proton Donors and Nucleophiles in Enzymes: How Adding Dynamics Helps Elucidate the Structure–Function Relationships journal February 2018
Predicting Binding Free Energies in a Large Combinatorial Chemical Space Using Multisite λ Dynamics journal May 2018
Connecting Protein Conformational Dynamics with Catalytic Function As Illustrated in Dihydrofolate Reductase journal January 2013
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 journal June 2011
Reproducing Crystal Binding Modes of Ligand Functional Groups Using Site-Identification by Ligand Competitive Saturation (SILCS) Simulations journal March 2011
Automation of the CHARMM General Force Field (CGenFF) I: Bond Perception and Atom Typing journal November 2012
Automation of the CHARMM General Force Field (CGenFF) II: Assignment of Bonded Parameters and Partial Atomic Charges journal November 2012
CHARMM-GUI Ligand Binder for Absolute Binding Free Energy Calculations and Its Application journal December 2012
CHARMM-GUI Micelle Builder for Pure/Mixed Micelle and Protein/Micelle Complex Systems journal July 2013
CHARMM-GUI PACE CG Builder for Solution, Micelle, and Bilayer Coarse-Grained Simulations journal March 2014
Docking Covalent Inhibitors: A Parameter Free Approach To Pose Prediction and Scoring journal June 2014
Structure-Based Virtual Screening Approach for Discovery of Covalently Bound Ligands journal June 2014
Mechanisms and Free Energies of Enzymatic Reactions journal August 2006
An Efficient Linear-Scaling Ewald Method for Long-Range Electrostatic Interactions in Combined QM/MM Calculations journal October 2004
Structural Determinants of Transmembrane β-Barrels journal May 2005
Distributed Multipole Analysis:  Stability for Large Basis Sets journal September 2005
Path Integral Simulations of Proton Transfer Reactions in Aqueous Solution Using Combined QM/MM Potentials journal January 2006
Free Energy Perturbation Hamiltonian Replica-Exchange Molecular Dynamics (FEP/H-REMD) for Absolute Ligand Binding Free Energy Calculations journal July 2010
DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB) journal March 2011
Path-Integral Calculations of Nuclear Quantum Effects in Model Systems, Small Molecules, and Enzymes via Gradient-Based Forward Corrector Algorithms journal April 2011
MSCALE: A General Utility for Multiscale Modeling journal March 2011
Boxed Molecular Dynamics: Decorrelation Time Scales and the Kinetic Master Equation journal April 2011
Constant pH Molecular Dynamics in Explicit Solvent with λ-Dynamics journal May 2011
Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of p K a Values journal June 2011
Continuous Constant pH Molecular Dynamics in Explicit Solvent with pH-Based Replica Exchange journal July 2011
CHARMM Additive All-Atom Force Field for Carbohydrate Derivatives and Its Utility in Polysaccharide and Carbohydrate–Protein Modeling journal August 2011
Multisite λ Dynamics for Simulated Structure–Activity Relationship Studies journal August 2011
Hybrid Quantum and Classical Simulations of the Dihydrofolate Reductase Catalyzed Hydride Transfer Reaction on an Accurate Semi-Empirical Potential Energy Surface journal September 2011
Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent journal December 2011
Optimization of the CHARMM Additive Force Field for DNA: Improved Treatment of the BI/BII Conformational Equilibrium journal December 2011
Practically Efficient and Robust Free Energy Calculations: Double-Integration Orthogonal Space Tempering journal February 2012
Advanced Corrections of Hydrogen Bonding and Dispersion for Semiempirical Quantum Mechanical Methods journal December 2011
CHARMM Additive All-Atom Force Field for Phosphate and Sulfate Linked to Carbohydrates journal January 2012
Momentum Distribution as a Fingerprint of Quantum Delocalization in Enzymatic Reactions: Open-Chain Path-Integral Simulations of Model Systems and the Hydride Transfer in Dihydrofolate Reductase journal March 2012
The Solvation Structure of Na + and K + in Liquid Water Determined from High Level ab Initio Molecular Dynamics Simulations journal March 2012
Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ 1 and χ 2 Dihedral Angles journal August 2012
Calculation of Free Energy Landscape in Multi-Dimensions with Hamiltonian-Exchange Umbrella Sampling on Petascale Supercomputer journal October 2012
Detection of Long-Range Concerted Motions in Protein by a Distance Covariance journal August 2012
Hybrid Quantum and Classical Simulations of the Formate Dehydrogenase Catalyzed Hydride Transfer Reaction on an Accurate Semiempirical Potential Energy Surface journal October 2012
A Modified QM/MM Hamiltonian with the Self-Consistent-Charge Density-Functional-Tight-Binding Theory for Highly Charged QM Regions journal October 2012
Parametrization and Benchmark of DFTB3 for Organic Molecules journal November 2012
Dynamic Heterogeneous Dielectric Generalized Born (DHDGB): An Implicit Membrane Model with a Dynamically Varying Bilayer Thickness journal March 2013
Generating Reservoir Conformations for Replica Exchange through the Use of the Conformational Space Annealing Method journal January 2013
Acceleration of Semiempirical Quantum Mechanical Calculations by Extended Lagrangian Molecular Dynamics Approach journal July 2013
Lennard-Jones Lattice Summation in Bilayer Simulations Has Critical Effects on Surface Tension and Lipid Properties journal July 2013
PRIMO: A Transferable Coarse-Grained Force Field for Proteins journal July 2013
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data journal June 2013
Comparison between Mean Forces and Swarms-of-Trajectories String Methods journal January 2014
Polarizable Force Field for Peptides and Proteins Based on the Classical Drude Oscillator journal November 2013
Leveraging Symmetries of Static Atomic Multipole Electrostatics in Molecular Dynamics Simulations journal November 2013
Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide journal November 2013
Multisurface Adiabatic Reactive Molecular Dynamics journal March 2014
Reaction Path Force Matching: A New Strategy of Fitting Specific Reaction Parameters for Semiempirical Methods in Combined QM/MM Simulations journal June 2014
Constant pH Replica Exchange Molecular Dynamics in Explicit Solvent Using Discrete Protonation States: Implementation, Testing, and Validation journal February 2014
Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes journal March 2014
Extension of the FACTS Implicit Solvation Model to Membranes journal June 2014
Constant pH Molecular Dynamics in Explicit Solvent with Enveloping Distribution Sampling and Hamiltonian Exchange journal June 2014
Transferring the PRIMO Coarse-Grained Force Field to the Membrane Environment: Simulations of Membrane Proteins and Helix–Helix Association journal June 2014
Acceleration of Ab Initio QM/MM Calculations under Periodic Boundary Conditions by Multiscale and Multiple Time Step Approaches journal September 2014
Specific Reaction Parametrization of the AM1/d Hamiltonian for Phosphoryl Transfer Reactions:  H, O, and P Atoms journal January 2007
Improving Convergence of Replica-Exchange Simulations through Coupling to a High-Temperature Structure Reservoir journal January 2007
An Integrated Path Integral and Free-Energy Perturbation−Umbrella Sampling Method for Computing Kinetic Isotope Effects of Chemical Reactions in Solution and in Enzymes journal April 2007
Development of a Polarizable Intermolecular Potential Function (PIPF) for Liquid Amides and Alkanes journal October 2007
Atomistic Simulation of Adiabatic Reactive Processes Based on Multi-State Potential Energy Surfaces journal June 2008
Molecular Mechanics Force Field for Octahedral Organometallic Compounds with Inclusion of the Trans Influence journal February 2009
Computations of Absolute Solvation Free Energies of Small Molecules Using Explicit and Implicit Solvent Model journal March 2009
CHARMM Additive All-Atom Force Field for Acyclic Polyalcohols, Acyclic Carbohydrates, and Inositol journal April 2009
Reaction Path Optimization with Holonomic Constraints and Kinetic Energy Potentials journal July 2009
Computation of Absolute Hydration and Binding Free Energy with Free Energy Perturbation Distributed Replica-Exchange Molecular Dynamics journal August 2009
An Evaluation of Explicit Receptor Flexibility in Molecular Docking Using Molecular Dynamics and Torsion Angle Molecular Dynamics journal September 2009
Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables journal December 2009
Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field journal January 2010
Accurate Calculation of Hydration Free Energies using Pair-Specific Lennard-Jones Parameters in the CHARMM Drude Polarizable Force Field journal March 2010
Solvation Free Energies of Small Amides and Amines from Molecular Dynamics/Free Energy Perturbation Simulations Using Pairwise Additive and Many-Body Polarizable Potentials journal July 1995
A Polarizable Intermolecular Potential Function for Simulation of Liquid Alcohols journal November 1995
Feynman path integral formulation of quantum mechanical transition-state theory journal August 1993
A quantized classical path approach for calculations of quantum mechanical rate constants journal September 1993
Simulations of quantum mechanical corrections for rate constants of hydride-transfer reactions in enzymes and solutions journal October 1991
Valence Bond Concepts Applied to the Molecular Mechanics Description of Molecular Shapes. 4. Transition Metals with π-Bonds journal November 2001
Free energy perturbation method for chemical reactions in the condensed phase: a dynamic approach based on a combined quantum and molecular mechanics potential journal December 1987
Peptide plane orientations determined by fundamental and overtone nitrogen 14 NMR journal September 1986
Development and use of quantum mechanical molecular models. 76. AM1: a new general purpose quantum mechanical molecular model journal June 1985
Ground states of molecules. 38. The MNDO method. Approximations and parameters journal June 1977
Atom dipole interaction model for molecular polarizability. Application to polyatomic molecules and determination of atom polarizabilities journal May 1972
Activation Energies from Bond Energies. I. Hydrogen Transfer Reactions journal September 1963
Atomic Radii and Interatomic Distances in Metals journal March 1947
Improved Treatment of the Protein Backbone in Empirical Force Fields journal January 2004
Proton Binding to Proteins:  p K a Calculations with Explicit and Implicit Solvent Models journal March 2004
Role of Hydration Force in the Self-Assembly of Collagens and Amyloid Steric Zipper Filaments journal July 2011
Dissecting Force Interactions in Cellulose Deconstruction Reveals the Required Solvent Versatility for Overcoming Biomass Recalcitrance journal September 2011
Intrinsic Contribution of the 2′-Hydroxyl to RNA Conformational Heterogeneity journal January 2012
Computational Analysis of the Binding Specificity of Gleevec to Abl, c-Kit, Lck, and c-Src Tyrosine Kinases journal September 2013
Computational Study of Gleevec and G6G Reveals Molecular Determinants of Kinase Inhibitor Selectivity journal October 2014
Determination of Biomembrane Bending Moduli in Fully Atomistic Simulations journal September 2014
Role of Hydrogen Bonding and Helix−Lipid Interactions in Transmembrane Helix Association journal April 2008
Many-Body Polarization Effects and the Membrane Dipole Potential journal February 2009
Multifrequency Electron Spin Resonance Spectra of a Spin-Labeled Protein Calculated from Molecular Dynamics Simulations journal February 2009
Catalyzing Racemizations in the Absence of a Cofactor: The Reaction Mechanism in Proline Racemase journal June 2009
Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids journal January 1996
Valence Bond Concepts Applied to the Molecular Mechanics Description of Molecular Shapes. 3. Applications to Transition Metal Alkyls and Hydrides journal March 1998
pH-Responsive Self-Assembly of Polysaccharide through a Rugged Energy Landscape journal September 2015
Role of Protein Dynamics in Allosteric Control of the Catalytic Phosphoryl Transfer of Insulin Receptor Kinase journal September 2015
Leaving Group Ability Observably Affects Transition State Structure in a Single Enzyme Active Site journal June 2016
Substrate and Transition State Binding in Alkaline Phosphatase Analyzed by Computation of Oxygen Isotope Effects journal August 2016
Novel Procedure for Modeling Ligand/Receptor Induced Fit Effects journal January 2006
A QM/MM Implementation of the Self-Consistent Charge Density Functional Tight Binding (SCC-DFTB) Method journal January 2001
ReaxFF:  A Reactive Force Field for Hydrocarbons journal October 2001
Introducing an Implicit Membrane in Generalized Born/Solvent Accessibility Continuum Solvent Models journal July 2002
Polarizable Atomic Multipole Water Model for Molecular Mechanics Simulation journal May 2003
p K a Calculations with QM/MM Free Energy Perturbations journal November 2003
Improved Formulas for the Calculation of the Electrostatic Contribution to the Intermolecular Interaction Energy from Multipolar Expansion of the Electronic Distribution journal December 2003
Generalized Hybrid Orbital (GHO) Method for Combining Ab Initio Hartree−Fock Wave Functions with Molecular Mechanics journal January 2004
A Critical Evaluation of Different QM/MM Frontier Treatments with SCC-DFTB as the QM Method journal May 2005
Finite Temperature String Method for the Study of Rare Events † journal April 2005
An ab Initio Study on the Torsional Surface of Alkanes and Its Effect on Molecular Simulations of Alkanes and a DPPC Bilayer journal March 2005
System-Size Dependence of Diffusion Coefficients and Viscosities from Molecular Dynamics Simulations with Periodic Boundary Conditions journal October 2004
Combining Self-Consistent-Charge Density-Functional Tight-Binding (SCC-DFTB) with Molecular Mechanics by the Generalized Hybrid Orbital (GHO) Method journal June 2004
p K a Calculations in Solution and Proteins with QM/MM Free Energy Perturbation Simulations:  A Quantitative Test of QM/MM Protocols journal August 2005
Molecular Dynamics Simulations of Large Integral Membrane Proteins with an Implicit Membrane Model journal January 2006
Development of Effective Quantum Mechanical/Molecular Mechanical (QM/MM) Methods for Complex Biological Processes journal April 2006
Coupling of Replica Exchange Simulations to a Non-Boltzmann Structure Reservoir journal March 2007
Long-Range Lennard-Jones and Electrostatic Interactions in Interfaces:  Application of the Isotropic Periodic Sum Method journal April 2007
Exploring SCC-DFTB Paths for Mapping QM/MM Reaction Mechanisms † journal July 2007
Finding Transition Pathways Using the String Method with Swarms of Trajectories journal March 2008
Absolute Binding Free Energy Calculations of Sparsomycin Analogs to the Bacterial Ribosome journal July 2010
Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types journal June 2010
Comparing Simulated and Experimental Translation and Rotation Constants: Range of Validity for Viscosity Scaling journal September 2010
CHARMM Additive All-Atom Force Field for Glycosidic Linkages in Carbohydrates Involving Furanoses journal September 2010
Development of CHARMM Polarizable Force Field for Nucleic Acid Bases Based on the Classical Drude Oscillator Model journal January 2011
Replica Exchange with Solute Scaling: A More Efficient Version of Replica Exchange with Solute Tempering (REST2) journal August 2011
Efficient Calculation of Molecular Configurational Entropies Using an Information Theoretic Approximation journal February 2012
Analysis and Elimination of a Bias in Targeted Molecular Dynamics Simulations of Conformational Transitions: Application to Calmodulin journal February 2012
Conformational Sampling of Peptides in the Presence of Protein Crowders from AA/CG-Multiscale Simulations journal April 2012
Unrestrained Computation of Free Energy along a Path journal August 2012
A Simplified Confinement Method for Calculating Absolute Free Energies and Free Energy and Entropy Differences journal January 2013
Restrained-Ensemble Molecular Dynamics Simulations Based on Distance Histograms from Double Electron–Electron Resonance Spectroscopy journal April 2013
Structural Refinement from Restrained-Ensemble Simulations Based on EPR/DEER Data: Application to T4 Lysozyme journal April 2013
Simulations of Anionic Lipid Membranes: Development of Interaction-Specific Ion Parameters and Validation Using NMR Data journal August 2013
A Polarizable Force Field of Dipalmitoylphosphatidylcholine Based on the Classical Drude Model for Molecular Dynamics Simulations of Lipids journal July 2013
Endoglucanase Peripheral Loops Facilitate Complexation of Glucan Chains on Cellulose via Adaptive Coupling to the Emergent Substrate Structures journal September 2013
Polarizable Empirical Force Field for Hexopyranose Monosaccharides Based on the Classical Drude Oscillator journal February 2014
Molecular Simulation of Water and Hydration Effects in Different Environments: Challenges and Developments for DFTB Based Models journal September 2014
Balancing the Interactions of Ions, Water, and DNA in the Drude Polarizable Force Field journal June 2014
Free Energy Simulations of Active-Site Mutants of Dihydrofolate Reductase journal August 2014
Representation of Ion–Protein Interactions Using the Drude Polarizable Force-Field journal September 2014
Computational Study of the “DFG-Flip” Conformational Transition in c-Abl and c-Src Tyrosine Kinases journal January 2015
Understanding the Dielectric Properties of Liquid Amides from a Polarizable Force Field journal March 2008
pKa of Residue 66 in Staphylococal nuclease. I. Insights from QM/MM Simulations with Conventional Sampling journal June 2008
Computations of Standard Binding Free Energies with Molecular Dynamics Simulations journal February 2009
Gaussian-Mixture Umbrella Sampling journal March 2009
A Coupled Polarization-Matrix Inversion and Iteration Approach for Accelerating the Dipole Convergence in a Polarizable Potential Function journal January 2009
Comparison of the Extended Isotropic Periodic Sum and Particle Mesh Ewald Methods for Simulations of Lipid Bilayers and Monolayers journal April 2009
Molecular Dynamics Study of a Polymeric Reverse Osmosis Membrane journal July 2009
CHARMM Additive All-Atom Force Field for Aldopentofuranoses, Methyl-aldopentofuranosides, and Fructofuranose journal September 2009
Ion Selectivity of α-Hemolysin with a β-Cyclodextrin Adapter. I. Single Ion Potential of Mean Force and Diffusion Coefficient journal December 2009
Ion Selectivity of α-Hemolysin with β-Cyclodextrin Adapter. II. Multi-Ion Effects Studied with Grand Canonical Monte Carlo/Brownian Dynamics Simulations journal February 2010
Conformational Sampling of Influenza Fusion Peptide in Membrane Bilayers as a Function of Termini and Protonation States journal December 2009
Boxed Molecular Dynamics: A Simple and General Technique for Accelerating Rare Event Kinetics and Mapping Free Energy in Large Molecular Systems journal December 2009
Current Status of the AMOEBA Polarizable Force Field journal March 2010
Simulation of Liquid Amides Using a Polarizable Intermolecular Potential Function † journal January 1996
Electric Polarizability and Hyperpolarizability of Carbon Monoxide journal January 1996
Effect of Electrostatic Force Truncation on Interfacial and Transport Properties of Water journal January 1996
All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins † journal April 1998
Molecular and Atomic Polarizabilities:  Thole's Model Revisited journal April 1998
A Generalized Hybrid Orbital (GHO) Method for the Treatment of Boundary Atoms in Combined QM/MM Calculations journal June 1998
Development of a Generalized Born Model Parametrization for Proteins and Nucleic Acids journal May 1999
Zeolite Structure and Reactivity by Combined Quantum-Chemical−Classical Calculations journal July 1999
High-Performance Scalable Molecular Dynamics Simulations of a Polarizable Force Field Based on Classical Drude Oscillators in NAMD journal December 2010
Toward Accurate Prediction of the Protonation Equilibrium of Nucleic Acids journal February 2013
Induced Polarization Influences the Fundamental Forces in DNA Base Flipping journal May 2014
Differential Impact of the Monovalent Ions Li + , Na + , K + , and Rb + on DNA Conformational Properties journal December 2014
Simulation of Osmotic Pressure in Concentrated Aqueous Salt Solutions journal November 2009
Nonequilibrium Measurements of Free Energy Differences for Microscopically Reversible Markovian Systems journal January 1998
Dynamics of folded proteins journal June 1977
SAM-dependent enzyme-catalysed pericyclic reactions in natural product biosynthesis journal September 2017
Unimolecular dissociation dynamics of vibrationally activated CH3CHOO Criegee intermediates to OH radical products journal April 2016
Mechanism of pH-dependent activation of the sodium-proton antiporter NhaA journal October 2016
CHARMM36m: an improved force field for folded and intrinsically disordered proteins journal November 2016
A plasmid-encoded dihydrofolate reductase from trimethoprim-resistant bacteria has a novel D2-symmetric active site journal November 1995
Structural mechanism of voltage-dependent gating in an isolated voltage-sensing domain journal February 2014
Conformational dynamics of ligand-dependent alternating access in LeuT journal April 2014
Unifying machine learning and quantum chemistry with a deep neural network for molecular wavefunctions journal November 2019
Highly accurate protein structure prediction for the human proteome journal July 2021
Promoting transparency and reproducibility in enhanced molecular simulations journal July 2019
Using metadynamics to explore complex free-energy landscapes journal March 2020
HSO3Cl: a prototype molecule for studying OH-stretching overtone induced photodissociation journal January 2016
Spectroscopy and dynamics of double proton transfer in formic acid dimer journal January 2016
Adaptive free energy sampling in multidimensional collective variable space using boxed molecular dynamics journal January 2016
ANI-1: an extensible neural network potential with DFT accuracy at force field computational cost journal January 2017
Crystal structure of LepI, a multifunctional SAM-dependent enzyme which catalyzes pericyclic reactions in leporin biosynthesis journal January 2019
The N(4S) + O2(X3Σ−g) ↔ O(3P) + NO(X2Π) reaction: thermal and vibrational relaxation rates for the 2A′, 4A′ and 2A′′ states journal January 2020
Large scale relative protein ligand binding affinities using non-equilibrium alchemy journal January 2020
Machine learning of solvent effects on molecular spectra and reactions journal January 2021
Facilitating ab initio QM/MM free energy simulations by Gaussian process regression with derivative observations journal January 2022
Computer simulation of zeolite structure and reactivity using embedded cluster methods journal January 1997
Accelerated, energy-conserving Born–Oppenheimer molecular dynamics via Fock matrix extrapolation journal January 2005
Halogen bonding: an electrostatically-driven highly directional noncovalent interaction journal January 2010
Convergence of QM/MM free-energy perturbations based on molecular-mechanics or semiempirical simulations journal January 2012
Elastic moduli for strongly curved monoplayers. Position of the neutral surface journal September 1991
Spatial and energetic-entropic decomposition of surface tension in lipid bilayers from molecular dynamics simulations journal September 2000
Multidimensional replica-exchange method for free-energy calculations journal October 2000
Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points journal December 2000
Generalized solvent boundary potential for computer simulations journal February 2001
Fast-growth thermodynamic integration: Error and efficiency analysis journal May 2001
Ab initio molecular dynamics: Propagating the density matrix with Gaussian orbitals journal June 2001
On the calculation of entropy from covariance matrices of the atomic fluctuations journal October 2001
Calculating free energies using average force journal November 2001
Novel generalized Born methods journal June 2002
Gradient symplectic algorithms for solving the Schrödinger equation with time-dependent potentials journal July 2002
Constant- p H molecular dynamics using stochastic titration journal September 2002
Optimization of quantum mechanical molecular mechanical partitioning schemes: Gaussian delocalization of molecular mechanical charges and the double link atom method journal December 2002
Calculation of the dielectric permittivity profile for a nonuniform system: Application to a lipid bilayer simulation journal February 2003
Modeling induced polarization with classical Drude oscillators: Theory and molecular dynamics simulation algorithm journal August 2003
A simple polarizable model of water based on classical Drude oscillators journal September 2003
A super-linear minimization scheme for the nudged elastic band method journal December 2003
Implicit solvation based on generalized Born theory in different dielectric environments journal January 2004
Computing time scales from reaction coordinates by milestoning journal June 2004
The Statistical Mechanical Theory of Transport Processes. IV. The Equations of Hydrodynamics journal June 1950
Statistical Mechanics of Fluid Mixtures journal May 1935
Overcoming free energy barriers using unconstrained molecular dynamics simulations journal August 2004
Curvy-steps approach to constraint-free extended-Lagrangian ab initio molecular dynamics, using atom-centered basis functions: Convergence toward Born–Oppenheimer trajectories journal December 2004
Isotropic periodic sum: A method for the calculation of long-range interactions journal January 2005
Simulation of conformational transitions by the restricted perturbation–targeted molecular dynamics method journal March 2005
Methodological problems in pressure profile calculations for lipid bilayers journal March 2005
A generalized Born formalism for heterogeneous dielectric environments: Application to the implicit modeling of biological membranes journal March 2005
Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules journal July 2005
Transition pathways in complex systems: Application of the finite-temperature string method to the alanine dipeptide journal October 2005
String method in collective variables: Minimum free energy paths and isocommittor surfaces journal July 2006
From A to B in free energy space journal February 2007
Computation of free energy profiles with parallel adaptive dynamics journal April 2007
Minimum free energy pathways and free energy profiles for conformational transitions based on atomistic molecular dynamics simulations journal April 2007
Simplified and improved string method for computing the minimum energy paths in barrier-crossing events journal April 2007
Enveloping distribution sampling: A method to calculate free energy differences from a single simulation journal May 2007
Molecular simulation with variable protonation states at constant pH journal April 2007
Proton momentum distribution in water: an open path integral molecular dynamics study journal June 2007
Multiple scaling replica exchange for the conformational sampling of biomolecules in explicit water journal December 2007
Adaptive biasing force method for scalar and vector free energy calculations journal April 2008
Computation of binding free energy with molecular dynamics and grand canonical Monte Carlo simulations journal March 2008
Multiple free energies from a single simulation: Extending enveloping distribution sampling to nonoverlapping phase-space distributions journal May 2008
Statistically optimal analysis of samples from multiple equilibrium states journal September 2008
Using the isotropic periodic sum method to calculate long-range interactions of heterogeneous systems journal October 2008
Markovian milestoning with Voronoi tessellations journal May 2009
Revisiting the finite temperature string method for the calculation of reaction tubes and free energies journal May 2009
Extended Lagrangian Born–Oppenheimer molecular dynamics with dissipation journal June 2009
Decomposition of energy and free energy changes by following the flow of work along reaction path journal October 2009
Free energy of conformational transition paths in biomolecules: The string method and its application to myosin VI journal February 2011
Product energy deposition of CN + alkane H abstraction reactions in gas and solution phases journal June 2011
Lagrangian formulation with dissipation of Born-Oppenheimer molecular dynamics using the density-functional tight-binding method journal July 2011
Improving the convergence of closed and open path integral molecular dynamics via higher order Trotter factorization schemes journal August 2011
Optimal pairwise and non-pairwise alchemical pathways for free energy calculations of molecular transformation in solution phase journal March 2012
A unified formulation of the constant temperature molecular dynamics methods journal July 1984
The lag between the Hamiltonian and the system configuration in free energy perturbation calculations journal December 1989
An adaptive umbrella sampling procedure in conformational analysis using molecular dynamics and its application to glycol journal November 1992
Particle mesh Ewald: An N ⋅log( N ) method for Ewald sums in large systems journal June 1993
A finite‐time variational method for determining optimal paths and obtaining bounds on free energy changes from computer simulations journal November 1993
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Random walk in orthogonal space to achieve efficient free-energy simulation of complex systems journal December 2008
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Density functional tight binding
  • Elstner, Marcus; Seifert, Gotthard
  • Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences, Vol. 372, Issue 2011 https://doi.org/10.1098/rsta.2012.0483
journal March 2014
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