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Top Articles

#TitleJournalYearCitations
1GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular SimulationJournal of Chemical Theory and Computation200814,046
2ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SBJournal of Chemical Theory and Computation20159,383
3PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory DataJournal of Chemical Theory and Computation20136,364
4MMPBSA.py: An Efficient Program for End-State Free Energy CalculationsJournal of Chemical Theory and Computation20124,059
5Optimization of the Additive CHARMM All-Atom Protein Force Field Targeting Improved Sampling of the Backbone ϕ, ψ and Side-Chain χ1 and χ2 Dihedral AnglesJournal of Chemical Theory and Computation20123,896
6GFN2-xTB—An Accurate and Broadly Parametrized Self-Consistent Tight-Binding Quantum Chemical Method with Multipole Electrostatics and Density-Dependent Dispersion ContributionsJournal of Chemical Theory and Computation20193,775
7PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKaPredictionsJournal of Chemical Theory and Computation20113,752
8NCIPLOT: A Program for Plotting Noncovalent Interaction RegionsJournal of Chemical Theory and Computation20113,721
9CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force FieldJournal of Chemical Theory and Computation20163,409
10P-LINCS:  A Parallel Linear Constraint Solver for Molecular SimulationJournal of Chemical Theory and Computation20083,381
11Design of Density Functionals by Combining the Method of Constraint Satisfaction with Parametrization for Thermochemistry, Thermochemical Kinetics, and Noncovalent InteractionsJournal of Chemical Theory and Computation20063,372
12Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh EwaldJournal of Chemical Theory and Computation20132,852
13gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACSJournal of Chemical Theory and Computation20212,821
14OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and ProteinsJournal of Chemical Theory and Computation20162,566
15ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in SolutionJournal of Chemical Theory and Computation20202,066
16The MARTINI Coarse-Grained Force Field: Extension to ProteinsJournal of Chemical Theory and Computation20082,032
17A Robust and Accurate Tight-Binding Quantum Chemical Method for Structures, Vibrational Frequencies, and Noncovalent Interactions of Large Molecular Systems Parametrized for All spd-Block Elements (Z = 1–86)Journal of Chemical Theory and Computation20171,832
18A Combined Charge and Energy Decomposition Scheme for Bond AnalysisJournal of Chemical Theory and Computation20091,773
19Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized BornJournal of Chemical Theory and Computation20121,714
20OPLS4: Improving Force Field Accuracy on Challenging Regimes of Chemical SpaceJournal of Chemical Theory and Computation20211,669
21Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force FieldJournal of Chemical Theory and Computation20101,668
22An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0Journal of Chemical Theory and Computation20111,658
23Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa ValuesJournal of Chemical Theory and Computation20111,652
24Performance of B3LYP Density Functional Methods for a Large Set of Organic MoleculesJournal of Chemical Theory and Computation20081,525
25g_wham—A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation EstimatesJournal of Chemical Theory and Computation20101,465
26Computational Thermochemistry: Scale Factor Databases and Scale Factors for Vibrational Frequencies Obtained from Electronic Model ChemistriesJournal of Chemical Theory and Computation20101,463
27Revised Basis Sets for the LANL Effective Core PotentialsJournal of Chemical Theory and Computation20081,299
28All-Electron Scalar Relativistic Basis Sets for Third-Row Transition Metal AtomsJournal of Chemical Theory and Computation20081,298
29Improved Parameters for the Martini Coarse-Grained Protein Force FieldJournal of Chemical Theory and Computation20131,212
30Efficient and Accurate Double-Hybrid-Meta-GGA Density Functionals—Evaluation with the Extended GMTKN30 Database for General Main Group Thermochemistry, Kinetics, and Noncovalent InteractionsJournal of Chemical Theory and Computation20111,195
31Benchmarking the Conductor-like Polarizable Continuum Model (CPCM) for Aqueous Solvation Free Energies of Neutral and Ionic Organic MoleculesJournal of Chemical Theory and Computation20051,141
32Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water ModelsJournal of Chemical Theory and Computation20101,105
33The Rosetta All-Atom Energy Function for Macromolecular Modeling and DesignJournal of Chemical Theory and Computation20171,100
34Psi4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and InteroperabilityJournal of Chemical Theory and Computation20171,094
35Exploring the Limit of Accuracy of the Global Hybrid Meta Density Functional for Main-Group Thermochemistry, Kinetics, and Noncovalent InteractionsJournal of Chemical Theory and Computation20081,082
36A Qualitative Index of Spatial Extent in Charge-Transfer ExcitationsJournal of Chemical Theory and Computation20111,075
37Long-Time-Step Molecular Dynamics through Hydrogen Mass RepartitioningJournal of Chemical Theory and Computation20151,071
38Intrinsic Atomic Orbitals: An Unbiased Bridge between Quantum Theory and Chemical ConceptsJournal of Chemical Theory and Computation20131,055
39Lipid14: The Amber Lipid Force FieldJournal of Chemical Theory and Computation20141,047
40OPLS3e: Extending Force Field Coverage for Drug-Like Small MoleculesJournal of Chemical Theory and Computation20191,002
41Exploration of Chemical Compound, Conformer, and Reaction Space with Meta-Dynamics Simulations Based on Tight-Binding Quantum Chemical CalculationsJournal of Chemical Theory and Computation2019999
42Extensive TD-DFT Benchmark: Singlet-Excited States of Organic MoleculesJournal of Chemical Theory and Computation2009996
43OpenMolcas: From Source Code to InsightJournal of Chemical Theory and Computation2019983
44Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion ProfilesJournal of Chemical Theory and Computation2011967
45DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB)Journal of Chemical Theory and Computation2011962
46Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular SimulationsJournal of Chemical Theory and Computation2015948
47PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov ModelsJournal of Chemical Theory and Computation2015944
48Using Hessian Updating To Increase the Efficiency of a Hessian Based Predictor-Corrector Reaction Path Following MethodJournal of Chemical Theory and Computation2005909
49Charge Model 5: An Extension of Hirshfeld Population Analysis for the Accurate Description of Molecular Interactions in Gaseous and Condensed PhasesJournal of Chemical Theory and Computation2012902
50Parametrization and Benchmark of DFTB3 for Organic MoleculesJournal of Chemical Theory and Computation2013898