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Top Articles

#TitleJournalYearCitations
1GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular SimulationJournal of Chemical Theory and Computation200814,191
2ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SBJournal of Chemical Theory and Computation20157,925
3PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory DataJournal of Chemical Theory and Computation20135,395
4Optimization 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 Computation20123,900
5Design of Density Functionals by Combining the Method of Constraint Satisfaction with Parametrization for Thermochemistry, Thermochemical Kinetics, and Noncovalent InteractionsJournal of Chemical Theory and Computation20063,402
6PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKaPredictionsJournal of Chemical Theory and Computation20113,357
7P-LINCS:  A Parallel Linear Constraint Solver for Molecular SimulationJournal of Chemical Theory and Computation20083,140
8MMPBSA.py: An Efficient Program for End-State Free Energy CalculationsJournal of Chemical Theory and Computation20123,140
9NCIPLOT: A Program for Plotting Noncovalent Interaction RegionsJournal of Chemical Theory and Computation20113,064
10CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force FieldJournal of Chemical Theory and Computation20162,842
11Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 2. Explicit Solvent Particle Mesh EwaldJournal of Chemical Theory and Computation20132,741
12OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and ProteinsJournal of Chemical Theory and Computation20162,490
13The MARTINI Coarse-Grained Force Field: Extension to ProteinsJournal of Chemical Theory and Computation20082,250
14GFN2-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 Computation20192,025
15Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized BornJournal of Chemical Theory and Computation20121,702
16Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa ValuesJournal of Chemical Theory and Computation20111,523
17An Automated Force Field Topology Builder (ATB) and Repository: Version 1.0Journal of Chemical Theory and Computation20111,491
18A Combined Charge and Energy Decomposition Scheme for Bond AnalysisJournal of Chemical Theory and Computation20091,440
19Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force FieldJournal of Chemical Theory and Computation20101,431
20g_wham—A Free Weighted Histogram Analysis Implementation Including Robust Error and Autocorrelation EstimatesJournal of Chemical Theory and Computation20101,355
21Improved Parameters for the Martini Coarse-Grained Protein Force FieldJournal of Chemical Theory and Computation20131,263
22Computational Thermochemistry: Scale Factor Databases and Scale Factors for Vibrational Frequencies Obtained from Electronic Model ChemistriesJournal of Chemical Theory and Computation20101,247
23A 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 Computation20171,223
24Revised Basis Sets for the LANL Effective Core PotentialsJournal of Chemical Theory and Computation20081,204
25All-Electron Scalar Relativistic Basis Sets for Third-Row Transition Metal AtomsJournal of Chemical Theory and Computation20081,124
26The Rosetta All-Atom Energy Function for Macromolecular Modeling and DesignJournal of Chemical Theory and Computation20171,117
27Lipid14: The Amber Lipid Force FieldJournal of Chemical Theory and Computation20141,107
28Efficient 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 Computation20111,082
29ff19SB: Amino-Acid-Specific Protein Backbone Parameters Trained against Quantum Mechanics Energy Surfaces in SolutionJournal of Chemical Theory and Computation20201,068
30Performance of B3LYP Density Functional Methods for a Large Set of Organic MoleculesJournal of Chemical Theory and Computation20081,042
31Benchmarking the Conductor-like Polarizable Continuum Model (CPCM) for Aqueous Solvation Free Energies of Neutral and Ionic Organic MoleculesJournal of Chemical Theory and Computation20051,018
32Psi4 1.1: An Open-Source Electronic Structure Program Emphasizing Automation, Advanced Libraries, and InteroperabilityJournal of Chemical Theory and Computation20171,012
33Long-Time-Step Molecular Dynamics through Hydrogen Mass RepartitioningJournal of Chemical Theory and Computation20151,004
34Exploring the Limit of Accuracy of the Global Hybrid Meta Density Functional for Main-Group Thermochemistry, Kinetics, and Noncovalent InteractionsJournal of Chemical Theory and Computation2008995
35Extensive TD-DFT Benchmark: Singlet-Excited States of Organic MoleculesJournal of Chemical Theory and Computation2009961
36PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov ModelsJournal of Chemical Theory and Computation2015950
37Implementation 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 Computation2010928
38Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion ProfilesJournal of Chemical Theory and Computation2011922
39Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular SimulationsJournal of Chemical Theory and Computation2015914
40A Qualitative Index of Spatial Extent in Charge-Transfer ExcitationsJournal of Chemical Theory and Computation2011904
41gmx_MMPBSA: A New Tool to Perform End-State Free Energy Calculations with GROMACSJournal of Chemical Theory and Computation2021903
42Combining Quantum Mechanics Methods with Molecular Mechanics Methods in ONIOMJournal of Chemical Theory and Computation2006876
43DFTB3: Extension of the Self-Consistent-Charge Density-Functional Tight-Binding Method (SCC-DFTB)Journal of Chemical Theory and Computation2011872
44S66: A Well-balanced Database of Benchmark Interaction Energies Relevant to Biomolecular StructuresJournal of Chemical Theory and Computation2011846
45Benchmark Databases for Nonbonded Interactions and Their Use To Test Density Functional TheoryJournal of Chemical Theory and Computation2005842
46Using Hessian Updating To Increase the Efficiency of a Hessian Based Predictor-Corrector Reaction Path Following MethodJournal of Chemical Theory and Computation2005840
47ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time ScaleJournal of Chemical Theory and Computation2009807
48Excitation Gaps of Finite-Sized Systems from Optimally Tuned Range-Separated Hybrid FunctionalsJournal of Chemical Theory and Computation2012797
49Parametrization and Benchmark of DFTB3 for Organic MoleculesJournal of Chemical Theory and Computation2013794
50TD-DFT Performance for the Visible Absorption Spectra of Organic Dyes:  Conventional versus Long-Range HybridsJournal of Chemical Theory and Computation2008787