Trackademia

Welcome to Trackademia

The idea behind Trackademia is to build on existing academic databases like Google Scholar and OpenAlex so that you can trust the data and use it for whatever you want. That comes down to two things.

More data, and more ways to use it. We aggregate publication data from every major source into a single dataset and add information pulled from faculty CVs. Then we let you slice it however you want: choose which sources to build from, write your own formulas, weight journals, adjust for department size.

More accurate, and honest about where it isn’t. We focus on a smaller set of schools so we can verify everything carefully. Faculty lists come from department websites rather than being inferred from publication records, so we know who should be in the data before we go looking. When we can’t find data on someone, we record the gap instead of dropping them. Every number comes with a coverage rate you can check against ground truth.

Everything in Trackademia is built from seven units. AI merges duplicate records across sources and tags each publication so these categories hold up:

  • Publication — citation counts, authors, journal, peer review status, and more
  • Publication group — versions of the same work combined into one entity, such as a working paper and the article it became
  • Academic
  • Department
  • University
  • Field
  • Journal

There are two modes. In Database mode you browse the underlying records and filter by any of the seven units. In Analytics mode you get graphs and comparisons, and you switch views to compare two departments, compare one department against the average of the others, or see them all at once. Tabs let you focus on a particular level of the data.

Back to the list
Academic

William Jorgensen

close

Academic

RankDistinguished
As of2012 · CV
DepartmentYale Chemistry
UniversityYale
FieldChemistry
Scholarprofile

Totals

Publications453
Citations159,542
h-index137 · Scholar
Citations per year in post3,128.3
Years in post51 from the CV positions

Coverage

Works with a count431 of 453
Share95%

Positions

Sterling Professor of Chemistry, Yale Univers…2009–
Director, Division of Physical Sciences and E…2009–2012
Whitehead Professor of Chemistry, Yale Univer…1990–2009
Visiting Professor, Harvard University1989–1989
Herbert C. Brown Professor of Chemistry, Purd…1985–1990
Head, Organic Chemistry Division, Purdue Univ…1984–1987
Professor, Department of Chemistry, Purdue Un…1982–1990
Associate Professor, Department of Chemistry,…1979–1982
and 1 more

Top venues 78 venues

The 8 holding the most of these works; 70 more hold at least one.

Journal of the American Chemical Society123
Bioorganic & Medicinal Chemistry Letters29
Journal of Chemical Theory and Computation29
The Journal of Organic Chemistry29
Journal of Medicinal Chemistry25
Journal of Computational Chemistry20
The Journal of Physical Chemistry20
The Journal of Physical Chemistry B20

Publications per year

Works this academic published in each year, by the year each work appeared; an undated work is in no year, and a work two colleagues wrote counts for each of them. The kind, works and year filters decide which works are here at all.

Citations per year

Citations received in each year, from this academic’s verified Scholar profile, which counts every citation to everything they ever wrote: no publication filter reaches this line - not the kinds, not the works switch, not the year window on publication - and no journal weight either. It is a profile total, so it does not match the works listed below.

Publications 453 works

Every work these filters select, most cited first and the works with no count at the end: a work nobody has a figure for is unknown, never a zero to be ranked among the works that have one, and it prints an em dash. Each figure is that work’s own citations - Scholar’s count where there is one, else OpenAlex’s - and is not weighted.

YearTitleVenueKindCitations
1983Comparison of Simple Potential Functions for Simulating Liquid Water.The Journal of Chemical Physicsarticle48,999
1996Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic LiquidsJournal of the American Chemical Societyarticle18,714
1988The OPLS Force Field for Proteins. Energy Minimizations for Crystals of Cyclic Peptides and Crambin.Journal of the American Chemical Societyarticle6,648
2001Evaluation and Reparameterization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides.The Journal of Physical Chemistry Barticle4,886
2016OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and ProteinsJournal of Chemical Theory and Computationarticle3,609
2000A five-site model for liquid water and the reproduction of the density anomaly by rigid, non-polarizable modelsThe Journal of Chemical Physicsarticle3,006
1984Optimized Intermolecular Potential Functions for Liquid Hydrocarbons.Journal of the American Chemical Societyarticle2,941
2004The Many Roles of Computation in Drug Discovery.Sciencearticle2,211
2008Performance of the B3LYP Density Functional Method for a Large Set of Organic Molecules.Journal of Chemical Theory and Computationarticle2,060
2017LigParGen web server: An automatic OPLS-AA parameter generator for organic molecules.Nucleic Acids Researcharticle2,056
2005Potential energy functions for atomic-level simulations of water, and organic and biomolecular systems.Proceedings of the National Academy of Sciencesarticle1,966
2015Accurate and Reliable Prediction of Relative Ligand Binding Potency in Prospective Drug Discovery by Way of a Modern Free-Energy Calculation Protocol and Force…Journal of the American Chemical Societyarticle1,539
1986Optimized Intermolecular Potential Functions for Liquid Alcohols.The Journal of Physical Chemistryarticle1,518
1981Transferable Intermolecular Potential Functions for Water, Alcohols, and Ethers. Application to Liquid Water.Journal of the American Chemical Societyarticle1,503
1990Aromatic-Aromatic Interactions: Free Energy Profiles for the Benzene Dimer in Water, Chloroform, and Liquid Benzene.Journal of the American Chemical Societyarticle1,499
1985Temperature and Size Dependence for Monte Carlo Simulations of TIP4P Water.Molecular Physicsarticle1,132
2002Prediction of Drug Solubility from Structure.Advanced Drug Delivery Reviewsarticle1,128
2015Improved Peptide and Protein Torsional Energetics with the OPLS-AA Force FieldJournal of Chemical Theory and Computationarticle1,034
1973The Organic Chemist's Book of Orbitalsbook1,034
2017Localized Bond Charge Corrected CM1A Charges for Condensed-Phase Simulations.The Journal of Physical Chemistry Barticle1,010
1985Monte Carlo Simulation of Differences in Free Energies of Hydration.The Journal of Chemical Physicsarticle978
1997The OPLS All-Atom Force Field for CarbohydratesJournal of Computational Chemistryarticle954
2009Efficient Drug Lead Discovery and Optimization.Accounts of Chemical Researcharticle880
1989Free energy calculations: a breakthrough for modeling organic chemistry in solutionAccounts of Chemical Researcharticle871
1991OPLS Potential Functions for Nucleotide Bases. Relative Association Constants of Hydrogen-Bonded Base Pairs in Chloroform.Journal of the American Chemical Societyarticle835
2002Energy component analysis for dilute aqueous solutions of lithium (1+), sodium (1+), fluoride (1-), and chloride (1-) ionsJournal of the American Chemical Societyarticle814
1999OPLS All-Atom Model for Amines: Resolution of the Amine Hydration ProblemJournal of the American Chemical Societyarticle810
1990The Importance of Secondary Interactions in Triply Hydrogen-Bonded Complexes: Guanine-Cytosine vs. Uracil-Diaminopyridine.Journal of the American Chemical Societyarticle783
2012Targeting the von Hippel-Landau E3 Ubiquitin Ligase using Small Molecules to Disrupt the VHL/HIF-1α Interaction.Journal of the American Chemical Societyarticle742
1982Revised TIPS for Simulations of Liquid Water and Aqueous Solutions.The Journal of Chemical Physicsarticle678
2001Gas-Phase and Liquid-State Properties of Esters, Nitriles, and Nitro Compounds with the OPLS-AA Force FieldJournal of Computational Chemistryarticle628
1990Relative Partition Coefficients for Organic Solutes from Fluid Simulations.The Journal of Physical Chemistryarticle621
2000Prediction of Properties from Simulations: Free Energies of Solvation in Hexadecane, Octanol, and WaterJournal of the American Chemical Societyarticle616
2001Perfluoroalkanes: Conformational Analysis and Liquid-State Properties from Ab Initio and Monte Carlo Calculations.The Journal of Physical Chemistry Aarticle615
1998Temperature Dependence of TIP3P, SPC, and TIP4P Water from NPT Monte Carlo Simulations: Seeking a Temperature of Maximum DensityJournal of Computational Chemistryarticle573
2006Halide, Ammonium, and Alkali Metal Ion Parameters for Modeling Aqueous Solutions.Journal of Chemical Theory and Computationarticle551
1983Quantum and statistical mechanical studies of liquids. 25. Solvation and conformation of methanol in waterJournal of the American Chemical Societyarticle548
2005Molecular Modeling of Organic and Biomolecular Systems Using BOSS and MCPRO.Journal of Computational Chemistryarticle535
1985Theoretical Examination of the SN2 Reaction Involving Chloride Ion and Methyl Chloride in the Gas Phase and Aqueous Solution.Journal of the American Chemical Societyarticle522
1998Ab Initio Calculations on Hydrogen-Bonded Complexes of Small Organic Molecules with WaterThe Journal of Physical Chemistry Aarticle507
2000Prediction of Drug Solubility from Monte Carlo SimulationsBioorganic & Medicinal Chemistry Lettersarticle496
1985Optimized Intermolecular Potential Functions for Amides and Peptides. Structure and Properties of Liquid Amides.Journal of the American Chemical Societyarticle479
2012Methyl Effects on Protein-Ligand Binding.Journal of Medicinal Chemistryarticle460
2001Diffusion constant of the TIP5P model of liquid waterThe Journal of Chemical Physicsarticle458
1994Free Energies of Hydration and Pure Liquid Properties of Hydrocarbons from the OPLS All-Atom ModelThe Journal of Physical Chemistryarticle431
2012Small Molecule Inhibitors of the Interaction between the E3 Ligase VHL and HIF1α.Angewandte Chemie International Editionarticle420
2008Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria.Journal of Chemical Theory and Computationarticle418
1986Monte Carlo Simulations of the Hydration of Ammonium and Carboxylate Ions.The Journal of Physical Chemistryarticle415
1998Development of an All-Atom Force Field for Heterocycles. Properties of Liquid Pyrrole, Furan, Diazoles, and OxazolesThe Journal of Physical Chemistry Barticle413
2002PDDG/PM3 and PDDG/MNDO: Improved Semiempirical Methods.Journal of Computational Chemistryarticle409
1988Efficient Computation of Absolute Free Energies of Binding by Computer Simulations. Application to the Methane Dimer in Water.The Journal of Chemical Physicsarticle397
1985Magnitude and Origin of the ß-Silicon Effect on Carbenium Ions.Journal of the American Chemical Societyarticle392
1996Performance of the AMBER94, MMFF94, and OPLS-AA Force Fields for Modeling Organic LiquidsThe Journal of Physical Chemistryarticle374
1991Rusting of the Lock and Key Model of Protein-Ligand Binding.Sciencearticle369
2000Developing a Dynamic Pharmacaphore Model for HIV-1 IntegraseJournal of Medicinal Chemistryarticle359
1979An Intermolecular Potential Function for the Methanol Dimer from Ab Initio Calculations.ChemInformarticle356
1984SN2 Reaction Profiles in the Gas Phase and Aqueous Solution.Journal of the American Chemical Societyarticle336
1998Development of an All-Atom Force Field for Heterocycles. Properties of Liquid Pyridine and DiazenesJournal of Molecular Structure THEOCHEMarticle332
1985Additions and Corrections - Optimized Intermolecular Potential Functions for Amides and Peptides. Hydration of Amides.Journal of the American Chemical Societyarticle324
1995An Extended Linear Response Method for Determining Free Energies of HydrationThe Journal of Physical Chemistryarticle316
1988Cis/Trans Energy Difference for the Peptide Bond in the Gas Phase and Aqueous Solution.Journal of the American Chemical Societyarticle315
2006Contribution of Conformer Focusing to the Uncertainty in Predicting Free Energies for Protein-Ligand Binding.Journal of Medicinal Chemistryarticle311
2009Energetics of Displacing Water Molecules from Protein Binding Sites: Consequences for Ligand Optimization.Journal of the American Chemical Societyarticle310
2010Advances in QM/MM Simulations for Organic and Enzymatic Reactions.Accounts of Chemical Researcharticle307
2012Treatment of Halogen Bonding in the OPLS-AA Force Field; Application to Potent Anti-HIV Agents.Journal of Chemical Theory and Computationarticle304
2021Potent non-covalent inhibitors of the main protease of SARS-CoV-2 from molecular sculpting of the drug parampanel guided by free-energy perturbation calculatio…ACS Central Sciencearticle300
1983Theoretical Studies of Medium Effects on Conformational Equilibria. (Feature Article)The Journal of Physical Chemistryarticle297
1991Solvent Effects on a Diels-Alder Reaction from Computer Simulations.Journal of the American Chemical Societyarticle292
1986Ab initio and Monte Carlo calculations for a nucleophilic addition reaction in the gas phase and in aqueous solutionJournal of the American Chemical Societyarticle285
1988Monte Carlo Simulations of Liquid Acetonitrile with a Three-Site Model.Molecular Physicsarticle283
1996Monte Carlo vs. Molecular Dynamics for Conformational SamplingThe Journal of Physical Chemistryarticle277
1990Structure and Basicity of Silyl Ethers: A Crystallographic and Ab Initio Inquiry into the Mode of Silicon-Oxygen Interactions.Journal of the American Chemical Societyarticle274
2005Discovery of a Potent, Selective, and Efficacious Class of Reversible α-Ketoheterocycle Inhibitors of Fatty Acid Amide Hydrolase Effective as Analgesics.Journal of Medicinal Chemistryarticle272
1991Molecular Dynamics Simulations of the Unfolding of an -Helical Analog of Ribonuclease-A S-Peptide in Water.Biochemistryarticle268
2014The Many Faces of Halogen Bonding: A Review of Theoretical Models and MethodsWiley Interdisciplinary Reviews Computational Molecular Sci…article262
1992Effects of Hydration on the Claisen Rearrangement of Allyl Vinyl Ether from Computer Simulations.Journal of the American Chemical Societyarticle258
2004Free Energies of Hydration from a Generalized Born Model and an All-Atom Force Field.The Journal of Physical Chemistry Barticle255
1989Free Energy of TIP4P Water and the Free Energies of Hydration of CH4 and Cl- from Statistical Perturbation Theory.Chemical Physicsarticle252
2009Prediction of the Water Content in Protein Binding Sites.The Journal of Physical Chemistry Barticle248
2020Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2.ACS Medicinal Chemistry Lettersarticle244
1985Monte Carlo Simulations of Alkanes in Water: Hydration Numbers and the Hydrophobic Effect.The Journal of Physical Chemistryarticle244
2010A Remote Arene Binding Site on Prostate Specific Membrane Antigen Revealed by Antibody-Recruiting Small Molecules.Journal of the American Chemical Societyarticle242
1997Molecular Dynamics of the Unfolding of Barnase in Water and 8M Aqueous UreaBiochemistryarticle229
1993Monte Carlo Simulations of Pure Liquid Substituted Benzenes with OPLS Potential Functions.Journal of Computational Chemistryarticle228
1993Ab Initio Study of Diels-Alder Reactions of Cyclopentadiene with Ethylene, Isoprene, Cyclopentadiene, Acrylonitrile, and Methyl Vinyl Ketone.Journal of the American Chemical Societyarticle226
2005Elucidation of Fatty Acid Amide Hydrolase Inhibition by Potent α-Ketoheterocycle Derivatives from Monte Carlo SimulationsJournal of the American Chemical Societyarticle225
2004Steric Retardation of SN2 Reactions in the Gas Phase and Solution.Journal of the American Chemical Societyarticle223
1997Binding Affinities for Sulfonamide Inhibitors with HumanThrombin using Monte Carlo Simulations with a Linear Response MethodJournal of Medicinal Chemistryarticle221
1993Monte Carlo Simulations of the Hydration of Substituted Benzenes with OPLS Potential Functions.Journal of Computational Chemistryarticle219
2002QM/MM Simulations of Cycloaddition Reactions in Water: Contribution of Enhanced Hydrogen Bonding at the Transition State to the Solvent Effects.The Journal of Physical Chemistry Barticle213
1981Transferable Intermolecular Potential Functions. Application to Liquid Methanol Including Internal Rotation.Journal of the American Chemical Societyarticle208
1985Energy Profile for a Non-Concerted SN2 Reaction in Solution.Journal of the American Chemical Societyarticle203
1994Enhanced Hydrogen Bonding of Water to Diels-Alder Transition States - Ab Initio Evidence.The Journal of Organic Chemistryarticle202
1997Computational Approaches to Molecular RecognitionCurrent Opinion in Chemical Biologyarticle201
1993Accuracy of Free Energies of Hydration for Organic Molecules from 6-31G* Derived Partial Charges.Journal of Computational Chemistryarticle201
1991Monte Carlo Simulations of Liquid Acetic Acid and Methyl Acetate with the OPLS Potential Functions.The Journal of Physical Chemistryarticle200
2001Quantum, intramolecular flexibility, and polarizability effects on the reproduction of the density anomaly of liquid water by simple potential functions.The Journal of Chemical Physicsarticle197
1980Quantum and statistical mechanical studies of liquids. 7. Structure and properties of liquid methanolJournal of the American Chemical Societyarticle197
1990Monte Carlo Simulations of Liquid Alkyl Ethers with the OPLS Potential Functions.Journal of Computational Chemistryarticle196
1993Do Denaturants Interact with Aromatic Hydrocarbons in Water?Journal of the American Chemical Societyarticle194
1980Computer Assisted Mechanistic Evaluation of Organic Reactions, l. Overview.The Journal of Organic Chemistryarticle194
1986Intermolecular potential functions and Monte Carlo simulations for liquid sulfur compoundsThe Journal of Physical Chemistryarticle193
1989A Priori pKa Calculations and the Hydration of Organic Anions.Journal of the American Chemical Societyarticle187
2016Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density PartitioningJournal of Chemical Theory and Computationarticle182
1982Monte Carlo Simulation of n-Butane in Water. Conformational Evidence for the Hydrophobic Effect.The Journal of Chemical Physicsarticle180
2009Chemical Control Over Immune Recognition: A Class of Antibody-Recruiting Small Molecules (ARMs) that Target Prostate Cancer.Journal of the American Chemical Societyarticle179
1990CAMEO: A Program for the Logical Prediction of the Products of Organic Reactions.Pure and Applied Chemistryarticle178
2004Accuracy of Free Energies of Hydration from CM1 and CM3 Atomic Charges.Journal of Computational Chemistryarticle169
2000Analysis of Binding Affinities for Celecoxib Analogs with COX-1 and COX-2 from Docking and Monte Carlo Simulations and Insight into COX-2/COX-1 SelectivityJournal of the American Chemical Societyarticle169
1989Ab Initio Investigation of the ß-Silicon Effect on Alkyl and Cyclopropyl Carbenium Ions and Radicals.Journal of the American Chemical Societyarticle169
1987Network Topology in Simulated Water.The Journal of Physical Chemistryarticle169
2006Comparison of SCC-DFTB and NDDO-Based Semiempirical Molecular Orbital Methods for Organic Molecules.The Journal of Physical Chemistry Aarticle168
2001New Linear Interaction Method for Binding Affinity Calculations Using a Continuum Solvent Model.The Journal of Physical Chemistry Barticle167
1986Ab Initio Study of the Structures and Binding Energies of Anion-Water Complexes.Journal of the American Chemical Societyarticle165
1993Molecular Dynamics Simulations of the Unfolding of Apomyoglobin in Water.Biochemistryarticle164
1987Hydration and energetics for tert-butyl chloride ion pairs in aqueous solutionJournal of the American Chemical Societyarticle164
1987A Priori Calculations of pKa's for Organic Compounds in Water. The pKa of Ethane.Journal of the American Chemical Societyarticle163
2006Computer-Aided Design of Non-Nucleoside Inhibitors of HIV-1 Reverse Transcriptase.Bioorganic & Medicinal Chemistry Lettersarticle162
2005Macrophomate Synthase: QM/MM Simulations Address the Diels-Alder versus Michael-Aldol Reaction Mechanism.Journal of the American Chemical Societyarticle162
2009Discovery of Human Macrophage Migration Inhibitory Factor (MIF)-CD74 Antagonists via Virtual Screening.Journal of Medicinal Chemistryarticle161
1989Substituent Effects and Transition Structures for Diels-Alder Reactions of Butadiene and Cyclopentadiene with Cyanoalkenes.Journal of the American Chemical Societyarticle160
1992Solvent Effects on the Barrier to Isomerization for a Tertiary Amide from Ab Initio and Monte Carlo Calculations.Journal of the American Chemical Societyarticle156
2007Why Urea Eliminates Ammonia Rather Than Hydrolyzes in Aqueous Solution.The Journal of Physical Chemistry Barticle155
1997Computational Investigations of Carbenium Ion Reactions Relevant to Sterol BiosynthesisJournal of the American Chemical Societyarticle151
1989Energetics and Hydration of the Constituent Ion Pairs of Tetramethylammonium Chloride.Journal of the American Chemical Societyarticle151
2011Computationally-Guided Optimization of a Docking Hit to Yield Catechol Diethers as Potent Anti-HIV Agents.Journal of Medicinal Chemistryarticle150
2007Special issue on polarizationJournal of Chemical Theory and Computationarticle146
1983The Origin and Consequences of Alkene Pyramidalization in Ground and Triplet Excited States.Journal of the American Chemical Societyarticle146
1998A QM/MM Method Based on CM1A Charges: Applications to Solvent Effects on Organic Equilibria and ReactionsThe Journal of Physical Chemistry Barticle143
2013Characterization of Biaryl Torsional Energetics and its Treatment in OPLS All-Atom Force Fields.Journal of Chemical Information and Modelingarticle141
2005Relationship between side chain structure and 14-helix stability of β3-peptides in water.Journal of the American Chemical Societyarticle140
1993Urea: Potential Functions, log P, and Free Energy of Hydration.Israel Journal of Chemistryarticle140
1982The Nature of Dilute Solutions of Sodium Ion in Water, Methanol, and THF.The Journal of Chemical Physicsarticle139
1997Monte Carlo Simulations for Proteins: Binding Affinities for Trypsin-Benzamidine Complexes via Free Energy PerturbationsThe Journal of Physical Chemistry Barticle137
2001Estimation of Binding Affinities for HEPT and Nevirapine Analogs with HIV-1 Reverse Transcriptase via Monte Carlo SimulationsJournal of Medicinal Chemistryarticle134
1990Molecular Dynamics of Proteins with the OPLS Potential Functions. Simulation of the Third Domain of Silver Pheasant Ovomucoid in WaterJournal of the American Chemical Societyarticle133
1984An Improved Intermolecular Potential Function for Simulations of Liquid Hydrogen Fluoride.Molecular Physicsarticle132
1980The Structure and Properties of Liquid Ammonia.Journal of the American Chemical Societyarticle130
1993Molecular Dynamics and Monte Carlo Simulations Favor the -Helical Form for Alanine-based Peptides in Water.Journal of the American Chemical Societyarticle127
2006Conformation of Alkanes in the Gas Phase and Pure Liquids.The Journal of Physical Chemistry Barticle126
2019Development and Testing of the OPLS-AA/M Force Field for RNA.Journal of Chemical Theory and Computationarticle124
JD Madura, RW Inpeyarticle124
1994Investigation of Solvent Effects on Pericyclic Reactions by Computer SimulationsJournal of the Chemical Society Faraday Transactionsarticle122
1982Ab Initio Study of Acid-Base Interactions. Proton, Lithium and Sodium Affinities of First and Second Row Bases.The Journal of Physical Chemistryarticle121
1998Prediction of Binding Affinities for TIBO Inhibitors of HIV-1 Reverse Transcriptase Using Monte Carlo Simulations in a Linear Response MethodJournal of Medicinal Chemistryarticle120
1989Interactions Between Amides in Solution and the Thermodynamics of Weak Binding.Journal of the American Chemical Societyarticle120
2004Solvent Effects and Mechanism for a Nucleophilic Aromatic Substitution from QM/MM Simulations.Organic Lettersarticle119
2008Catalytic Mechanism and Performance of Computationally Designed Enzymes for Kemp Elimination.Journal of the American Chemical Societyarticle118
1981Structures and Properties of Organic Liquids: n-Butane and 1,2-Dichloroethane and Their Conformational Equilibria.Journal of the American Chemical Societyarticle118
1997Free Energies of Solvation in Chloroform and Water from a Linear Response ApproachJournal of Physical Organic Chemistryarticle117
1999Host-Guest Chemistry of Rotaxanes and Catenanes: Application of a Polarizable All- Atom Force Field to Cyclobis(paraquat-p-phenylene) Complexes with Disubstitu…Journal of the Chemical Society Perkin Transactions 2article116
1983Impey RW and Klein MLThe Journal of Chemical Physicsarticle115
2006FEP-Guided Selection of Bicyclic Heterocycles in Lead Optimization for Non-Nucleoside Inhibitors of HIV-1 Reverse TranscriptaseJournal of the American Chemical Societyarticle113
2004Extension of the PDDG/PM3 and PDDG/MNDO Semiempirical Molecular Orbital Methods to the Halogens.Journal of Computational Chemistryarticle113
1993Limited Effects of Polarization for Cl-(H2O)n and Na+(H2O)n Clusters.The Journal of Chemical Physicsarticle113
2003Monte Carlo backbone sampling for polypeptides with variable bond angles and dihedral angles using concerted rotations and a Gaussian bias.The Journal of Chemical Physicsarticle112
2013Picomolar Inhibitors of HIV Reverse Transcriptase Featuring Bicyclic Replacement of a Cyanovinylphenyl GroupJournal of the American Chemical Societyarticle111
2008Optimization of Azoles as Anti-HIV Agents Guided by Free-Energy Calculations.Journal of the American Chemical Societyarticle111
1991Computational Insights on Intermolecular Interactions and Binding in Solution.article111
1987Use of Statistical Perturbation Theory for Computing Solvent Effects on Molecular Conformation. Butane in Water.The Journal of Physical Chemistryarticle111
2014Wiley Interdisciparticle109
2002Prediction of Activity for Non-nucleoside Inhibitors with HIV Reverse Transcriptase Based on Monte Carlo Simulations.Journal of Medicinal Chemistryarticle109
2007Polarization Effects for Hydrogen-Bonded Complexes of Substituted Phenols with Water and Chloride Ion.Journal of Chemical Theory and Computationarticle108
2006Cope Elimination: Elucidation of Solvent Effects from QM/MM Simulations.Journal of the American Chemical Societyarticle108
1997Elucidation of Transition Structures and Solvent Effects for Epoxidations by DimethyldioxiraneJournal of the American Chemical Societyarticle108
1987Ab initio study of the SN2 reactions of hydroxide and hydroperoxide with chloromethaneJournal of the American Chemical Societyarticle108
2007Understanding Rate Accelerations for Diels-Alder Reactions in Solution using Enhanced QM/MM Methodology.Journal of Chemical Theory and Computationarticle106
2007Search for Non-Nucleoside Inhibitors of HIV-1 Reverse Transcriptase using Chemical Similarity, Molecular Docking, and MM-GB/SA Scoring.Journal of Chemical Information and Modelingarticle104
1991Chemical Chameleons: Hydrogen Bonding with Imides and Lactams in Chloroform.Journal of the American Chemical Societyarticle104
2005Extension of the PDDG/PM3 semiempirical molecular orbital method to sulfur, silicon, and phosphorus.Journal of Chemical Theory and Computationarticle101
2003Validation of a Model for the Complex of HIV-1 Reverse Transcriptase with the Novel Non-nucleoside Inhibitor TMC125.Journal of the American Chemical Societyarticle101
2015Design, Synthesis, and Protein Crystallography of Biaryltriazoles as Potent Tautomerase Inhibitors of Macrophage Migration Inhibitory FactorJournal of the American Chemical Societyarticle100
2010Effects of Water Placement on Predictions of Binding Affinities for p38α MAP Kinase Inhibitors.Journal of Chemical Theory and Computationarticle99
1995An Empirical Boundary Potential for Water Droplet SimulationsJournal of Computational Chemistryarticle99
1988Theoretical Examination of Hexanol-Water Interfaces.The Journal of Physical Chemistryarticle99
1981Simulation of Liquid Ethanol Including Internal Rotation.Journal of the American Chemical Societyarticle99
2010Mif modulatorsarticle98
2007Elucidation of Rate Variations for a Diels-Alder Reaction in Ionic Liquids from QM/MM Simulations.Journal of Chemical Theory and Computationarticle98
1999Estimation of the Binding Affinities of FKBP12 Inhibitors Using a Linear Response MethodBioorganic & Medicinal Chemistryarticle98
1995A Comprehensive Study of the Rotational Profiles of Some Organic Systems by Ab Initio MO Theory, Forming a Basis for Peptide Torsional ParametersJournal of Computational Chemistryarticle98
1982Convergence of Monte Carlo Simulations of Liquid Water in the NPT Ensemble.Chemical Physics Lettersarticle98
2013Limiting Cardiac Ischemic Injury by Pharmacological Augmentation of Macrophage Migration Inhibitory Factor–AMP-Activated Protein Kinase Signal TransductionCirculationarticle97
2004Polypeptide Folding using Monte Carlo Sampling, Concerted Rotation, and Continuum Solvation.Journal of the American Chemical Societyarticle95
1981Pressure Dependence of the Structure and Properties of Liquid n-Butane.Journal of the American Chemical Societyarticle95
2003Contributions of Conformational Compression and Preferential Transition State Stabilization to the Rate Enhancement by Chorismate Mutase.Journal of the American Chemical Societyarticle94
2006Elucidation of Hydrolysis Mechanisms for Fatty Acid Amide Hydrolase and Its Lys142Ala Variant.Journal of the American Chemical Societyarticle92
1995Dielectric Constants of Formamide and Dimethylformamide via Computer SimulationsThe Journal of Physical Chemistryarticle92
2025The need to implement FAIR principles in biomolecular simulationsNature Methodsarticle91
2011Efficient Discovery of Potent Anti-HIV Agents Especially Targeting the Tyr181Cys Variant of HIV Reverse Transcriptase.Journal of the American Chemical Societyarticle91
2015Molecular Dynamics and Monte Carlo Simulations for Protein-Ligand Binding and Inhibitor DesignBiochimica et Biophysica Acta (BBA) - General Subjectsarticle90
2015Evaluation of CM5 Charges for Nonaqueous Condensed-Phase ModelingJournal of Chemical Theory and Computationarticle90
2015Illustrating Concepts in Physical Organic Chemistry with 3D Printed OrbitalsJournal of Chemical Educationarticle89
2014Evaluation of CM5 Charges for Condensed-Phase ModelingJournal of Chemical Theory and Computationarticle89
2010Optimization of N-benzyl-benzoxazol-2-ones as receptor antagonists of macrophage migration inhibitory factor (MIF).Bioorganic & Medicinal Chemistry Lettersarticle88
1995The Importance of Polarization for Dipolar Solutes in Low-Dielectric Media: 1,2- Dichloroethane and Water in CyclohexaneJournal of the American Chemical Societyarticle77
2009Steric and Solvation Effects in Ionic SN2 Reactions.Journal of the American Chemical Societyarticle76
2013Exploring Adsorption of Water and Ions on Carbon Surfaces using a Polarizable Force Field.The Journal of Physical Chemistry Lettersarticle69
2009In silico improvement of β3-peptide inhibitors of p53•hDM2 and p53•hDMX.Journal of the American Chemical Societyarticle68
2012Role of macrophage migration inhibitory factor in the regulatory T-cell response of tumor-bearing mice.The Journal of Immunologyarticle66
2007From Docking False-Positive to Active Anti-HIV Agent.Journal of Medicinal Chemistryarticle66
1990Computer-Assisted Mechanistic Evaluation of Organic Reactions, 17. Free Radical Chain Reactions.The Journal of Organic Chemistryarticle66
1978Monte Carlo Simulations of Liquid Hydrogen Fluoride.Journal of the American Chemical Societyarticle66
2010QM/MM Modeling Finds Diels-Alder Reactions are Accelerated Less On Water than In Water.Journal of the American Chemical Societyarticle65
2010Discovery of Novel FGFR1 Kinase Inhibitors by Structure-Based Virtual Screening.Journal of Medicinal Chemistryarticle64
2021Structural insights into a novel perampanel-derived pharmacophore targeting the SARS- CoV-2 main protease.Structurearticle63
1998Monte Carlo Investigations of Selective Anion Complexation by a Bis(phenylurea)-p- tert-Butylcalix(4]areneJournal of the American Chemical Societyarticle63
2016Computer-Aided Discovery of Anti-HIV AgentsBioorganic & Medicinal Chemistryarticle62
2009Exploiting structural analysis, in silico screening, and serendipity to identify novel inhibitors of drug-resistant falciparum malaria.ACS Chemical Biologyarticle62
1979Deriving Intermolecular Potential Functions for the Water Dimer from Ab Initio Calculations.Journal of the American Chemical Societyarticle62
2010Exploring Solvent Effects on the Menshutkin Reaction using a Polarizable Force Field.The Journal of Physical Chemistry Barticle61
1993Comparison of 6-31G* Based MST/SCRF and FEP Evaluations of the Free Energies of Hydration for Small Neutral Molecules.Journal of Computational Chemistryarticle61
1989Variational Transition State for the Reaction of Cl2C: with Ethylene and the Thermodynamics of Carbene Additions.Journal of the American Chemical Societyarticle61
2012Challenges for Academic Drug Discovery.Angewandte Chemie International Editionarticle60
1982Quantum and statistical mechanical studies of liquids. 20. Pressure dependence of hydrogen bonding in liquid methanolJournal of the American Chemical Societyarticle60
1998Conformational Complexity of Succinic Acid and Its Monoanion in the Gas Phase and in Solution: Ab Initio Calculations and Monte Carlo SimulationsJournal of the American Chemical Societyarticle59
2021Optimization of Triarylpyridinone Inhibitors of the Main Protease of SARS-CoV-2 to Low-Nanomolar Antiviral Potency.ACS Medicinal Chemistry Lettersarticle58
1987Ab Initio Study of the Displacement Reactions of Chloride Ion with Formyl and Acetyl Chloride.Journal of the American Chemical Societyarticle58
2005Influence of Inter- and Intramolecular Hydrogen Bonding on Kemp Decarboxylations from QM/MM Simulations.Journal of the American Chemical Societyarticle57
2000Validation of a Model for the Complex of HIV-1 Reverse Transcriptase with Sustiva through Computation of Resistance ProfilesJournal of the American Chemical Societyarticle56
1996Monte Carlo Investigations of Solvent Effects on the Chorismate to Prephenate RearrangementJournal of the American Chemical Societyarticle56
1994Solvent Effects on the Ring Opening of Cyclopropanones to Oxyallyls - A Combined Ab Initio and Monte Carlo StudyJournal of the American Chemical Societyarticle56
2004Monte Carlo Backbone Sampling for Nucleic Acids using Concerted Rotations including Variable Bond Angles.The Journal of Physical Chemistry Barticle55
1981Structures and Properties of Organic Liquids: n-Alkyl Ethers and Their Conformational Equilibria.Journal of the American Chemical Societyarticle55
1978An Intermolecular Potential Function for the HF Dimer from Ab Initio 6-3lG Computations.Journal of the American Chemical Societyarticle55
2012Crystal Structures of HIV-1 Reverse Transcriptase with Picomolar Inhibitors Reveal Key Interactions for Drug Design.Journal of the American Chemical Societyarticle54
2006Optimization of Pyrimidinyl- and Triazinyl-amines as Non-Nucleoside Inhibitors of HIV-1 Reverse Transcriptase.Bioorganic & Medicinal Chemistry Lettersarticle54
1982Quantum and statistical mechanical studies of liquids. 21. The nature of dilute solutions of sodium and methoxide ions in methanolJournal of the American Chemical Societyarticle54
1992Computer-Assisted Mechanistic Analysis of Organic Reactions. 20. Ene and Retro-ene Chemistry.The Journal of Organic Chemistryarticle53
1982Monte Carlo Simulations of Liquid Tetrahydrofuran Including Pseudorotation.The Journal of Chemical Physicsarticle53
1980Monte Carlo Results for Hydrogen Bond Distributions in Liquid Water.Chemical Physics Lettersarticle53
2010Pulled from a protein’s embrace.Naturearticle52
2003Investigation of Solvent Effects for the Claisen Rearrangement of Chorismate to Prephenate: Mechanistic Interpretation via Near Attack Conformations.Journal of the American Chemical Societyarticle52
1995The Energy Difference Between the Classical and the Nonclassical 2-Norbornyl Cation in Solution. A Combined Ab Initio - Monte Carlo StudyJournal of the American Chemical Societyarticle52
1990Origin of the Strong Binding of Adenine to a Molecular Tweezer.Journal of the American Chemical Societyarticle52
2018Advances and Insights for Small Molecule Inhibition of Macrophage Migration Inhibitory Factor.Journal of Medicinal Chemistryarticle51
2017Covalent inhibitors for eradication of drug-resistant HIV-1 reverse transcriptase: from design to protein crystallography.Proceedings of the National Academy of Sciencesarticle51
1994Monte Carlo Results for the Effect of Solvation on the Anomeric Equilibrium for 2- MethoxytetrahydropyranJournal of the American Chemical Societyarticle51
2013Automated ligand- and structure-based protocol for in silico prediction of Human Serum Albumin binding.Journal of Chemical Information and Modelingarticle50
2010Receptor agonists of macrophage migration inhibitory factor.Bioorganic & Medicinal Chemistry Lettersarticle50
2018Enhanced Monte Carlo Methods for Modeling Proteins Including Computation of Absolute Free Energies of Binding.Journal of Chemical Theory and Computationarticle49
2017Improved Description of Sulfur Anisotropy in OPLS Force Fields. Model Development and Parameterization.The Journal of Physical Chemistry Barticle49
2017Identification and Characterization of Small Molecules Binding to the JAK2 Pseudokinase Domain.ACS Medicinal Chemistry Lettersarticle49
2015Structure-based Evaluation of Non-nucleoside Inhibitors with Improved Potency and Solubility that Target HIV Reverse Transcriptase VariantsJournal of Medicinal Chemistryarticle49
2013Small Molecular Modulation of Macrophage Migration Inhibitory Factor (MIF) in the Hyperoxia-Induced Mouse Model of Bronchopulmonary Dysplasia.Respiratory Researcharticle49
2015Endothelial CD74 mediates macrophage migration inhibitory factor protection in hyperoxic lung injuryThe FASEB Journalarticle48
2004General Model for Estimation of the Inhibition of Protein Kinases Using Monte Carlo Simulations.Journal of Medicinal Chemistryarticle47
2016A Fluorescence Polarization Assay for Binding to Macrophage Migration Inhibitory Factor and Crystal Structures for Two Potent ComplexesJournal of the American Chemical Societyarticle46
2011Improving MM-GB/SA Scoring through the Application of the Variable Dielectric Model.Journal of Chemical Theory and Computationarticle46
2008Optical Rotatory Dispersion of 2,3-Hexadiene and 2,3-Pentadiene.The Journal of Physical Chemistry Aarticle46
2006Optimization of Diarylamines as Non-Nucleoside Inhibitors of HIV-1 Reverse Transcriptase.Bioorganic & Medicinal Chemistry Lettersarticle45
1995Free Energies of Hydration for Organic Molecules from Monte Carlo SimulationsPerspectives in Drug Discovery and Designarticle45
1981Sampling Methods for Monte Carlo Simulations of n-Butane in Dilute Solution.The Journal of Chemical Physicsarticle44
2017Systematic Study of Effects of Structural Modifications on the Aqueous Solubilities of Drug-like Molecules.ACS Medicinal Chemistry Lettersarticle43
2014Enhanced Monte Carlo Sampling through Replica Exchange with Solute TemperingJournal of Chemical Theory and Computationarticle43
2014Picomolar Inhibitors of HIV-1 Reverse Transcriptase: Design and Crystallography of Naphthyl Phenyl EthersACS Medicinal Chemistry Lettersarticle43
1986Effect of hydration on the structure of an SN2 transition stateThe Journal of Physical Chemistryarticle43
1975Chemical Consequences of Orbital Interactions. II. Ethylene and Butadiene Bridged Polycyclic Hydrocarbons Contain Three- and Four-Membered Rings.Journal of the American Chemical Societyarticle43
2013Polarized Protein-Specific Charges from AIM Electron Density Partitioning.Journal of Chemical Theory and Computationarticle42
2006NO-MNDO: Reintroduction of the Overlap Matrix into MNDO.Journal of Chemical Theory and Computationarticle42
1976Computer-Assisted Synthetic Analysis. Synthetic Strategies Based on Appendages and the Use of Reconnective Transforms.Journal of the American Chemical Societyarticle42
2001Antiviral Drug Design: Computational Analyses of the Effects of the L100I Mutation for HIV-RT on the Binding of NNRTIs.Bioorganic & Medicinal Chemistry Lettersarticle41
1993Mechanism for the Rotamase Activity of FK506 Binding Protein from Molecular Dynamics Simulations.Biochemistryarticle41
2013Extension into the entrance channel of HIV-1 reverse transcriptase—Crystallography and enhanced solubilityBioorganic & Medicinal Chemistry Lettersarticle40
1995Elucidation of Transition States and Solvent Effects for the Mislow-Evans Rearrangement of Allylic SulfoxidesJournal of the American Chemical Societyarticle40
2003Molecular Modeling Calculations of HIV-1 Reverse Transcriptase Nonnucleoside Inhibitors: Correlation of Binding Energy with Biological Activity for Novel 2-Ary…Journal of Medicinal Chemistryarticle39
1976The Cyclic Structure of Monomeric Dilithioacetylene.Tetrahedron Lettersarticle39
2020Explicit Representation of Cation-π Interactions in Force Fields with 1/r4 Non-bonded Terms.Journal of Chemical Theory and Computationarticle38
2013Foundations of Biomolecular ModelingCellarticle38
2009Discovery of Wild-type and Y181C Mutant Non-nucleoside HIV-1 Reverse Transcriptase Inhibitors Using Virtual Screening with Multiple Protein Structures.Journal of Chemical Information and Modelingarticle38
2006Medium Effects on the Decarboxylation of a Biotin Model in Pure and Mixed Solvents from QM/MM Simulations.The Journal of Organic Chemistryarticle38
2001Estimation of Binding Affinities for Selective Thrombin Inhibitors via Monte Carlo SimulationsJournal of Medicinal Chemistryarticle38
1986Computer Simulation of Chemical and Biomolecular Systems.PubMededited volume38
2018From In Silico Hit to Long-Acting Late-Stage Preclinical Candidate to Combat HIV Infection.Proceedings of the National Academy of Sciencesarticle36
2014Structural studies provide clues for analog design of specific inhibitors of Cryptosporidium hominis thymidylate synthase-dihydrofolate reductaseBioorganic & Medicinal Chemistry Lettersarticle36
2004Structural and Energetic Analyses for the Effects of the K103N Mutation of HIV-1 Reverse Transcriptase on Efavirenz Analogs.Journal of Medicinal Chemistryarticle36
2000Monte Carlo Calculations on HIV-1 Reverse Transcriptase Complexed with the Nonnucleoside Inhibitor 8-Cl TIBO: Contribution of the L100I and Y181C Variants to P…Protein Engineering Design and Selectionarticle36
1999Selective Anion Complexation by a Calix[4]pyrrole Investigated by Monte Carlo SimulationsThe Journal of Organic Chemistryarticle36
1997The Origin of Self-Assembling Ternary Complex Stabilities and Template Ratios in Carceplex FormationJournal of the American Chemical Societyarticle36
1994Synthesis and Investigations of Enetetraynes.Tetrahedronarticle36
1986Computer Simulations of Organic Reactions in SolutionaAnnals of the New York Academy of Sciencesarticle36
2013Optimization of diarylazines as anti-HIV agents with dramatically enhanced solubilityBioorganic & Medicinal Chemistry Lettersarticle35
2010Thorpe-Ingold Acceleration of Oxirane Formation is Mostly a Solvent Effect.Journal of the American Chemical Societyarticle35
1995Generalized Alteration of Structure and Parameters (GASP); a New Method for Free Energy Perturbations in Systems Containing Flexible and/or Fixed Degrees of Fr…Journal of Computational Chemistryarticle35
1970Structural and Energetic Predictions for Simple Hydrocarbons from the NDDO and CNDO Semiempirical Molecular Orbital Methods.Journal of the American Chemical Societyarticle35
2014Cooperative Effects and Optimal Halogen Bonding Motifs for Self-Assembling SystemsThe Journal of Physical Chemistry Aarticle34
2011On the Mechanism and Rate of Spontaneous Decomposition of Amino Acids.The Journal of Physical Chemistry Barticle34
2010Eastern extension of azoles as non-nucleoside inhibitors of HIV-1 reverse transcriptase; cyano group alternatives.Bioorganic & Medicinal Chemistry Lettersarticle34
2002Estimation of Binding Affinities for Celecoxib Analogues with COX-2 via Monte Carlo – Extended Linear Response.Bioorganic & Medicinal Chemistry Lettersarticle34
2018Molecular Dynamics Simulations of a Conformationally Mobile Peptide-Based Catalyst for Atroposelective Bromination.ACS Catalysisarticle33
2012Virtual Screening and Optimization Yield Low-Nanomolar Inhibitors of the Tautomerase Activity of Plasmodium falciparum MIF.Journal of Medicinal Chemistryarticle33
2010E/Z Energetics for Molecular Modeling and Design.Journal of Chemical Theory and Computationarticle33
2007Computation of Accurate Activation Barriers for Methyl Transfer Reactions of Sulfonium and Ammonium Salts in Aqueous Solution.Journal of Chemical Theory and Computationarticle33
1981Internal Rotation in Liquid 1,2-Dichloroethane and n-Butane.Journal of the American Chemical Societyarticle33
2005Effects of Arg90 Neutralization on the Enzyme-Catalyzed Rearrangement of Chorismate to Prephenate.Journal of Chemical Theory and Computationarticle32
1989Structure and Binding for Rebek's Diacid in Chloroform. A Demure Host for Pyrazine.Journal of the American Chemical Societyarticle32
1971Charge Density Analysis of Rotational Barriers.Journal of the American Chemical Societyarticle32
2019Computation of Protein-Ligand Binding Free Energies Using Quantum Mechanical Bespoke Force Fields.MedChemCommarticle31
2019Absolute Free Energy of Binding Calculations for Macrophage Migration Inhibitory Factor in Complex with a Drug-like Inhibitor.The Journal of Physical Chemistry Barticle31
2002Three- vs. Four-Coordinate Phosphorus in the Gas Phase and in Solution: Treacherous Relative Energies for Phosphine Oxide and Phosphinous Acid.The Journal of Chemical Physicsarticle31
2001Efficient Exploration of Conformational Space Using the Stochastic Search Method: Application to -Peptide OligomersJournal of Computational Chemistryarticle31

The 300 most cited are listed; 153 more are not.