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List of works by William L. Jorgensen

1.14*CM1A-LBCC: Localized Bond-Charge Corrected CM1A Charges for Condensed-Phase Simulations

scientific article

A Fluorescence Polarization Assay for Binding to Macrophage Migration Inhibitory Factor and Crystal Structures for Complexes of Two Potent Inhibitors

scientific article

A Reflection on Norman Louis Allinger

scientific article published on 17 March 2021

A five-site model for liquid water and the reproduction of the density anomaly by rigid, nonpolarizable potential functions

scientific article (publication date: 22 May 2000)

A mechanistic and structural investigation of modified derivatives of the diaryltriazine class of NNRTIs targeting HIV-1 reverse transcriptase

scientific article

A nanotherapy strategy significantly enhances anticryptosporidial activity of an inhibitor of bifunctional thymidylate synthase-dihydrofolate reductase from Cryptosporidium

scientific article published on 4 April 2015

A remote arene-binding site on prostate specific membrane antigen revealed by antibody-recruiting small molecules

scientific article

Absolute Free Energy of Binding Calculations for Macrophage Migration Inhibitory Factor in Complex with a Druglike Inhibitor

scientific article published on 07 October 2019

Accuracy of free energies of hydration using CM1 and CM3 atomic charges

scientific article

Accurate and reliable prediction of relative ligand binding potency in prospective drug discovery by way of a modern free-energy calculation protocol and force field

scientific article

Activity predictions for efavirenz analogues with the K103N mutant of HIV reverse transcriptase

scientific article published in October 2003

Adding a Hydrogen Bond May Not Help: Naphthyridinone vs Quinoline Inhibitors of Macrophage Migration Inhibitory Factor

scientific article published on 14 November 2017

Advances and Insights for Small Molecule Inhibition of Macrophage Migration Inhibitory Factor

scientific article published on 04 June 2018

Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions

scientific article

Analyses of activity for factor Xa inhibitors based on Monte Carlo simulations

scientific article published in December 2003

Application of a BOSS-Gaussian interface for QM/MM simulations of Henry and methyl transfer reactions

scientific article

Aryl extensions of thienopyrimidinones as fibroblast growth factor receptor 1 kinase inhibitors ⬇️

scientific article published on April 27, 2011

Assault on resistance: the use of computational chemistry in the development of anti-HIV drugs

scientific article

Automated Ligand- and Structure-Based Protocol forin SilicoPrediction of Human Serum Albumin Binding ⬇️

scientific article published on April 2, 2013

Benzisothiazolones as modulators of macrophage migration inhibitory factor ⬇️

scientific article published on June 12, 2011

Bifunctional inhibition of human immunodeficiency virus type 1 reverse transcriptase: mechanism and proof-of-concept as a novel therapeutic design strategy

scientific article published on 9 May 2013

Biochemical assays for the discovery of TDP1 inhibitors

scientific article

Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning

scientific article

Catalytic mechanism and performance of computationally designed enzymes for Kemp elimination

scientific article

Characterization of Biaryl Torsional Energetics and its Treatment in OPLS All-Atom Force Fields ⬇️

scientific article published on May 13, 2013

Chemical control over immune recognition: a class of antibody-recruiting small molecules that target prostate cancer

scientific article published on December 2009

Comparison of simple potential functions for simulating liquid water

scientific article

Computation of Accurate Activation Barriers for Methyl-Transfer Reactions of Sulfonium and Ammonium Salts in Aqueous Solution

scientific article published in May 2007

Computation of protein-ligand binding free energies using quantum mechanical bespoke force fields

scientific article published on 27 February 2019

Computationally-guided optimization of a docking hit to yield catechol diethers as potent anti-HIV agents

scientific article published on 29 November 2011

Computationally-guided optimization of small-molecule inhibitors of the Aurora A kinase-TPX2 protein-protein interaction

scientific article published on 8 August 2017

Computer-aided discovery of anti-HIV agents

scientific article

Computer-assisted mechanistic evaluation of organic reactions. 20. Ene and retro-ene chemistry

article

Confronting Racism in Chemistry Journals

scientific article published on 19 June 2020

Contribution of conformer focusing to the uncertainty in predicting free energies for protein-ligand binding

scientific article published in October 2006

Contributions of conformational compression and preferential transition state stabilization to the rate enhancement by chorismate mutase.

scientific article

Cooperative effects and optimal halogen bonding motifs for self-assembling systems

scientific article published on 08 April 2014

Covalent inhibitors for eradication of drug-resistant HIV-1 reverse transcriptase: From design to protein crystallography

scientific article

Crystal Structures of HIV-1 Reverse Transcriptase with Picomolar Inhibitors Reveal Key Interactions for Drug Design ⬇️

scientific article published on November 19, 2012

Design, Conformation, and Crystallography of 2-Naphthyl Phenyl Ethers as Potent Anti-HIV Agents

scientific article published on 31 October 2016

Design, synthesis, and protein crystallography of biaryltriazoles as potent tautomerase inhibitors of macrophage migration inhibitory factor

scientific article

Determination of partial molar volumes from free energy perturbation theory

scientific article published on 15 January 2015

Development and Testing of the OPLS-AA/M Force Field for RNA

scientific article published on 12 March 2019

Discovery and crystallography of bicyclic arylaminoazines as potent inhibitors of HIV-1 reverse transcriptase

scientific article

Discovery of Novel Fibroblast Growth Factor Receptor 1 Kinase Inhibitors by Structure-Based Virtual Screening

scientific article

Discovery of a potent, selective, and efficacious class of reversible alpha-ketoheterocycle inhibitors of fatty acid amide hydrolase effective as analgesics

scientific article published on March 2005

Discovery of dimeric inhibitors by extension into the entrance channel of HIV-1 reverse transcriptase

scientific article published on 5 January 2012

Discovery of human macrophage migration inhibitory factor (MIF)-CD74 antagonists via virtual screening

scientific article published on January 2009

Discovery of wild-type and Y181C mutant non-nucleoside HIV-1 reverse transcriptase inhibitors using virtual screening with multiple protein structures

scientific article

Drug discovery: Pulled from a protein's embrace

scientific article published in July 2010

E/Z Energetics for Molecular Modeling and Design ⬇️

scientific article published on September 14, 2010

Eastern extension of azoles as non-nucleoside inhibitors of HIV-1 reverse transcriptase; cyano group alternatives

scientific article

Effects of Water Placement on Predictions of Binding Affinities for p38α MAP Kinase Inhibitors

scientific article

Efficient Discovery of Potent Anti-HIV Agents Targeting the Tyr181Cys Variant of HIV Reverse Transcriptase ⬇️

scientific article published on September 9, 2011

Efficient drug lead discovery and optimization

scientific article published on June 2009

Elucidation of fatty acid amide hydrolase inhibition by potent alpha-ketoheterocycle derivatives from Monte Carlo simulations

scientific article

Elucidation of hydrolysis mechanisms for fatty acid amide hydrolase and its Lys142Ala variant via QM/MM simulations

scientific article published in December 2006

Endothelial CD74 mediates macrophage migration inhibitory factor protection in hyperoxic lung injury

scientific article published on 21 January 2015

Energetic effects for observed and unobserved HIV-1 reverse transcriptase mutations of residues L100, V106, and Y181 in the presence of nevirapine and efavirenz

scientific article

Energetic preferences for alpha,beta versus beta,gamma unsaturation

scientific article

Energetics of displacing water molecules from protein binding sites: consequences for ligand optimization

scientific article published on October 2009

Enhanced Monte Carlo Methods for Modeling Proteins Including Computation of Absolute Free Energies of Binding

scientific article published on 08 May 2018

Estimation of binding affinities for celecoxib analogues with COX-2 via Monte Carlo-extended linear response

scientific article published in February 2002

Evaluation of CM5 Charges for Condensed-Phase Modeling.

scientific article

Evaluation of CM5 Charges for Nonaqueous Condensed-Phase Modeling

scientific article published on 27 August 2015

Explicit Representation of Cation-π Interactions in Force Fields with 1/r4 Nonbonded Terms

scientific article published on 13 October 2020

Exploiting Structural Analysis, in Silico Screening, and Serendipity To Identify Novel Inhibitors of Drug-Resistant Falciparum Malaria

scientific article

Exploring Adsorption of Water and Ions on Carbon Surfaces Using a Polarizable Force Field ⬇️

scientific article published on January 17, 2013

Exploring solvent effects upon the Menshutkin reaction using a polarizable force field

scientific article

Extension into the entrance channel of HIV-1 reverse transcriptase—Crystallography and enhanced solubility

scientific article

Extension of the PDDG/PM3 Semiempirical Molecular Orbital Method to Sulfur, Silicon, and Phosphorus

scientific article published on January 2005

Foundations of biomolecular modeling

scientific article published on December 2013

From docking false-positive to active anti-HIV agent

scientific article

From in silico hit to long-acting late-stage preclinical candidate to combat HIV-1 infection.

scientific article published on 26 December 2017

General model for estimation of the inhibition of protein kinases using Monte Carlo simulations

scientific article published in May 2004

HIV-1 reverse transcriptase variants: molecular modeling of Y181C, V106A, L100I, and K103N mutations with nonnucleoside inhibitors using Monte Carlo simulations in combination with a linear response method

scientific article published in January 2003

Hydration Properties and Solvent Effects for All-Atom Solutes in Polarizable Coarse-Grained Water

scientific article published on 22 February 2016

Identification and Characterization of JAK2 Pseudokinase Domain Small Molecule Binders.

scientific article published on 17 May 2017

Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2

scientific article published on 28 August 2020

Improved Description of Sulfur Charge Anisotropy in OPLS Force Fields: Model Development and Parameterization

scientific article published on 19 June 2017

Improved Peptide and Protein Torsional Energetics with the OPLSAA Force Field

scientific article published in June 2015

Improved Treatment of Nucleosides and Nucleotides in the OPLS-AA Force Field

scientific article published on 16 February 2017

Improving MM-GB/SA Scoring through the Application of the Variable Dielectric Model ⬇️

scientific article published on November 14, 2011

In Silico Improvement of beta3-peptide inhibitors of p53 x hDM2 and p53 x hDMX

scientific article published on May 2009

Influence of inter- and intramolecular hydrogen bonding on kemp decarboxylations from QM/MM simulations

scientific article published in June 2005

Introducing the Journal of Chemical Theory and Computation

scientific article published in January 2005

Investigation of Solvent Effects on the Rate and Stereoselectivity of the Henry Reaction ⬇️

scientific article published on December 14, 2011

Investigation of solvent effects for the Claisen rearrangement of chorismate to prephenate: mechanistic interpretation via near attack conformations

scientific article published in June 2003

Irregularities in enzyme assays: The case of macrophage migration inhibitory factor

scientific article

JAK2 JH2 Fluorescence Polarization Assay and Crystal Structures for Complexes with Three Small Molecules

scientific article published on 17 May 2017

LigParGen web server: an automatic OPLS-AA parameter generator for organic ligands

scientific article published on 21 April 2017

Limiting cardiac ischemic injury by pharmacological augmentation of macrophage migration inhibitory factor-AMP-activated protein kinase signal transduction

scientific article published on 10 June 2013

Macrophage Migration Inhibitory Factor Is Detrimental in Pneumococcal Pneumonia and a Target for Therapeutic Immunomodulation

scientific article

Macrophomate synthase: QM/MM simulations address the Diels-Alder versus Michael-Aldol reaction mechanism

scientific article

Methyl effects on protein-ligand binding

scientific article

Molecular Dynamics Simulations of a Conformationally Mobile Peptide-Based Catalyst for Atroposelective Bromination

article

Molecular Modeling Calculations of HIV-1 Reverse Transcriptase Nonnucleoside Inhibitors: Correlation of Binding Energy with Biological Activity for Novel 2-Aryl-Substituted Benzimidazole Analogues ⬇️

scientific article published on May 8, 2003

Molecular dynamics and Monte Carlo simulations for protein-ligand binding and inhibitor design

scientific article

Molecular modeling of organic and biomolecular systems using BOSS and MCPRO.

scientific article

Monte Carlo simulations of liquid acetic acid and methyl acetate with the OPLS potential functions

article

Monte Carlo vs Molecular Dynamics for Conformational Sampling

NO-MNDO:  Reintroduction of the Overlap Matrix into MNDO.

scientific article published in March 2006

Novel non-active site inhibitor of Cryptosporidium hominis TS-DHFR identified by a virtual screen

scientific article

OPLS all‐atom force field for carbohydrates

article

OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins

scientific article published on 17 November 2015

On the mechanism and rate of spontaneous decomposition of amino acids ⬇️

scientific article published on October 31, 2011

Optical rotatory dispersion of 2,3-hexadiene and 2,3-pentadiene

scientific article

Optimization of N-benzyl-benzoxazol-2-ones as receptor antagonists of macrophage migration inhibitory factor (MIF) ⬇️

scientific article published on August 3, 2010

Optimization of Pyrazoles as Phenol Surrogates to Yield Potent Inhibitors of Macrophage Migration Inhibitory Factor.

scientific article published on 25 March 2018

Optimization of azoles as anti-human immunodeficiency virus agents guided by free-energy calculations

scientific article published on 28 June 2008

Optimization of benzyloxazoles as non-nucleoside inhibitors of HIV-1 reverse transcriptase to enhance Y181C potency

scientific article published on 12 December 2012

Optimization of diarylamines as non-nucleoside inhibitors of HIV-1 reverse transcriptase

scientific article published on 17 November 2005

Optimization of diarylazines as anti-HIV agents with dramatically enhanced solubility

scientific article published on 08 July 2013

Origin of the activity drop with the E50D variant of catalytic antibody 34E4 for Kemp elimination

scientific article published on January 2009

PDDG/PM3 and PDDG/MNDO: improved semiempirical methods

scientific article published in December 2002

Performance of Protein-Ligand Force Fields for the Flavodoxin-Flavin Mononucleotide System

scientific article published on 21 July 2016

Perspective on Free-Energy Perturbation Calculations for Chemical Equilibria

scientific article published on May 2008

Picomolar Inhibitors of HIV Reverse Transcriptase Featuring Bicyclic Replacement of a Cyanovinylphenyl Group

scientific article

Picomolar Inhibitors of HIV-1 Reverse Transcriptase: Design and Crystallography of Naphthyl Phenyl Ethers

scientific article

Polarization Effects for Hydrogen-Bonded Complexes of Substituted Phenols with Water and Chloride Ion ⬇️

scientific article published on November 1, 2007

Polarized Protein-Specific Charges from Atoms-in-Molecule Electron Density Partitioning

scientific article published on 11 June 2013

Polypeptide folding using Monte Carlo sampling, concerted rotation, and continuum solvation

scientific article

Potent Inhibitors Active against HIV Reverse Transcriptase with K101P, a Mutation Conferring Rilpivirine Resistance

scientific article

Potential energy functions for atomic-level simulations of water and organic and biomolecular systems

scientific article

Prediction of Binding Affinities for TIBO Inhibitors of HIV-1 Reverse Transcriptase Using Monte Carlo Simulations in a Linear Response Method

scientific article

Prediction of activity for nonnucleoside inhibitors with HIV-1 reverse transcriptase based on Monte Carlo simulations

scientific article published in July 2002

Prediction of drug solubility from structure

scientific article

Prediction of the water content in protein binding sites

scientific article

QM/MM Calculations for the Cl- + CH3Cl SN2 Reaction in Water Using CM5 Charges and Density Functional Theory

scientific article published on 27 June 2019

Quantum mechanical/molecular mechanical modeling finds Diels-Alder reactions are accelerated less on the surface of water than in water

scientific article

Ramipril-induced generalized pustular psoriasis: case report and literature review

scientific article published on January 2010

Receptor agonists of macrophage migration inhibitory factor ⬇️

scientific article published on September 29, 2010

Relationship between side chain structure and 14-helix stability of beta3-peptides in water

scientific article

Reply to Pandey et al.: Understanding the efficacy of a potential antiretroviral drug candidate in humanized mouse model of HIV infection

article published in the Proceedings of the National Academy of Sciences of the United States of America

Revised TIPS for simulations of liquid water and aqueous solutions

article

Robust Free Energy Perturbation Protocols for Creating Molecules in Solution

scientific article published on 24 June 2019

Role of Macrophage Migration Inhibitory Factor in the Regulatory T Cell Response of Tumor-Bearing Mice ⬇️

scientific article published on September 12, 2012

Search for non-nucleoside inhibitors of HIV-1 reverse transcriptase using chemical similarity, molecular docking, and MM-GB/SA scoring

scientific article

Small molecular modulation of macrophage migration inhibitory factor in the hyperoxia-induced mouse model of bronchopulmonary dysplasia

scientific article published on 28 February 2013

Small-Molecule Inhibitors of the Interaction between the E3 Ligase VHL and HIF1α

scientific article

Steric and solvation effects in ionic S(N)2 reactions

scientific article published in November 2009

Steric retardation of SN2 reactions in the gas phase and solution

scientific article

Structural and Preclinical Studies of Computationally Designed Non-Nucleoside Reverse Transcriptase Inhibitors for Treating HIV infection

scientific article

Structural and energetic analyses of the effects of the K103N mutation of HIV-1 reverse transcriptase on efavirenz analogues

scientific article published in April 2004

Structural studies provide clues for analog design of specific inhibitors of Cryptosporidium hominis thymidylate synthase-dihydrofolate reductase

scientific article published on 24 July 2014

Structure-Based Evaluation of C5 Derivatives in the Catechol Diether Series Targeting HIV-1 Reverse Transcriptase

scientific article

Structure-based evaluation of non-nucleoside inhibitors with improved potency and solubility that target HIV reverse transcriptase variants

scientific article

Synthesis and Evaluation of Selected Key Methyl Ether Derivatives of Vancomycin Aglycon ⬇️

scientific article published on October 14, 2010

Systematic Study of Effects of Structural Modifications on the Aqueous Solubility of Drug-like Molecules.

scientific article

Targeting the von Hippel–Lindau E3 Ubiquitin Ligase Using Small Molecules To Disrupt the VHL/HIF-1α Interaction

scientific article

Temperature and size dependence for Monte Carlo simulations of TIP4P water

article

The many faces of halogen bonding: a review of theoretical models and methods

scientific article published on 9 June 2014

The many roles of computation in drug discovery

scientific article

Thorpe-Ingold acceleration of oxirane formation is mostly a solvent effect

scientific article

Treatment of Halogen Bonding in the OPLS-AA Force Field: Application to Potent Anti-HIV Agents ⬇️

scientific article published on April 3, 2012

Unbinding Dynamics of Non-Nucleoside Inhibitors from HIV-1 Reverse Transcriptase

scientific article published on 03 January 2019

Understanding Rate Accelerations for Diels-Alder Reactions in Solution Using Enhanced QM/MM Methodology.

scientific article

Update to Our Reader, Reviewer, and Author Communities-April 2020

scientific article published on 22 April 2020

Update to Our Reader, Reviewer, and Author Communities-April 2020

scientific article published on 23 April 2020

Validation of a model for the complex of HIV-1 reverse transcriptase with nonnucleoside inhibitor TMC125.

scientific article

Vancomycin analogs: Seeking improved binding of d-Ala-d-Ala and d-Ala-d-Lac peptides by side-chain and backbone modifications

scientific article

Vancomycin resistance: modeling backbone variants with D-Ala-D-Ala and D-Ala-D-Lac peptides

scientific article published on 24 December 2008

Virtual Screening and Optimization Yield Low-Nanomolar Inhibitors of the Tautomerase Activity of Plasmodium falciparum Macrophage Migration Inhibitory Factor ⬇️

scientific article published on October 26, 2012

Virtual screening reveals allosteric inhibitors of the Toxoplasma gondii thymidylate synthase-dihydrofolate reductase

scientific article published on 31 December 2013

Why urea eliminates ammonia rather than hydrolyzes in aqueous solution

scientific article

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