Publications by authors named "Jennifer L Knight"

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Harnessing free energy calculations for kinome-wide selectivity in drug discovery campaigns with a Wee1 case study.
Jennifer Lynn Knight, Anthony J Clark, Jiashi Wang, Andrew Placzek, Pieter H Bos

Nat Commun· August 2025

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AutoDesigner - Core Design, a De Novo Design Algorithm for Chemical Scaffolds: Application to the Design and Synthesis of Novel Selective Wee1 Inhibitors.
Pieter H Bos, Fabio Ranalli, Emelie Flood, Shawn Watts, Daigo Inoyama, Jennifer L Knight

J Chem Inf Model· October 2024

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Exploiting high-energy hydration sites for the discovery of potent peptide aldehyde inhibitors of the SARS-CoV-2 main protease with cellular antiviral activity.
Daniel W Carney, Abba E Leffler, Jeffrey A Bell, Asela S Chandrasinghe, Cecilia Cheng, Jennifer L Knight

Bioorg Med Chem· April 2024

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OPLS3: A Force Field Providing Broad Coverage of Drug-like Small Molecules and Proteins.
Edward Harder, Wolfgang Damm, Jon Maple, Chuanjie Wu, Mark Reboul, Jennifer L Knight

J Chem Theory Comput· January 2016

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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.
Lingle Wang, Yujie Wu, Yuqing Deng, Byungchan Kim, Levi Pierce, Jennifer L Knight

J Am Chem Soc· February 2015

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Leveraging Data Fusion Strategies in Multireceptor Lead Optimization MM/GBSA End-Point Methods.
Jennifer L Knight, Goran Krilov, Kenneth W Borrelli, Joshua Williams, John R Gunn

J Chem Theory Comput· August 2014

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Deconstructing activation events in rhodopsin.
Elena N Laricheva, Karunesh Arora, Jennifer L Knight, Charles L Brooks

J Am Chem Soc· July 2013

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Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes.
Jennifer L Knight, Joseph D Yesselman, Charles L Brooks

J Comput Chem· April 2013

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Towards Accurate Prediction of Protonation Equilibrium of Nucleic Acids.
Garrett B Goh, Jennifer L Knight, Charles L Brooks

J Phys Chem Lett· March 2013

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Modeling Local Structural Rearrangements Using FEP/REST: Application to Relative Binding Affinity Predictions of CDK2 Inhibitors.
Lingle Wang, Yuqing Deng, Jennifer L Knight, Yujie Wu, Byungchan Kim

J Chem Theory Comput· February 2013

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pH-dependent dynamics of complex RNA macromolecules.
Garrett B Goh, Jennifer L Knight, Charles L Brooks

J Chem Theory Comput· February 2013

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MATCH: an atom-typing toolset for molecular mechanics force fields.
Joseph D Yesselman, Daniel J Price, Jennifer L Knight, Charles L Brooks

J Comput Chem· January 2012

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Constant pH Molecular Dynamics Simulations of Nucleic Acids in Explicit Solvent.
Garrett B Goh, Jennifer L Knight, Charles L Brooks

J Chem Theory Comput· January 2012

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Applying efficient implicit nongeometric constraints in alchemical free energy simulations.
Jennifer L Knight, Charles L Brooks

J Comput Chem· December 2011

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Surveying implicit solvent models for estimating small molecule absolute hydration free energies.
Jennifer L Knight, Charles L Brooks

J Comput Chem· October 2011

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Multi-Site λ-dynamics for simulated Structure-Activity Relationship studies.
Jennifer L Knight, Charles L Brooks

J Chem Theory Comput· September 2011

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On the mechanism of crystalline polymorph selection by polymer heteronuclei.
Vilmalí López-Mejías, Jennifer L Knight, Charles L Brooks, Adam J Matzger

Langmuir· June 2011

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Lambda-dynamics free energy simulation methods.
Jennifer L Knight, Charles L Brooks

J Comput Chem· August 2009

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Validating CHARMM parameters and exploring charge distribution rules in structure-based drug design.
Jennifer L Knight, Charles L Brooks

J Chem Theory Comput· January 2009

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Exploring structural variability in X-ray crystallographic models using protein local optimization by torsion-angle sampling.
Jennifer L Knight, Zhiyong Zhou, Emilio Gallicchio, Daniel M Himmel, Richard A Friesner

Acta Crystallogr D Biol Crystallogr· April 2008

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HIV-1 reverse transcriptase structure with RNase H inhibitor dihydroxy benzoyl naphthyl hydrazone bound at a novel site.
Daniel M Himmel, Stefan G Sarafianos, Sanjeewa Dharmasena, Mohammed M Hossain, Kessler McCoy-Simandle, Jennifer L Knight

ACS Chem Biol· December 2006

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Distance-restrained docking of rifampicin and rifamycin SV to RNA polymerase using systematic FRET measurements: developing benchmarks of model quality and reliability.
Jennifer L Knight, Vladimir Mekler, Jayanta Mukhopadhyay, Richard H Ebright, Ronald M Levy

Biophys J· February 2005

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