Publications by authors named "Nathan M Lim"

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Characterization of JNJ-2482272 [4-(4-Methyl-2-(4-(Trifluoromethyl)Phenyl)Thiazole-5-yl) Pyrimidine-2-Amine] As a Strong Aryl Hydrocarbon Receptor Activator in Rat and Human.
Kevin J Coe, Mark Feinstein, J William Higgins, Perry Leung, Brian P Scott, Nathan M Lim

Drug Metab Dispos· August 2022

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Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo.
Teresa Danielle Bergazin, Ido Y Ben-Shalom, Nathan M Lim, Sam C Gill, Michael K Gilson

J Comput Aided Mol Des· February 2021

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Insights on small molecule binding to the Hv1 proton channel from free energy calculations with molecular dynamics simulations.
Victoria T Lim, Andrew D Geragotelis, Nathan M Lim, J Alfredo Freites, Francesco Tombola

Sci Rep· August 2020

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Fragment Pose Prediction Using Non-equilibrium Candidate Monte Carlo and Molecular Dynamics Simulations.
Nathan M Lim, Meghan Osato, Gregory L Warren, David L Mobley

J Chem Theory Comput· April 2020

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An optimized chemical-genetic method for cell-specific metabolic labeling of RNA.
Sarah Nainar, Bonnie J Cuthbert, Nathan M Lim, Whitney E England, Ke Ke

Nat Methods· March 2020

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Sampling Conformational Changes of Bound Ligands Using Nonequilibrium Candidate Monte Carlo and Molecular Dynamics.
Sukanya Sasmal, Samuel C Gill, Nathan M Lim, David L Mobley

J Chem Theory Comput· March 2020

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Binding Modes and Metabolism of Caffeine.
Zuzana Jandova, Samuel C Gill, Nathan M Lim, David L Mobley, Chris Oostenbrink

Chem Res Toxicol· July 2019

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Enhancing Side Chain Rotamer Sampling Using Nonequilibrium Candidate Monte Carlo.
Kalistyn H Burley, Samuel C Gill, Nathan M Lim, David L Mobley

J Chem Theory Comput· March 2019

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Escaping Atom Types in Force Fields Using Direct Chemical Perception.
David L Mobley, Caitlin C Bannan, Andrea Rizzi, Christopher I Bayly, John D Chodera, Victoria T Lim, Nathan M Lim

J Chem Theory Comput· November 2018

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Refining Protein Penetration into the Lipid Bilayer Using Fluorescence Quenching and Molecular Dynamics Simulations: The Case of Diphtheria Toxin Translocation Domain.
Alexander Kyrychenko, Nathan M Lim, Victor Vasquez-Montes, Mykola V Rodnin, J Alfredo Freites

J Membr Biol· June 2018

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Binding Modes of Ligands Using Enhanced Sampling (BLUES): Rapid Decorrelation of Ligand Binding Modes via Nonequilibrium Candidate Monte Carlo.
Samuel C Gill, Nathan M Lim, Patrick B Grinaway, Ariën S Rustenburg, Josh Fass

J Phys Chem B· May 2018

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Sensitivity in Binding Free Energies Due to Protein Reorganization.
Nathan M Lim, Lingle Wang, Robert Abel, David L Mobley

J Chem Theory Comput· September 2016

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Blind prediction of HIV integrase binding from the SAMPL4 challenge.
David L Mobley, Shuai Liu, Nathan M Lim, Karisa L Wymer, Alexander L Perryman

J Comput Aided Mol Des· April 2014

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Blind prediction of solvation free energies from the SAMPL4 challenge.
David L Mobley, Karisa L Wymer, Nathan M Lim, J Peter Guthrie

J Comput Aided Mol Des· March 2014

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Lead optimization mapper: automating free energy calculations for lead optimization.
Shuai Liu, Yujie Wu, Teng Lin, Robert Abel, Jonathan P Redmann, Nathan M Lim

J Comput Aided Mol Des· September 2013

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