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Theoretical and Computational Chemistry

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FEP Protocol Builder: Optimization of Free Energy Perturbation Protocols using Active Learning

Cesar de Oliveira, Karl Leswing, Shulu Feng, Rene Kanters, Robert Abel, Sathesh Bhat

Version 1 posted 03 May 2023

1,360

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Theoretical and Computational Chemistry

Working Paper

Relative Binding Free Energy Predictions for Inhibitors of Tetrameric Influenza Virus Neuraminidase

Billy J Williams-Noonan, Elizabeth Yuriev, David K Chalmers

Version 1 posted 14 September 2021

284

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Theoretical and Computational Chemistry

Working Paper

Absolute Binding Free Energy Calculations for Buried Water Molecules

Yunhui Ge, Hannah Baumann, David Mobley

Version 2 posted 29 September 2022

549

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1

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Theoretical and Computational Chemistry

Working Paper

Encoding prior knowledge in ensemble refinement

Jürgen Köfinger, Gerhard Hummer

Version 3 posted 20 February 2024

359

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Biological and Medicinal Chemistry

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Discovery of a Novel Mutant-Selective Epidermal Growth Factor Receptor Inhibitor Using in silico Enabled Drug Discovery Platform

Hideyuki Igawa, Zef A. Konst, Eric Therrien, Mee Shelley, Heidi Koldsø, Pieter H. Bos, Ana Negri, Andreas Verras, Jiaye Guo, Markus Dahlgren, Adam Levinson, Brendan T. Parr, Suresh E. Kurhade, Prashant Latthe, Rajesha Shetty, Sridhar Santhanakrishnan, Katherine Amberg-Johnson, Alan Futran, Christian Atsriku, Robert Pelletier, Zhijian Liu, Jeffery A. Bell, Sathesh Bhat, Mats Svensson, Aleksey I. Gerasyuto

Version 2 posted 21 June 2024

339

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1

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Theoretical and Computational Chemistry

Working Paper

Is the functional response of a receptor determined by the thermodynamics of ligand binding?

Martin Vögele, Bin W. Zhang, Jonas Kaindl, Lingle Wang

Version 2 posted 27 September 2023

1,171

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Theoretical and Computational Chemistry

Working Paper

Q-RepEx: A Python Pipeline to Increase the Sampling of Empirical Valence Bond Simulations

Sebastian Brickel, Andrey O. Demkiv, Rory M. Crean, Gaspar P. Pinto, Shina Caroline Lynn Kamerlin

Version 1 posted 18 November 2022

220

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Biological and Medicinal Chemistry

Working Paper

Accurate physics-based prediction of binding affinities of RNA and DNA targeting ligands

Ara M. Abramyan, Anna Bochicchio, Chuanjie Wu, Wolfgang Damm, David R. Langley, Devleena Shivakumar, Dmitry Lupyan, Lingle Wang, Edward Harder, Eliud O. Oloo

Version 2 posted 26 August 2024

425

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Theoretical and Computational Chemistry

Working Paper

Basic residues at position 11 of α-conotoxin LvIA influence subtype selectivity between α3β2 and α3β4 nicotinic receptors via an electrostatic mechanism

Yves Haufe, Veeresh Kuruva, Ziyana Samanani, Guy Kamnesky, Gonxhe Lokaj, Pranavkumar Shadarmarshan, Rezvan Shahoei, Dana Katz, Jared Sampson, Michael Pusch, Ashraf Brik, Annette Nicke, Abba Leffler

Version 2 posted 19 July 2023

237

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Theoretical and Computational Chemistry

Working Paper

Using AlphaFold and Experimental Structures for the Prediction of the Structure and Binding Affinities of GPCR Complexes via Induced Fit Docking and Free Energy Perturbation

Dilek Coskun, Muyun Lihan, Joao Rodrigues, Marton Vass, Daniel Robinson, Richard Friesner, Edward Miller

Version 3 posted 03 August 2023

1,336

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37 results in Free Energy Perturbation in Keywords: Free Energy Perturbation

FEP Protocol Builder: Optimization of Free Energy Perturbation Protocols using Active Learning

Relative Binding Free Energy Predictions for Inhibitors of Tetrameric Influenza Virus Neuraminidase

Absolute Binding Free Energy Calculations for Buried Water Molecules

Encoding prior knowledge in ensemble refinement

Discovery of a Novel Mutant-Selective Epidermal Growth Factor Receptor Inhibitor Using in silico Enabled Drug Discovery Platform

Is the functional response of a receptor determined by the thermodynamics of ligand binding?

Q-RepEx: A Python Pipeline to Increase the Sampling of Empirical Valence Bond Simulations

Accurate physics-based prediction of binding affinities of RNA and DNA targeting ligands

Basic residues at position 11 of α-conotoxin LvIA influence subtype selectivity between α3β2 and α3β4 nicotinic receptors via an electrostatic mechanism

Using AlphaFold and Experimental Structures for the Prediction of the Structure and Binding Affinities of GPCR Complexes via Induced Fit Docking and Free Energy Perturbation

37 results in Keywords: Free Energy Perturbation