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Theoretical and Computational Chemistry

Working Paper

Phase-field modelling of molecular dynamics with diffusive motions

Kairi Masuda

Version 1 posted 30 August 2022

139

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Theoretical and Computational Chemistry

Working Paper

Calculating Absorption and Fluorescence Spectra for Chromophores in Solution with Ensemble Franck-Condon Methods

Ajay Khanna, Sapana Shedge, Tim Zuehlsdorff, Christine Isborn

Version 2 posted 01 July 2024

262

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Theoretical and Computational Chemistry

Working Paper

An automated Calculation Pipeline for Differential Pair Interaction Energies with Molecular Force Fields using the Tinker Molecular Modeling Package

Felix Bänsch, Mirco Daniel, Harald Lanig, Christoph Steinbeck, Achim Zielesny

Version 1 posted 08 February 2024

196

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Theoretical and Computational Chemistry

Working Paper

Unveiling the Full Dynamical and Reactivity Profiles of Acetylcholinesterase: A Comprehensive All-Atom Investigation

Frédéric Célerse, Louis Lagardère, Yasmine Bouchibti, Florian Nachon, Laurent Verdier, Jean-Philip Piquemal, Etienne Derat

Version 1 posted 17 November 2023

298

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Biological and Medicinal Chemistry

Review

Molecular Mechanisms for Stabilizing Biologics in the Solid State

Jing Ling, Yong Du, W. Peter Wuelfing, Nicole Buist, Yogita Krishnamachari, Hanmi Xi, Allen C. Templeton, Yongchao Su

Version 1 posted 26 August 2024

246

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Theoretical and Computational Chemistry

Working Paper

Understanding and Fine Tuning the Propensity of ATP-Driven Liquid-Liquid Phase Separation with Oligolysine

Qiang Zhu, Yongxian Wu, Ray Luo

Version 2 posted 30 January 2024

316

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Theoretical and Computational Chemistry

Working Paper

Utilization of AlphaFold Models for Drug Discovery: Feasibility and Challenges. Histone Deacetylase 11 as a Case Study

Fady Baselious, Dina Robaa, Wolfgang Sippl

Version 1 posted 26 October 2023

280

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Theoretical and Computational Chemistry

Working Paper

QMrebind: Incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations

Anupam Anand Ojha, Lane Votapka, Rommie Amaro

Version 2 posted 16 October 2023

490

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Theoretical and Computational Chemistry

Working Paper

A Cutoff-based Method with Charge-distribution-data Driven Pair Potentials for Efficiently Estimating Electrostatic Interactions in Molecular System

Ikuo Fukuda, Kei Moritsugu, Junichi Higo, Yoshifumi Fukunishi

Version 1 posted 21 August 2023

151

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Theoretical and Computational Chemistry

Working Paper

Accelerating Fragment Based Drug Discovery using Grand Canonical Nonequilibrium Candidate Monte Carlo

William Poole, Marley Samways, Davide Branduardi, Richard Taylor, Marcel Verdonk, Jonathan Essex

Version 1 posted 30 September 2024

291

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41 results in Molecular dynamics in Keywords: Molecular dynamics

Phase-field modelling of molecular dynamics with diffusive motions

Calculating Absorption and Fluorescence Spectra for Chromophores in Solution with Ensemble Franck-Condon Methods

An automated Calculation Pipeline for Differential Pair Interaction Energies with Molecular Force Fields using the Tinker Molecular Modeling Package

Unveiling the Full Dynamical and Reactivity Profiles of Acetylcholinesterase: A Comprehensive All-Atom Investigation

Molecular Mechanisms for Stabilizing Biologics in the Solid State

Understanding and Fine Tuning the Propensity of ATP-Driven Liquid-Liquid Phase Separation with Oligolysine

Utilization of AlphaFold Models for Drug Discovery: Feasibility and Challenges. Histone Deacetylase 11 as a Case Study

QMrebind: Incorporating quantum mechanical force field reparameterization at the ligand binding site for improved drug-target kinetics through milestoning simulations

A Cutoff-based Method with Charge-distribution-data Driven Pair Potentials for Efficiently Estimating Electrostatic Interactions in Molecular System

Accelerating Fragment Based Drug Discovery using Grand Canonical Nonequilibrium Candidate Monte Carlo

41 results in Keywords: Molecular dynamics