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17 results in Keywords: Markov State Model

Biological and Medicinal Chemistry

Working Paper

Allosteric Modulation of PCSK9-LDLR Interaction: Can Structureless Loops be Drug Targets?

Ipsita Basu, Krishnendu Sinha, Zacharia Shah, Salim Shah, Suman Chakrabarty

Version 1 posted 31 October 2022

452

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Physical Chemistry

Working Paper

SARS-CoV-2 RdRp Follows Asynchronous Translocation Pathway for Viral Transcription and Replication

Xiaowei Wang, Yuan Yao, Xin Gao, Lu Zhang

Version 1 posted 15 June 2022

221

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Theoretical and Computational Chemistry

Working Paper

Exploring Transition States of Protein Conformational Changes via Out-of-Distribution Detection in the Hyperspherical Latent Space

Bojun Liu, Jordan G. Boysen, Ilona Christy Unarta, Xuefeng Du, Yixuan Li, Xuhui Huang

Version 1 posted 23 January 2024

915

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Theoretical and Computational Chemistry

Working Paper

Tutorials on How to Build Non-Markovian Dynamic Models from Molecular Dynamics Simulations for Studying Protein Dynamics

Yue Wu, Siqin Cao, Yunrui Qiu, Xuhui Huang

Version 1 posted 28 November 2023

861

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Citations

Theoretical and Computational Chemistry

Working Paper

Deciphering the Allosteric Process of Phaeodactylum tricornutum Aureochrome 1a LOV Domain

Hao Tian, Francesco Trozzi, Brian Zoltowski, Peng Tao

Version 1 posted 30 June 2020

385

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Theoretical and Computational Chemistry

Working Paper

Intramolecular proton transfer reaction dynamics using machine learned ab initio potential energy surfaces

Shampa Raghunathan

Version 2 posted 05 July 2021

376

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Theoretical and Computational Chemistry

Working Paper

Solution-State Preorganization of Cyclic β-Hairpin Ligands Determines Binding Mechanism and Affinities for MDM2

Yunhui Ge, Si Zhang, Mate Erdelyi, Vincent Voelz

Version 3 posted 20 April 2021

589

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Theoretical and Computational Chemistry

Working Paper

A Markov State Model of Solvent Features Reveals Water Dynamics in Protein-Peptide Binding

Robert Raddi, Vincent Voelz

Version 1 posted 04 April 2023

216

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Theoretical and Computational Chemistry

Working Paper

Integrative Generalized Master Equation: A Theory to Study Long-timescale Biomolecular Dynamics via the Integrals of Memory Kernels

Siqin Cao, Yunrui Qiu, Michael Kalin, Xuhui Huang

Version 2 posted 17 January 2023

654

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Citations

Theoretical and Computational Chemistry

Working Paper

Dissociation pathways of the p53 DNA binding domain from DNA and critical roles of key residues elucidated by dPaCS-MD/MSM

Mohamed Sobeh, Akio kitao

Version 1 posted 13 December 2021

267

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17 results in Markov State Model in Keywords: Markov State Model

Allosteric Modulation of PCSK9-LDLR Interaction: Can Structureless Loops be Drug Targets?

SARS-CoV-2 RdRp Follows Asynchronous Translocation Pathway for Viral Transcription and Replication

Exploring Transition States of Protein Conformational Changes via Out-of-Distribution Detection in the Hyperspherical Latent Space

Tutorials on How to Build Non-Markovian Dynamic Models from Molecular Dynamics Simulations for Studying Protein Dynamics

Deciphering the Allosteric Process of Phaeodactylum tricornutum Aureochrome 1a LOV Domain

Intramolecular proton transfer reaction dynamics using machine learned ab initio potential energy surfaces

Solution-State Preorganization of Cyclic β-Hairpin Ligands Determines Binding Mechanism and Affinities for MDM2

A Markov State Model of Solvent Features Reveals Water Dynamics in Protein-Peptide Binding

Integrative Generalized Master Equation: A Theory to Study Long-timescale Biomolecular Dynamics via the Integrals of Memory Kernels

Dissociation pathways of the p53 DNA binding domain from DNA and critical roles of key residues elucidated by dPaCS-MD/MSM

17 results in Keywords: Markov State Model