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Theoretical and Computational Chemistry

Working Paper

Association/dissociation Mechanisms of Intrinsically Disordered Region of Protein Beyond Conformational Selection and Induced Fit

Duy Phuoc Tran, Akio Kitao

Version 1 posted 24 September 2019

668

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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

583

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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

370

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Biological and Medicinal Chemistry

Working Paper

Inhibition of the Hexamerization of SARS-CoV-2 Endoribonuclease and Modeling of RNA Structures Bound to the Hexamer

Duy Tran, Yuta Taira, Takumi Ogawa, Ryoga Misu, Yoshiki Miyazawa, Akio Kitao

Version 1 posted 13 July 2021

290

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Theoretical and Computational Chemistry

Working Paper

Markov State Models with Weighted Ensemble Simulation: How to Eliminate the Trajectory Merging Bias

Samik Bose, Ceren Kilinc, Alex Dickson

Version 1 posted 28 August 2024

165

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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

374

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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

639

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1

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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

213

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Theoretical and Computational Chemistry

Working Paper

A Step-by-step Guide on How to Construct quasi-Markov State Models to Study Functional Conformational Changes of Biological Macromolecules

Andrew Kai-hei Yik, Yunrui Qiu, Ilona Christy Unarta, Siqin Cao, Xuhui Huang

Version 1 posted 17 February 2022

2,802

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1

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Theoretical and Computational Chemistry

Working Paper

Energetic and Kinetic Origin of CALB Interfacial Activation Revealed by PaCS-MD/MSM

Tegar Wijaya, Akio Kitao

Version 1 posted 28 March 2023

189

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Refine Search

17 results in Markov state model in Keywords: Markov state model

Association/dissociation Mechanisms of Intrinsically Disordered Region of Protein Beyond Conformational Selection and Induced Fit

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

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

Inhibition of the Hexamerization of SARS-CoV-2 Endoribonuclease and Modeling of RNA Structures Bound to the Hexamer

Markov State Models with Weighted Ensemble Simulation: How to Eliminate the Trajectory Merging Bias

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

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

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

A Step-by-step Guide on How to Construct quasi-Markov State Models to Study Functional Conformational Changes of Biological Macromolecules

Energetic and Kinetic Origin of CALB Interfacial Activation Revealed by PaCS-MD/MSM

17 results in Keywords: Markov state model