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8 results in Authors: Siqin Cao

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

2,899

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Physical Chemistry

Review

Memory unlocks the future of biomolecular dynamics: Transformative tools to uncover physical insights accurately and efficiently

Anthony Dominic III, Siqin Cao, Andres Montoya-Castillo, Xuhui Huang

Version 2 posted 27 April 2023

389

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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

Memory Kernel Minimization Based Neural Networks for Discovering Slow Collective Variables of Biomolecular Dynamics

Bojun Liu, Siqin Cao, Jordan G Boysen, Mingyi Xue, Xuhui Huang

Version 1 posted 04 September 2024

340

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Theoretical and Computational Chemistry

Working Paper

Sub-millisecond Atomistic Simulations Reveal Hydrogen Bond-Driven Diffusion of a Guest Peptide in Protein-RNA Condensate

Ilona C. Unarta, Siqin Cao, Eshani C. Goonetilleke, Jiani Niu, Samuel H. Gellman, Xuhui Huang

Version 1 posted 12 December 2023

285

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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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Physical Chemistry

Working Paper

EPISOL: A Software Package with Expanded Functions to Perform 3D-RISM Calculations for the Solvation of Chemical and Biological Molecules

Siqin Cao, Michael Kalin, Xuhui Huang

Version 1 posted 31 October 2022

433

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Biological and Medicinal Chemistry

Working Paper

FeatureDock: Protein-Ligand Docking Guided by Physicochemical Feature-Based Local Environment Learning using Transformer

Mingyi Xue, Bojun Liu, Siqin Cao, Xuhui Huang

Version 1 posted 11 July 2024

861

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8 results in Siqin Cao in Authors: Siqin Cao

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

Memory unlocks the future of biomolecular dynamics: Transformative tools to uncover physical insights accurately and efficiently

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

Memory Kernel Minimization Based Neural Networks for Discovering Slow Collective Variables of Biomolecular Dynamics

Sub-millisecond Atomistic Simulations Reveal Hydrogen Bond-Driven Diffusion of a Guest Peptide in Protein-RNA Condensate

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

EPISOL: A Software Package with Expanded Functions to Perform 3D-RISM Calculations for the Solvation of Chemical and Biological Molecules

FeatureDock: Protein-Ligand Docking Guided by Physicochemical Feature-Based Local Environment Learning using Transformer

8 results in Authors: Siqin Cao