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8 results in Authors: Siqin Cao

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

791

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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

268

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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

414

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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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Citations

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

372

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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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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

279

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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

753

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8 results in Siqin Cao in Authors: Siqin Cao

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

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

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

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

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

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

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

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

8 results in Authors: Siqin Cao