Elastic network model

Bridging Sequence and Structure with Evol

Personal Evol Workshop Notes

Yu Zhu

Last updated on Aug 9, 2021 1 min read Protein, Elastic network model, co-evolution

Bridging Sequence and Structure with Evol

Collective Dynamics of Proteins Using Elastic Network Models

Personal ProDy Workshop Notes

Yu Zhu

Last updated on Aug 9, 2021 1 min read Protein, Elastic network model

Collective Dynamics of Proteins Using Elastic Network Models

Journal of Chemical Information and Modeling | Comparative Dynamics and Functional Mechanisms of the CYP17A1 Tunnels Regulated by Ligand Binding

An integrated calculation strategy to systematically study the mechanism of ligand binding and channel tunneling dynamics at the atomic level

Yu Zhu

Last updated on Oct 3, 2020 6 min read Protein, Elastic network model, Ligand, Biological Network

Journal of Chemical Information and Modeling | Comparative Dynamics and Functional Mechanisms of the CYP17A1 Tunnels Regulated by Ligand Binding

Both intra and inter-domain interactions define the intrinsic dynamics and allosteric mechanism in DNMT1s

Highlights in the publication include 1)Dynamics and allosteric potentials of the RFTS domain are proposed. 2)Hinge sites located at the RFTS-CD interface are key regulators for inter-domain interactions. 3)Network analysis reveals local allosteric networks and inter-domain communication pathways in DNMT1. 4)A potential allosteric site at the TRD interface for DNMT1 is identified.

Zhongjie Liang, Yu Zhu, Jie Long, Fei Ye, Guang Hu

Both intra and inter-domain interactions define the intrinsic dynamics and allosteric mechanism in DNMT1s