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Updated: Sep 20, 2026

Modeling an Enzyme Active Site using Molecular Visualization Freeware
Published on: December 25, 2021
[Modeling of the SARS coronavirus main proteinase and conformational flexibility of the active site]
Shiyong Liu1, Jianfeng Pei, Hao Chen
1State Key Laboratory of Structural Chemistry of Stable and Unstable Species, College of Chemistry and Molecular Engineering & Center for Theoretical Biology, Peking University, Beijing 100871, China.
Abstract:
SARS coronavirus 3CL proteinase is the key enzyme for virus replication which may serve as the target for drug discovery against SARS. A 3D structure model has been built for SARS coronavirus 3CL proteinase by comparative protein modeling. A homodimer model of the proteinase was also built. Analysis of the dimeric interface suggests the 3CL proteinase may have dimer form in solution. The conformational flexibility of the active site has been simulated by molecular dynamics combined with multi-canonical sampling. The active site loops have two typical conformations which may be related to the conformational movement associated with the enzymatic reaction.
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