Examining asymmetric pairwise pre-reaction and transition states in enzymatic catalysis by molecular dynamics simulation and quantum mechanics/molecular mechanics calculation-Reference-Cited by-全球学者库

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Examining asymmetric pairwise pre-reaction and transition states in enzymatic catalysis by molecular dynamics simulation and quantum mechanics/molecular mechanics calculation

Published:2023-06 Issue:2 Volume:4 Page:102263
ISSN:2666-1667
Container-title:STAR Protocols
language:en
Short-container-title:STAR Protocols

Author:

Luo Shenggan,Lyu Chu-Jun,Mao Yong,Liu Yihan,Shi Ting,Zhao Yi-Lei^ORCID

Funder

National Key Research and Development Program of China

National Key Project for Synthetic Biology

Center for High Performance Computing, Shanghai Jiao Tong University

National Natural Science Foundation of China

Publisher

Elsevier BV

Subject

General Immunology and Microbiology,General Biochemistry, Genetics and Molecular Biology,General Neuroscience

Reference17 articles.

1. Understanding the effectiveness of enzyme pre-reaction state by a quantum-based machine learning model;Luo;Cell Rep. Phys. Sci.,2022

2. ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB;Maier;J. Chem. Theory Comput.,2015

3. Development and testing of a general amber force field;Wang;J. Comput. Chem.,2004

4. Molecular dynamics simulations of alcohol dehydrogenase with a four- or five-coordinate catalytic zinc ion;Ryde;Proteins,1995

5. Structural survey of zinc-containing proteins and development of the zinc AMBER force field (ZAFF);Peters;J. Chem. Theory Comput.,2010

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