scholarly journals Molecular Model Construction of the Dense Medium Component Scaffold in Coal for Molecular Aggregate Simulation

ACS Omega ◽  
2020 ◽  
Vol 5 (22) ◽  
pp. 13375-13383
Author(s):  
Lulu Lian ◽  
Zhihong Qin ◽  
Chunsheng Li ◽  
Jinglan Zhou ◽  
Qiang Chen ◽  
...  
Keyword(s):  
Molecular Model ◽  
Model Construction ◽  
Dense Medium ◽  
Molecular Aggregate ◽  
Medium Component

scholarly journals Characterization of coal-based fulvic acid and the construction of a fulvic acid molecular model

RSC Advances ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 5468-5477 ◽  
Author(s):  
Guan-qun Gong ◽  
Xin Yuan ◽  
Ying-jie Zhang ◽  
Ya-jun Li ◽  
Wei-xin Liu ◽  
...  
Keyword(s):  
Fulvic Acid ◽  
Molecular Model ◽  
Scientific Basis ◽  
Applied Science ◽  
Model Construction

Fulvic acid (FA) is composed of many molecular units with similar characteristic structures. The characterization and molecular model construction of coal-based FA is the key for the scientific basis and applied science of FA.

scholarly journals Molecular Model Construction and Evaluation of Jincheng Anthracite

ACS Omega ◽  
2020 ◽  
Vol 5 (19) ◽  
pp. 10663-10670
Author(s):  
Guochao Yan ◽  
Gang Ren ◽  
Longjian Bai ◽  
Jianping Feng ◽  
Zhiqiang Zhang
Keyword(s):  
Molecular Model ◽  
Model Construction

scholarly journals EnzyHTP: A High-Throughput Computational Platform for Enzyme Modeling

2021 ◽  
Author(s):  
Qianzhen Shao ◽  
Yaoyukun Jiang ◽  
Zhongyue Yang
Keyword(s):  
High Throughput ◽  
Structural Model ◽  
Molecular Model ◽  
Molecular Simulations ◽  
Model Construction ◽  
Single Amino Acid ◽  
Manual Operation ◽  
Modeling Data ◽  
Dynamics Simulations ◽  
Enzyme Modeling

Molecular simulations, including quantum mechanics (QM), molecular mechanics (MM), and multiscale QM/MM modeling, have been extensively applied to understand the mechanism of enzyme catalysis and to design new enzymes. However, molecular simulations typically require specialized, manual operation ranging from model construction to post-analysis to complete the entire life-cycle of enzyme modeling. The dependence on manual operation makes it challenging to simulate enzymes and enzyme variants in a high-throughput fashion. In this work, we developed a Python software, EnzyHTP, to automate molecular model construction, QM, MM, and QM/MM computation, and analyses of modeling data for enzyme simulations. To test the EnzyHTP, we used fluoroacetate dehalogenase (FAcD) as a model system and simulated the enzyme interior electrostatics for 100 FAcD mutants with a random single amino acid substitution. For each enzyme mutant, the workflow involves structural model construction, 1 ns molecular dynamics simulations, and quantum mechnical calculations in 100 MD-sampled snapshots. The entire simulation workflow for 100 mutants was completed in 7 hours with 10 GPUs and 160 CPUs. EnzyHTP is expected to improve the efficiency and reproducibility of computational enzyme, facilitate the fundamental understanding of catalytic origins across enzyme families, and accelerate the optimization of biocatalysts for non-native substrate transformation.

Molecular Model Construction and Study of Gas Adsorption of Zhaozhuang Coal

2018 ◽  
Vol 32 (9) ◽  
pp. 9727-9737 ◽  
Author(s):  
Junqing Meng ◽  
Ruquan Zhong ◽  
Shichao Li ◽  
Feifei Yin ◽  
Baisheng Nie
Keyword(s):  
Gas Adsorption ◽  
Molecular Model ◽  
Model Construction

Large Scale Molecular Model Construction of Xishan Bituminous Coal

2017 ◽  
Vol 31 (2) ◽  
pp. 1310-1317 ◽  
Author(s):  
Zhiqiang Zhang ◽  
Qiannan Kang ◽  
Shuai Wei ◽  
Tao Yun ◽  
Guochao Yan ◽  
...  
Keyword(s):  
Large Scale ◽  
Bituminous Coal ◽  
Molecular Model ◽  
Model Construction
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