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A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules
Edited by
Yong Wang;
Yong Wang
College of Life Sciences,
Shanghai Institute for Advanced Study, Institute of Quantitative Biology, Zhejiang University
, Hangzhou, 310027, China
The Provincial International Science and Technology Cooperation Base on Engineering Biology,
International Campus of Zhejiang University
, Haining, Zhejiang, 314400, China
Search for other works by this author on:
Ruhong Zhou
Ruhong Zhou
College of Life Sciences,
Shanghai Institute for Advanced Study, Institute of Quantitative Biology, Zhejiang University
, Hangzhou, 310027, China
Search for other works by this author on:
AIP Publishing LLC
ISBN electronic:
978-0-7354-2527-9
ISBN print:
978-0-7354-2524-8
Publication date:
2023
A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules
Edited by: Yong Wang, Ruhong Zhou
https://doi.org/10.1063/9780735425279
ISBN (print): 978-0-7354-2524-8
ISBN (electronic): 978-0-7354-2527-9
Publisher: AIP Publishing LLC
Download citation file:
Pay-Per-View Access
$135.00
Table of Contents
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Front MatterByYong Wang;Yong WangCollege of Life Sciences,Shanghai Institute for Advanced Study, Institute of Quantitative Biology, Zhejiang University, Hangzhou, 310027,ChinaThe Provincial International Science and Technology Cooperation Base on Engineering Biology,International Campus of Zhejiang University, Haining, Zhejiang, 314400,ChinaSearch for other works by this author on:Ruhong ZhouRuhong ZhouCollege of Life Sciences,Shanghai Institute for Advanced Study, Institute of Quantitative Biology, Zhejiang University, Hangzhou, 310027,ChinaSearch for other works by this author on:
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Chapter 1: A Practical Introduction to Martini 3 and its Application to Protein-Ligand Binding SimulationsByRiccardo Alessandri;Riccardo AlessandriPritzker School of Molecular Engineering,University of Chicago, Chicago, Illinois 60637,USASearch for other works by this author on:Sebastian Thallmair;Sebastian ThallmairFrankfurt Institute for Advanced Studies, Ruth-Moufang-Str. 1, 60438 Frankfurt am Main,GermanySearch for other works by this author on:Cristina Gil Herrero;Cristina Gil HerreroFrankfurt Institute for Advanced Studies, Ruth-Moufang-Str. 1, 60438 Frankfurt am Main,GermanySearch for other works by this author on:Raúl Mera-Adasme;Raúl Mera-AdasmeDepartamento de Ciencias del Ambiente, Facultad de Qúímica y Biología,Universidad de Santiago de Chile (USACH),ChileSearch for other works by this author on:Siewert J. Marrink;Siewert J. MarrinkGroningen Biomolecular Sciences and Biotechnology Institute and Zernike Institute for Advanced Materials,University of Groningen, Groningen,The NetherlandsSearch for other works by this author on:Paulo C. T. SouzaPaulo C. T. SouzaMolecular Microbiology and Structural Biochemistry,UMR 5086 CNRS and University of Lyon, Lyon,FranceSearch for other works by this author on:
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Chapter 2: Multiscale Theoretical Studies for Molecular MotorsByKewei Xie;Kewei XieDepartment of Physics,University of Science and Technology of China, Hefei, Anhui 230026,ChinaSearch for other works by this author on:Qian WangQian WangDepartment of Physics,University of Science and Technology of China, Hefei, Anhui 230026,ChinaSearch for other works by this author on:
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Chapter 3: Simulating Transmembrane Proteins with the Coarse-Grained SIRAH Force Field: Tips and Tricks for Setting Up and Running in AMBERByExequiel E. Barrera;Exequiel E. BarreraLaboratorio de Integración de Señales Celulares, IHEM, Universidad Nacional de Cuyo, CONICET, Mendoza,Argentina, CP 5500Institut Pasteur de Montevideo, Montevideo, Uruguay,Mataojo2020, CP 11400Search for other works by this author on:Sergio PantanoSergio PantanoInstitut Pasteur de Montevideo, Montevideo, Uruguay,Mataojo2020, CP 11400Search for other works by this author on:
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Chapter 4: A Guide to Titratable Martini SimulationsBySelim Sami;Selim SamiGroningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Groningen,The Netherlands
a) b) Search for other works by this author on:Fabian Grünewald;Fabian GrünewaldGroningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Groningen,The Netherlandsa) c) Search for other works by this author on:Paulo C. T. Souza;Paulo C. T. SouzaMolecular Microbiology and Structural Biochemistry, UMR 5086 CNRS and University of Lyon, Lyon,Franced) Search for other works by this author on:Siewert J. MarrinkSiewert J. MarrinkGroningen Biomolecular Sciences and Biotechnology Institute & Zernike Institute for Advanced Materials, University of Groningen, Groningen,The Netherlandse) Search for other works by this author on: -
Chapter 5: Simulating Membrane Proteins with Constant pH Molecular DynamicsByYandong HuangYandong HuangCollege of Computer Engineering,Jimei University, Xiamen 361021,ChinaSearch for other works by this author on:
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Chapter 6: Learning DeePMD-Kit: A Guide to Building Deep Potential ModelsByWenshuo Liang;Wenshuo LiangDP Technology, Beijing 100080,ChinaSearch for other works by this author on:Jinzhe Zeng;Jinzhe ZengLaboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, Rutgers the State University of New Jersey, New Brunswick, New Jersey 08901-8554,United StatesSearch for other works by this author on:Darrin M. York;Darrin M. YorkLaboratory for Biomolecular Simulation Research, Institute for Quantitative Biomedicine, and Department of Chemistry and Chemical Biology, Rutgers the State University of New Jersey, New Brunswick, New Jersey 08901-8554,United StatesSearch for other works by this author on:Linfeng Zhang;Linfeng ZhangDP Technology, Beijing 100080,ChinaAI for Science Institute, Beijing 100080,ChinaSearch for other works by this author on:Han WangHan WangLaboratory of Computational Physics, Institute of Applied Physics and Computational Mathematics, Fenghao East Road 2, Beijing 100094,P.R. ChinaSearch for other works by this author on:
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Chapter 7: Enhanced Sampling Based on Collective VariablesByHaohao Fu;Haohao FuCollege of Chemistry, Nankai University, Tianjin 300071,ChinaSearch for other works by this author on:Wensheng Cai;Wensheng CaiCollege of Chemistry, Nankai University, Tianjin 300071,ChinaSearch for other works by this author on:Christophe Chipot;Christophe ChipotLaboratoire International Associé CNRS and University of Illinois at Urbana−Champaign, UMR n°7019, Université de Lorraine, BP 70239, F-54506 Vandœuvre-lès-Nancy,FranceSearch for other works by this author on:Xueguang ShaoXueguang ShaoCollege of Chemistry, Nankai University, Tianjin 300071,ChinaSearch for other works by this author on:
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Chapter 8: A Practical Guide to Kinetics Calculation of Protein Conformational Change using Frequency Adaptive MetadynamicsByRongfeng Zou;Rongfeng ZouShenzhen Jingtai Technology Co., Ltd. (XtalPi), Floor 3, Sf Industrial Plant, No. 2 Hongliu Road, Fubao Community, Fubao Street, Futian District, Shenzhen 518045,ChinaSearch for other works by this author on:Tiefeng Song;Tiefeng SongThe Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining 314400,ChinaSearch for other works by this author on:Liangdong Wang;Liangdong WangCollege of Life Sciences, Zhejiang University, Hangzhou,ChinaSearch for other works by this author on:Lingyuan Ye;Lingyuan YeThe Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining 314400,ChinaSearch for other works by this author on:Yong WangYong WangThe Provincial International Science and Technology Cooperation Base on Engineering Biology, International Campus of Zhejiang University, Haining 314400,ChinaCollege of Life Sciences, Shanghai Institute for Advanced Study, Institute of Quantitative Biology, Zhejiang University, Hangzhou,ChinaSearch for other works by this author on:
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Chapter 9: TAPS: A Traveling-Salesman Based Automated Path Searching Method for Functional Dynamics of Complex Biomolecular SystemsByKun Xi;Kun XiWarshel Institute for Computational Biology, School of Life and Health Sciences,The Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong, 518172,ChinaSearch for other works by this author on:Lizhe ZhuLizhe ZhuWarshel Institute for Computational Biology, School of Life and Health Sciences,The Chinese University of Hong Kong (Shenzhen), Shenzhen, Guangdong, 518172,ChinaSearch for other works by this author on:
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Chapter 10: A Step-by-Step Guide on How to Construct Quasi-Markov State Models to Study Functional Conformational Changes of Biological MacromoleculesByAndrew Kai-Hei Yik;Andrew Kai-Hei YikDepartment of Chemistry,University of Wisconsin-Madison, Madison, WI 53706,USASearch for other works by this author on:Yunrui Qiu;Yunrui QiuDepartment of Chemistry,University of Wisconsin-Madison, Madison, WI 53706,USASearch for other works by this author on:Ilona Christy Unarta;Ilona Christy UnartaDepartment of Chemistry,University of Wisconsin-Madison, Madison, WI 53706,USASearch for other works by this author on:Siqin Cao;Siqin CaoDepartment of Chemistry,University of Wisconsin-Madison, Madison, WI 53706,USASearch for other works by this author on:Xuhui HuangXuhui HuangDepartment of Chemistry,University of Wisconsin-Madison, Madison, WI 53706,USASearch for other works by this author on:
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Chapter 11: Calculation of Relative Binding Free Energy for Mutations in Protein Complexes: The Alchemical PathByMei Feng;Mei FengLanzhou Center for Theoretical Physics, Key Laboratory of Theoretical Physics of Gansu Province, Lanzhou University, Lanzhou, Gansu 730000,ChinaInstitute of Quantitative Biology, Department of Physics, and College of Life Sciences, Zhejiang University, 310027 Hangzhou,ChinaSearch for other works by this author on:Yi Song;Yi SongInstitute of Quantitative Biology, Department of Physics, and College of Life Sciences, Zhejiang University, 310027 Hangzhou,ChinaSearch for other works by this author on:Ruhong ZhouRuhong ZhouInstitute of Quantitative Biology, Department of Physics, and College of Life Sciences, Zhejiang University, 310027 Hangzhou,ChinaDepartment of Chemistry,Columbia University, New York, NY 10027,USASearch for other works by this author on:
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AppendixByYong Wang;Yong WangCollege of Life Sciences,Shanghai Institute for Advanced Study, Institute of Quantitative Biology, Zhejiang University, Hangzhou, 310027,ChinaThe Provincial International Science and Technology Cooperation Base on Engineering Biology,International Campus of Zhejiang University, Haining, Zhejiang, 314400,ChinaSearch for other works by this author on:Ruhong ZhouRuhong ZhouCollege of Life Sciences,Shanghai Institute for Advanced Study, Institute of Quantitative Biology, Zhejiang University, Hangzhou, 310027,ChinaSearch for other works by this author on:
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IndexByYong Wang;Yong WangCollege of Life Sciences,Shanghai Institute for Advanced Study, Institute of Quantitative Biology, Zhejiang University, Hangzhou, 310027,ChinaThe Provincial International Science and Technology Cooperation Base on Engineering Biology,International Campus of Zhejiang University, Haining, Zhejiang, 314400,ChinaSearch for other works by this author on:Ruhong ZhouRuhong ZhouCollege of Life Sciences,Shanghai Institute for Advanced Study, Institute of Quantitative Biology, Zhejiang University, Hangzhou, 310027,ChinaSearch for other works by this author on: