Modeling Biomolecular Site Dynamics
Modeling Biomolecular Site Dynamics: Methods and Protocols
by William S. Hlavacek
English | 2019 | ISBN: 1493991000 | 423 Pages | PDF | 18 MB
by William S. Hlavacek
English | 2019 | ISBN: 1493991000 | 423 Pages | PDF | 18 MB
This volume covers a variety of topics related to the practice of rule-based modeling, a type of mathematical modeling useful for studying biomolecular site dynamics. There is an emphasis on software tools and detailed descriptions of techniques. The chapters in this book discuss topics such as software tools and frameworks for compartmental modeling (Pycellerator, RuleBuilder, Prgy, rxncon, MSMB, and ML-Rules); tools for spatial modeling (Simmune, Smoldyn, MCell-R, SRSim, and CellOrganizer); rule-based models to analyze proteomic data; model annotation; Markov chain aggregation; BioJazz; and methods to identify model parameters (Data2Dynamics, RKappa, and BioNetFit). Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary resources, step-by-step, readily reproducible protocols, and tips on troubleshooting and avoiding known pitfalls.