Modeling Biomolecular Site Dynamics

Methods and Protocols

  • William S. Hlavacek

Part of the Methods in Molecular Biology book series (MIMB, volume 1945)

Table of contents

  1. Front Matter
    Pages i-xix
  2. Bruce E. Shapiro, Eric Mjolsness
    Pages 1-32
  3. Ryan Suderman, G. Matthew Fricke, William S. Hlavacek
    Pages 33-42
  4. Oana Andrei, Maribel Fernández, Hélène Kirchner, Bruno Pinaud
    Pages 43-70
  5. Jesper Romers, Sebastian Thieme, Ulrike Münzner, Marcus Krantz
    Pages 71-118
  6. Alida Palmisano, Stefan Hoops, Layne T. Watson, Thomas C. Jones Jr, John J. Tyson, Clifford A. Shaffer
    Pages 119-139
  7. Tobias Helms, Tom Warnke, Adelinde M. Uhrmacher
    Pages 141-160
  8. Bastian R. Angermann, Martin Meier-Schellersheim
    Pages 161-177
  9. Jose-Juan Tapia, Ali Sinan Saglam, Jacob Czech, Robert Kuczewski, Thomas M. Bartol, Terrence J. Sejnowski et al.
    Pages 203-229
  10. Richard Henze, Gerd Grünert, Bashar Ibrahim, Peter Dittrich
    Pages 231-249
  11. Timothy D. Majarian, Ivan Cao-Berg, Xiongtao Ruan, Robert F. Murphy
    Pages 251-264
  12. Matteo Cavaliere, Vincent Danos, Ricardo Honorato-Zimmer, William Waites
    Pages 271-296
  13. Bernhard Steiert, Clemens Kreutz, Andreas Raue, Jens Timmer
    Pages 341-362
  14. Anatoly Sorokin, Oksana Sorokina, J. Douglas Armstrong
    Pages 363-390
  15. William S. Hlavacek, Jennifer A. Csicsery-Ronay, Lewis R. Baker, María del Carmen Ramos Álamo, Alexander Ionkov, Eshan D. Mitra et al.
    Pages 391-419
  16. Back Matter
    Pages 421-423

About this book


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.

Cutting-edge and thorough, Modeling Biomolecular Site Dynamics: Methods and Protocols is a valuable resource for both the novice and expert rule-based modeler. It will also appeal to systems biologists and help them enhance their studies with easy-to-read and write rule-based models.


mathematical models cellular regulatory systems rule-based modeling spatial modeling genetic programming compartmental modeling spatial modeling proteomics Markov chain aggregation model parameters

Editors and affiliations

  • William S. Hlavacek
    • 1
  1. 1.Theoretical Biology and Biophysics Group, Theoretical DivisionLos Alamos National LaboratoryLos AlamosUSA

Bibliographic information

  • DOI
  • Copyright Information Springer Science+Business Media, LLC, part of Springer Nature 2019
  • Publisher Name Humana Press, New York, NY
  • eBook Packages Springer Protocols
  • Print ISBN 978-1-4939-9100-6
  • Online ISBN 978-1-4939-9102-0
  • Series Print ISSN 1064-3745
  • Series Online ISSN 1940-6029
  • Buy this book on publisher's site
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