Biomolecular Simulations

1. Integrative Approaches for Biomolecular Simulations

   1. Coarse Graining of a Giant Molecular System: The Chromatin Fiber

      • Guido Tiana, Luca Giorgetti

      Pages 399-411

2. Analyzing, Visualizing, and Comparing Biomolecular Simulations

   1. Front Matter

      Pages 413-413

      PDF

   2. Analyzing Biomolecular Ensembles

      • Matteo Lambrughi, Matteo Tiberti, Maria Francesca Allega, Valentina Sora, Mads Nygaard, Agota Toth et al.

      Pages 415-451

   3. Using Data-Reduction Techniques to Analyze Biomolecular Trajectories

      • Gareth A. Tribello, Piero Gasparotto

      Pages 453-502

   4. Analysis Libraries for Molecular Trajectories: A Cross-Language Synopsis

      • Toni Giorgino

      Pages 503-527

   5. Analyzing and Biasing Simulations with PLUMED

      • Giovanni Bussi, Gareth A. Tribello

      Pages 529-578

3. Back Matter

   Pages 579-581

   PDF

This volume explores the recent advancements in biomolecular simulations of proteins, small molecules, and nucleic acids, with a primary focus on classical molecular dynamics (MD) simulations at atomistic, coarse-grained, and quantum/ab-initio levels. The chapters in this book are divided into four parts: Part One looks at recent techniques used in the development of physic-chemical models of proteins, small molecules, nucleic acids, and lipids; Part Two discusses enhanced sampling and free-energy calculations; Part Three talks about integrative computational and experimental approaches for biomolecular simulations; and Part Four focuses on analyzing, visualizing, and comparing biomolecular simulations. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls.

 
Cutting-edge and comprehensive, Biomolecular Simulations: Methods and Protocols is a valuable resource for both novice and expert researchers who are interested in studying different areas of biomolecular simulations, and discovering new tools to progress their future projects.

• bioinformatics
• force fields
• kinetics calculations
• ligand binding
• maximum Entropy

• Structural Bioinformatics Unit, Institut Pasteur, CNRS UMR 3528, Paris, France

  Massimiliano Bonomi

• Dipartimento di Bioscienze, Università degli Studi di Milano, Milano, Italy

  Carlo Camilloni

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