Biomolecular Simulations : Methods and Protocols / edited by Massimiliano Bonomi, Carlo Camilloni.

Format:

Book

Contributor:

Bonomi, Massimiliano, editor.

Camilloni, Carlo, editor.

SpringerLink (Online service)

Series:

Springer Protocols (Springer-12345)

Methods in molecular biology 1064-3745 ; 2022.

Methods in Molecular Biology, 1064-3745 ; 2022

Language:

English

Subjects (All):

Bioinformatics.

Proteins.

Computational biology.

Protein Science.

Computer Appl. in Life Sciences.

Local Subjects:

Bioinformatics.

Protein Science.

Computer Appl. in Life Sciences.

Physical Description:

1 online resource (XIII, 581 pages) : 185 illustrations, 155 illustrations in color.

Edition:

First edition 2019.

Contained In:

Springer eBooks

Place of Publication:

New York, NY : Springer New York : Imprint: Humana, 2019.

System Details:

text file PDF

Summary:

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.

Contents:

Atomistic Force Fields for Proteins

Force Fields for Small Molecules

Improvement of RNA Simulations with Torsional Revisions of the AMBER Force Field

Quantum Chemical and QM/MM Models in Biochemistry

A Practical View of the Martini Force Field

Using SMOG 2 to Simulate Complex Biomolecular Assemblies

Replica Exchange Methods for Biomolecular Simulations

Metadynamics to Enhance Sampling in Biomolecular Simulations

Protein-Ligand Binding Free Energy Calculations with FEP+

Ligand Binging Calculations with Metadynamics

The Adaptive Path Collective Variable - A Versatile Biasing Approach to compute the Average Transition Path and Free Energy of Molecular Transitions

Google-Accelerated Biomolecular Simulations

A Practical Guide to the Simultaneous Determination of Protein Structure and Dynamics using Metainference

Inferring Structural Ensembles of Flexible and Dynamic Macromolecules using Bayesian, Maximum Entropy, and Minimal-Ensemble Refinement Methods

Modeling Biological Complexes using Integrative Modeling Platform

Co-Evolutionary Analysis of Protein Sequences for Molecular Modeling

Coarse Graining of a Giant Molecular System: The Chromatin Fiber

Analyzing Biomolecular Ensembles

Using Data-Reduction Techniques to Analyze Biomolecular Trajectories

Analysis Libraries for Molecular Trajectories: A Cross-Language Synopsis

Analyzing and Biasing Simulations with PLUMED.

Other Format:

Printed edition:

ISBN:

978-1-4939-9608-7

9781493996087

Access Restriction:

Restricted for use by site license.