Biomolecular Simulations : Methods and Protocols - Bonomi, Massimiliano; Camilloni, Carlo; SpringerLink (Online service) (New York, NY : Springer New York : Imprint: Humana, 2019)
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.
Keywords: Bioinformatics; Proteins .; Bioinformatics .; Computational biology .; Bioinformatics; Protein Science; Computer Appl. in Life Sciences