Innovations in Biomolecular Modeling and Simulations

"This two-volume set contains contributions from many distinguished computational chemists and will catch the attention of computational chemists, computational biologists, and biophysicists (both experimental and theoretical)""Even though some areas have already been extensively reviewed in recent papers, as a theoretician with an interest in nucleic acid chemistry, I still found information that I did not know before. Both volumes are typical examples.""To summarize, this is an interesting book, with interesting chapters in both volumes."

• Volume 1 Beginnings;Personal Perspective;Fashioning NAMD, a History of Risk and Reward: Klaus Schulten Reminisces;Towards Biomolecular Simulations with Explicit Inclusion of Polarizability: Development of a CHARMM Polarizable Force Field based on the Classical Drude Oscillator Model;Integral Equation Theory of Biomolecules and Electrolytes;Molecular Simulation in the Energy Biosciences;Sampling and rates;Dynamics Simulations with Trajectory Fragments;Computing Reaction Rates in Biomolecular Systems using discrete macrostates;Challenges in applying Monte Carlo sampling to biomolecular systems;Coarse graining and multiscale models;Coarse Grained Protein Models;Generalized Multi-Level Coarse-Grained Molecular Simulation and Its Applucation to Myosin-V Movement;Top-down Mesoscale Models and Free Energy Calculations of Multivalent Protein-Protein and Protein-Membrane Interactions in Nanocarrier Adhesion and Receptor Trafficking;Studying Proteins and Peptides at Material Surfaces;Multiscale Design: From Theory to Practice. Volume 2 Atomistic simulations of nucleic acids and nucleic acid complexes;Modeling nucleic acid structure and flexibility: from atomic to mesoscopic scale;Molecular dynamics and force field based methods for studying quadruplex nucleic acids;Opposites attract: Shape and Electrostatic Complementarity in Protein/DNA Complexes;Intrinsic motions of DNA polymerases underlie their remarkable specificity and selectivity and suggest a hybrid substrate binding mechanism;Molecular Dynamics Structure Prediction of a Novel Protein/DNA Complex: Two HU Proteins with a DNA Four-way Junction;Molecular Dynamics Simulations of RNA Molecules;The Structure and Folding of Helical Junctions in RNA;DNA folding, knotting, sliding and hopping;Simulations of DNA Knots and Catenanes;Monte Carlo Simulations of Nucleosome Chains to Idenitfy Factors that control DNA Compaction and Access;Sliding Dynamics Along DNA: a Molecular Perspective;Drug design;Structure-based design technology: CONTOUR and its aplication to drug discovery;Molecular simulation in computer-aided drug design: algorithms and applications;Computer-aided drug discovery: two antiviral drugs for HIV AIDS