The chemical and biological sciences face unprecedented opportunities in the 21st century. A confluence of factors from parallel universes - advances in experimental techniques in biomolecular structure determination, progress in theoretical modeling and simulation for large biological systems, and breakthroughs in computer technology - has opened new avenues of opportunity as never before. Now, experimental data can be interpreted and further analysed by modeling, and predictions from any approach can be tested and advanced through companion methodologies and technologies. This two volume set describes innovations in biomolecular modeling and simulation, in both the algorithmic and application fronts. With contributions from experts in the field, the books describe progress and innovation in areas including: simulation algorithms for dynamics and enhanced configurational sampling, force field development, implicit solvation models, coarse-grained models, quantum-mechanical simulations, protein folding, DNA polymerase mechanisms, nucleic acid complexes and simulations, RNA structure analysis and design and other important topics in structural biology modeling. The books are aimed at graduate students and experts in structural biology and chemistry and the emphasis is on reporting innovative new approaches rather than providing comprehensive reviews on each subject.
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