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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.

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Innovations in Biomolecular Modeling and Simulations Volume 2

The Royal Society of Chemistry

Contents

Volume 1, 
Beginnings, 
Chapter 1 Personal Perspective Harold A. Scheraga, 3, 
Chapter 2 Fashioning NAMD, a History of Risk and Reward: Klaus Schulten Reminisces Lisa Pollack, 8, 
Force Fields and Electrostatics, 
Chapter 3 Towards Biomolecular Simulations with Explicit Inclusion of Polarizability: Development of a CHARMM Polarizable Force Field based on the Classical Drude Oscillator Model C. M. Baker, E. Darian and A. D. MacKerell Jr, 23, 
Chapter 4 Integral Equation Theory of Biomolecules and Electrolytes Tyler Luchko, In Suk Joung and David A. Case, 51, 
Chapter 5 Molecular Simulation in the Energy Biosciences Xiaolin Cheng, Jerry M. Parks, Loukas Petridis, Benjamin Lindner, Roland Schulz, Hao-Bo Guo, Goundla Srinivas and Jeremy C. Smith, 87, 
Sampling and Rates, 
Chapter 6 Enhancing the Capacity of Molecular Dynamics Simulations with Trajectory Fragments Alfredo E. Cardenas and Ron Elber, 117, 
Chapter 7 Computing Reaction Rates in Bio-molecular Systems Using Discrete Macro-states Eric Darve and Ernest Ryu, 138, 
Chapter 8 Challenges in Applying Monte Carlo Sampling to Biomolecular Systems M. Mezei, 207, 
Coarse Graining and Multiscale Models, 
Chapter 9 Coarse-grain Protein Models N. Ceres and R. Lavery, 219, 
Chapter 10 Generalised Multi-level Coarse-grained Molecular Simulation and its Application to Myosin-V Movement William R. Taylor and Zoe Katsimitsoulia, 249, 
Chapter 11 Top-down Mesoscale Models and Free Energy Calculations of Multivalent Protein-Protein and Protein-Membrane Interactions in Nanocarrier Adhesion and Receptor Trafficking Jin Liu, Neeraj J. Agrawal, David M. Eckmann, Portonovo S. Ayyaswamy and Ravi Radhakrishnan, 272, 
Chapter 12 Studying Proteins and Peptides at Material Surfaces Jun Feng, Gillian C. Lynch and B. Montgomery Pettitt, 293, 
Chapter 13 Multiscale Design: From Theory to Practice J. Fish, V. Filonova and Z. Yuan, 321, 
Subject Index, 345, 
Volume 2, 
Atomistic Simulations of Nucleic Acids and Nucleic Acid Complexes, 
Chapter 1 Modelling Nucleic Acid Structure and Flexibility: From Atomic to Mesoscopic Scale Filip Lankas, 3, 
Chapter 2 Molecular Dynamics and Force Field Based Methods for Studying Quadruplex Nucleic Acids Shozeb M Haider and Stephen Neidle, 33, 
Chapter 3 Opposites Attract: Shape and Electrostatic Complementarity in Protein-DNA Complexes Robert C. Harris, Travis Mackoy, Ana Carolina Dantas Machado, Darui Xu, Remo Rohs and Marcia Oliveira Fenley, 53, 
Chapter 4 Intrinsic Motions of DNA Polymerases Underlie Their Remarkable Specificity and Selectivity and Suggest a Hybrid Substrate Binding Mechanism Meredith C. Foley, Karunesh Arora and Tamar Schlick, 81, 
Chapter 5 Molecular Dynamics Structure Prediction of a Novel Protein–DNA Complex: Two HU Proteins with a DNA Four-way Junction Elizabeth G. Wheatley, Susan N. Pieniazek, Iulia Vitoc, Ishita Mukerji and D.L. Beveridge, 111, 
Chapter 6 Molecular Dynamics Simulations of RNA Molecules J. Šponer, M. Otyepka, P. Banáš, K. Réblová and N. G. Walter, 129, 
Chapter 7 The Structure and Folding of Helical Junctions in RNA David M. J. Lilley, 156, 
DNA Folding, Knotting, Sliding and Hopping, 
Chapter 8 Structure and Dynamics of Supercoiled DNA Knots and Catenanes Guillaume Witz and Andrzej Stasiak, 179, 
Chapter 9 Monte Carlo Simulations of Nucleosome Chains to Identify Factors that Control DNA Compaction and Access Karsten Rippe, Rene Stehr and Gero Wedemann, 198, 
Chapter 10 Sliding Dynamics Along DNA: A Molecular Perspective Amir Marcovitz and Yaakov Levy, 236, 
Drug Design, 
Chapter 11 Structure-based Design Technology CONTOUR and its Application to Drug Discovery Zhijie Liu, Peter Lindblom, David A. Claremon and Suresh B. Singh, 265, 
Chapter 12 Molecular Simulation in Computer-aided Drug Design: Algorithms and Applications Robert V. Swift and Rommie E. Amaro, 281, 
Chapter 13 Computer-aided Drug Discovery: Two Antiviral Drugs for HIV/AIDS J. Andrew McCammon, 316, 
Subject Index, 320,