- Broad coverage of computational chemistry and up-to-date information- Topics covered include bioinformatics, drug discovery, protein NMR, simulation methodologies, and applications in academic and industrial settings- Each chapter reviews the most recent literature on a specific topic of interest to computational chemists
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Section A 1. Advancements in Molecular Dynamics Simulations of Biomolecules on Graphical Processing Units Dong Xu, Mark J. Williamson, Ross C. Walker 2. Quantum Chemistry on Graphics Processing Units Andreas W. Gotz, Thorsten Wole, Ross C. Walker 3. Computing Free-Energy Profiles using Multidimensional Potentials of Mean Force and Polynomial Quadrature Methods Jonah Z. Vilseck and Orlando Acevedo 4. QM/MM Alchemical Free Energy Simulations: Challenges and Recent Developments Wei Yang, Qiang Cui, Donghong Min, and Hongzhi Li
Section B 5. Deciphering Structural Fingerprints for Metalloproteins with Quantum Chemical Calculations Yan Ling and Yong Zhang 6. Ab initio Electron Propagator Methods:Applications to Fullerenes and Nucleic Acid Fragments Viatcheslav G. Zakrzewski, Olga Dolgounitcheva, Alexander V. Zakjevskii and J. V. Ortiz
Section C 7. Using Density Functional Theory methods for modeling induction and dispersion interactions in ligand-protein complexes Hunter Utkov, Maura Livengood, and Mauricio Cafiero 8. Theoretical Calculations of Acid Dissociation Constants: A Review Article Kristin S. Alongi and George C. Shields 9. Antibiotics Targeting the Ribosome: Structure Based Design and the Nobel Prize Edward C. Sherer
Section D 10. Insights into the role of conformational transitions and metal ion binding in RNA catalysis from molecular simulations Tai-Sung Lee, George M. Giambasu, Darrin M. York 11. Atomistic Modeling of Solid Oxide Fuel Cells C. Heath Turner, Xian Wang, Kah Chun Lau, Wei An, and Brett I. Dunlap
Section E 12. Modelling signalling processes across cellular membranes using a mesoscopic approach George Khelashvili and Daniel Harries 13. Folding of conjugated proteins Dalit Shental-Bechor, Oshrit Arviv, Tzachi Hagai, and Yaakov Levy
Section F 14. Mean-force scoring functions for protein-ligand binding Sheng-You Huang and Xiaoqin Zou
David Spellmeyer, PhD is an Advisor to startup and early venture companies providing technical and scientific guidance on overcoming technological, scientific and business development challenges. He brings broad business and technical expertise from companies both large (IBM, DuPont) and small (Chiron, CombiChem, Signature BioScience, Nodality). David has been involved in the development of advanced functional assays such as Nodality's Single Cell Network Profiling (SCNP) and Signature's label-free molecular and cellular screening systems. He has extensive experience in the management and analysis of high dimensional data (combinatorial chemistry and SCNP). He has worked closely with business development teams in establishing over 20 non-dilutive strategic corporate partnerships, 4 mergers and acquisitions, several rounds of venture financing, and two joint ventures. David received his Ph.D. in theoretical organic chemistry from UCLA. He completed his post-doctoral training in pharmaceutical chemistry at UCSF, where he remains an active Adjunct Associate Professor.