Molecular Modeling of Proteins (Methods in Molecular Biology (443))

Molecular modeling has undergone a remarkable transformation in the last 20 years, as biomolecular simulation moves from the realm of specialists to the wider academic community. Molecular Modeling of Proteins provides thorough introductions and a compilation of step-by-step methods applicable to problems faced by non-specialists {u2013} especially those new to the software packages used in molecular modeling. Tips on troubleshooting and avoiding common pitfalls are included in this book, along with chapters covering a wide range of subjects ranging from free energy calculation to applications for drug design. Written by an internationally distinguished panel of investigators and outlining the most striking developments in the field, Molecular Modeling of Proteins is an invaluable resource for those in the industry, as well as a cutting-edge reference for students and professionals in the fields of chemistry, biochemistry, biology, biophysics and bioinformatics Molecular Dynamics Simulations / Erik R. Lindahl -- Monte Carlo Simulations / David J. Earl And Michael W. Deem -- Hybrid Quantum And Classical Methods For Computing Kinetic Isotope Effects Of Chemical Reactions In Solutions And In Enzymes / Jiali Gao [and Others] -- Comparison Of Protein Force Fields For Molecular Dynamics Simulations / Olgun Guvench And Alexander D. Mackerell, Jr. -- Normal Modes And Essential Dynamics / Steven Hayward And Bert L. De Groot -- Calculation Of Absolute Protein-ligand Binding Constants With The Molecular Dynamics Free Energy Perturbation Method / Hyung-june Woo -- Free Energy Calculations Applied To Membrane Proteins / Christophe Chipot -- Molecular Dynamics Simulations Of Membrane Proteins / Philip C. Biggin And Peter J. Bond -- Membrane-associated Proteins And Peptides / Marc F. Lensink -- Implicit Membrane Models For Membrane Protein Simulation / Michael Feig -- Comparative Modeling Of Proteins / Gerald H. Lushington -- Transmembrane Protein Models Based On High-throughput Molecular Dynamics Simulations With Experimental Constraints / Andrew J. Beevers And Andreas Kukol -- Nuclear Magnetic Resonance-based Modeling And Refinement Of Protein Three-dimensional Structures And Their Complexes / Gloria Fuentes, Aalt D.j. Van Dijk, And Alexandre M.j.j. Bonvin -- Conformational Changes In Protein Function / Haiguang Liu [and Others] -- Protein Folding And Unfolding By All-atom Molecular Dynamics Simulations / Hongxin Lei And Yong Duan -- Modeling Of Protein Misfolding In Disease / Edyta B. Małolepsza -- Identifying Putative Drug Targets And Potential Drug Leads : Starting Points For Virtual Screening And Docking / David S. Wishart -- Receptor Flexibility For Large-scale In Silico Ligand Screens : Chances And Challenges / B. Fischer, H. Merlitz, And W. Wenzel -- Molecular Docking / Garrett M. Morris And Marguerita Lim-wilby. Andreas Kukol [editor]. Includes Bibliographical References And Index. Molecular dynamics simulations / Erik R. Lindahl Monte Carlo simulations / David J. Earl and Michael W. Deem Hybrid quantum and classical methods for computing kinetic isotope effects of chemical reactions in solutions and in enzymes / Jiali Gao ... [et al.] Comparison of protein force fields for molecular dynamics simulations / Olgun Guvench and Alexander D. MacKerell, Jr. Normal modes and essential dynamics / Steven Hayward and Bert L. de Groot Calculation of absolute protein-ligand binding constants with the molecular dynamics free energy perturbation method / Hyung-June Woo Free energy calculations applied to membrane proteins / Christophe Chipot Molecular dynamics simulations of membrane proteins / Philip C. Biggin and Peter J. Bond Membrane-associated proteins and peptides / Marc F. Lensink Implicit membrane models for membrane protein simulation / Michael Feig Comparative modeling of proteins / Gerald H. Lushington Transmembrane protein models based on high-throughput molecular dynamics simulations with experimental constratints / Andrew J. Beevers and Andreas Kukol Nuclear magnetic resonance-based modeling and refinement of protein three-dimensional structures and their complexes / Gloria Fuentes, Aalt D.J. van Dijk, and Alexandre M.J.J. Bonvin Conformational changes in protein function / Haiguang Liu ... [et al.] Protein folding and unfolding by all-atom molecular dynamics simulations / Hongxin Lei and Yong Duan Modeling of protein misfolding in disease / Edyta B. Małolepsza Identifying putative drug targets and potential drug leads : starting points for virtual screening and docking / David S. Wishart Receptor flexibility for large-scale in silico ligand screens : chances and challenges / B. Fischer, H. Merlitz, and W. Wenzel Molecular docking / Garrett M. Morris and Marguerita Lim-Wilby. Front Matter....Pages i-xi Back Matter....Pages 3-23 ....Pages 25-36