Molecular Modeling of Proteins [Paperback]

Molecular modeling has undergone a remarkable transformation in the last 20 years. This book provides thorough introductions and a compilation of step-by-step methods applicable to problems faced by non-specialists  especially those new to the software packages used in molecular modeling. Tips on troubleshooting and avoiding common pitfalls are included in the book, along with chapters covering a wide range of subjects. Links to downloadable software are also provided.

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  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.

Methodology 1 Molecular dynamics simulationsErik R. Lindahl 2 Monte Carlo simulationsMichael W. Deem, David J. Earl 3 Hybrid quantum and classical methods for computing kinetic isotope effects of chemical reactions in solutions and in enzymesJiali Gao, Dan. T. Major, Yao Fan, Yen-lin Lin, Shuhua Ma and Kin-Yiu Wong 4 Comparison of forcefields for molecular dynamics simulationsOlgun Guvench and Alexander D. MacKerell, Jr. 5 Normal modes and essential dynamicsSteven Hayward and Bert L. de Groot Free energy calcull3,