Description
Springer Guide To Biomolecular Simulations by Oren M. Becker , Martin Karplus
Molecular dynamics simulations have become instrumental in replacing our view of proteins as relatively rigid structures with the realization that they were dynamic systems, whose internal motions play a functional role. Over the years, such simulations have become a central part of biophysics. Applications of molecular dynamics in biophysics range over many areas. They are used in the structure determination of macromolecules with x-ray and NMR data, the modelling of unknown structures from their sequence, the study of enzyme mechanisms, the estimation of ligand-binding free energies, the evaluation of the role of conformational change in protein function, and drug design for targets of known structures. _x000D__x000D__x000D_The widespread application of molecular dynamics and related methodologies suggests that it would be useful to have available an introductory self-contained course by which students with a relatively limited background in chemistry, biology and computer literacy, can learn the fundamentals of the field. This Guide to Biomolecular Simulations tries to fill this need. The Guide consists of six chapters which provide the fundamentals of the field and six chapters which introduce the reader to more specialized but important applications of the methodology._x000D_ _x000D_Introduction: Note to the Student; _x000D_
Introduction: Note to the Instructor; _x000D_
Introduction: UNIX; _x000D_
Introduction: CHARMM Primer; _x000D_
Introduction: CHARMM Template Files; _x000D_
Lab 1: Introduction to Molecular Visualization; _x000D_
Lab 2: Energy and Minimization; _x000D_
Lab 3: Minimization and Analysis; _x000D_
Lab 4: Conformational Analysis; _x000D_
Lab 5:Basic Molecular Dynamics in Vacuum and in Solution; _x000D_
Lab 6: Molecular Dynamics and Analysis: Myoglobin; _x000D_
Lab 7: Ligand Dynamics in Myoglobin; _x000D_
Lab 8: Normal Mode Analysis; _x000D_
Lab 9: Free Energy Calculations; _x000D_
Lab 10: Minimum Energy Paths; _x000D_
Lab 11: Multiple Copy Simultaneous Search; _x000D_
Lab 12: Hemoglobin Cooperativity: the T-R transition._x000D_