Guide to Biomolecular Simulations

ISBN-13: 9789401776356 / Angielski / Miękka / 2016 / 203 str.

Oren M. Becker; Martin Karplus

Opis

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.

Recenzje

From the reviews:

"The Guide to Biomolecular Simulations intends to provide students and nonexperts with an introductory, self-contained course about the application of molecular dynamics and related methodologies. The book emerged from a biophysics course held at Harvard in the 1990s and is therefore suited for standalone self-study as well as for classroom use ... . And finally, a reader who successfully worked through the book obtained significant experience in using CHARMM, one of the most widely used molecular dynamics packages in biomolecular simulations." (Anselm H. C. Horn, Journal of Chemical Information and Modeling, Vol. 46 (6), 2006)

Spis treści

Introduction: Note to the Student; Introduction: Note to the Instructor; Introduction: UNIX; Introduction: CHARMM Primer; Introduction: CHARMM Template Files; Lab 1: Introduction to Molecular Visualization; Lab 2: Energy and Minimization; Lab 3: Minimization and Analysis; Lab 4: Conformational Analysis; Lab 5:Basic Molecular Dynamics in Vacuum and in Solution; Lab 6: Molecular Dynamics and Analysis: Myoglobin; Lab 7: Ligand Dynamics in Myoglobin; Lab 8: Normal Mode Analysis; Lab 9: Free Energy Calculations; Lab 10: Minimum Energy Paths; Lab 11: Multiple Copy Simultaneous Search; Lab 12: Hemoglobin Cooperativity: the T-R transition.