This note explores the
concepts and algorithms that enable computational modeling of biological
molecules, in both theory and practice. Topics covered includes: The basics of
protein structure, Rosetta and structural modeling, Optimization techniques,
Analysis of protein structures and assessment of model quality, Full atom
refinement and side chain modeling, Hands-on: Side chain modeling, Homology
modelin, Protein-protein docking.
The aim of this book is that a non expert
can gain some appreciation for the intricacies involved, and in the current
state of affairs. The expert meanwhile, can gain a deeper understanding of the
topic.