These are notes about
using mathematics to study the molecular structure of molecules, especially long
organic molecules like DNA and proteins. Topics covered includes: Molecular
Genetics: DNA, Proteins, Frames and moving frames, Orthogonal transformations
and Rotations, Torsion angles and pdb files, X-ray Crystallography, Lattices,
and Fourier Series, Nuclear Magnetic Resonance and distance geometry, Protein
Folding.
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.