This course covers modeling at the molecular level, with a focus on topics relevant to protein-ligand binding and cheminformatics. The first half of the course will cover topics in basic macromolecular structure and thermodynamics relevant to prediction and analysis of macromolecular interactions, and includes crystallography, energetics of hydrogen-bonding and hydrophobic interactions, and structure-based docking. The second half of the course will introduce the basics of cheminformatics, covering chemical structures, chemical descriptors, and methods for clustering and similarity-searching for compounds.
At the end of the course, students will be able to:
Recognize intermolecular interactions given a PDB structure, and understand the thermodynamic basis for each type of intermolecular interaction.
Read a protein structure paper critically.
Interpret enzyme kinetics data.
Recognize and calculate basic physiochemical properties of small molecule compounds.
Describe the underlying basis for cheminformatics techniques, and apply them to compare small molecule compounds.