Bioinformatics 2052

Lecture Date	Lecture Notes	Lecture Topic

March 1	Lecture 1 General References	Course Outline
March 12	Lecture 2	Conformations: Models and Definitions (see Erratum below)
March 15	Lecture 3	Structural & Functional Properties of Proteins
March 19	Lecture 4	Atomic Structure of Proteins
March 27	Lecture 5a Lecture 5b	Protein Conformation
March 29	Lecture 6 Miyazawa & Jernigan, 1996, JMB Residue-specific empirical potentials	Energetics: Interaction Potentials (I)
April 2	Lecture 7 Homework 3 Table IV.6.1	Energetics: Interaction Potentials (II)
April 5	Lecture 8 (ppt) (pdf)	Molecular Dynamics (MD) Simulations
April 9	Lecture 8.1 (ppt) (pdf)	Trajectory Analysis
April 16	Lecture 9	Solvation Thermodynamics
April 18	Bahar et al., 1997, Biochemistry	Monte Carlo (MC) Simulations
April 23	Lecture 10 Phi-Value Analysis	Folding Kinetics
April 26	Lecture 11 Protein Folding Kinetics	Kinetic Modeling
	Lecture 12	Topology-based models
	Lecture 13	Protein Structure Prediction