1. Overview-the many levels of systems biology 2. Experimental methods for measuring protein-protein interactions and their limitations 3. Data sources for information about proteins and their

Algorithms for detecting structure similarity Dynamic Programming works on 1D strings- reduce problem to this cant accommodate topological changes example: Secondary Structure Alignment Program(SSAP) 3D Comparison/Clustering

For a molecular simulation or model you need 1. a representation of the protein 2. An energy function 3. a search algorithm or optimizer

1. Grow crystals-structure determination by X-ray crystallography relies on the repeating structure of a crystalline lattice 2. Collect a diffraction pattern-periodically spaced atoms in the crystal give specific\spots\where x-rays interfere constructively

Review of protein structure hierarchy Nonpolar, Hydrophobic R-grou Primary structure Glycin (Gly, G) Aa,A≌ alina (VaL V. Leucine(Lou, L) Isoleucine{,非 MAAAAAAGPEMVRGQVE 20 amino acids Phenylalanine(Ph,月

Review -Homology Modeling Identify a protein with similar sequence for which a structure has been solved (the template) Align the target sequence with the template Use the alignment to build an approximate structure for the target

Review of markov HMM Models for dna Markov Models for splice sites Hidden Markov models looking under the hood The Viterbi algorithm Real World HMMs

Outline Brief review of protein structure chou -Fasman- predictions Garnier, Osguthorpe and Robson Helical wheels and hydrophobic moments Neural networks Nearest neighbor methods Consensus prediction approaches

Markov Hidden markov models for dna Markov Models for splice sites Hidden Markov models looking under the hood The Viterbi algorithm Real World HMMs

Review of markov models DNA Evolution CpG Island HMM The viterbi algorithm Real World HMMs Markov models for dna evolution Ch. 4 of Mount