Determine protein structure from amino acid sequence

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UC Berkeley :: EECS :: rluo@uclink Determine protein structure from amino acid sequence. Ray Luo UC Berkeley EECS ? UC Berkeley :: EECS :: rluo@uclink

UC Berkeley :: EECS :: rluo@uclink Information flows from DNA to RNA to polypeptide string to folded protein. Polypeptide: amino acid sequence Folded protein: 3D structure UC Berkeley :: EECS :: rluo@uclink

UC Berkeley :: EECS :: rluo@uclink Amino acid sequence encodes the 3D structure and function of a protein. UC Berkeley :: EECS :: rluo@uclink

UC Berkeley :: EECS :: rluo@uclink Comparative methods align sequence against known proteins in a database. New protein Protein in database : Protein in database : New protein Alignment { UC Berkeley :: EECS :: rluo@uclink

UC Berkeley :: EECS :: rluo@uclink De novo methods search for a stable structure by simulating protein folding. Folded protein Unfolded protein Transition state - Free energy Reaction coordinate UC Berkeley :: EECS :: rluo@uclink

UC Berkeley :: EECS :: rluo@uclink Most proteins have complicated 3D structures requiring efficient algorithms. ? De novo Comparative UC Berkeley :: EECS :: rluo@uclink

UC Berkeley :: EECS :: rluo@uclink Utilize de novo simulation to support comparative alignment and vice versa. Protein folding Sequence alignment Sampling Clustering Cooperative Approach: UC Berkeley :: EECS :: rluo@uclink

UC Berkeley :: EECS :: rluo@uclink Determine protein structure from amino acid sequence using comparative alignment and protein folding simulation. Protein folding Sequence alignment UC Berkeley :: EECS :: rluo@uclink

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