UC Berkeley :: EECS :: rluo@uclink
Determine protein structure from amino acid
sequence.Ray Luo
UC Berkeley EECS
UC Berkeley :: EECS :: rluo@uclink
Information flows from DNA to RNA to polypeptide string to folded protein.
Polypeptide:amino acidsequence
Folded protein:3D structure
UC Berkeley :: EECS :: rluo@uclink
Amino acid sequence encodes the 3D structure and function of a protein.
UC Berkeley :: EECS :: rluo@uclink
Comparative methods align sequence against known proteins in a database.
Newprotein
Protein in database
: Protein in database: New proteinAlignment {
UC Berkeley :: EECS :: rluo@uclink
De novo methods search for a stable structure by simulating protein folding.
Folded proteinUnfolded protein
Transition state
- Fr
ee e
nerg
y
Reaction coordinate
UC Berkeley :: EECS :: rluo@uclink
Most proteins have complicated 3D structures requiring efficient algorithms.
De novo
Comparative
UC Berkeley :: EECS :: rluo@uclink
Utilize de novo simulation to support comparative alignment and vice versa.
Proteinfolding
Sequencealignment
SamplingClustering
Cooperative Approach:
UC Berkeley :: EECS :: rluo@uclink
Determine protein structure from amino acid sequence using comparative alignment and protein folding simulation.
Proteinfolding
Sequencealignment