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

2. 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 ::

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

4. 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 ::

5. 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 ::

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

7. 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 ::

8. 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 ::