Statistical and Computational Issues in

Ab Initio Protein Structure

Prediction

Ingo Ruczinski,

John Hopkins School of Public Health

The prediction of protein tertiary structure solely from its amino acid sequence (``de novo'' or ``ab initio'' protein structure prediction) is one of the most important unsolved problems in molecular biology. We recently developed the Rosetta algorithm for ab initio protein structure prediction which generates protein structures from fragment libraries using simulated annealing. I will describe the basics of the folding algorithm, and discuss some of the statistical and computational issues related to ab initio structure

prediction.

[1] Bonneau R, Tsai J, Ruczinski I, Baker D:

"Functional inferences from blind ab initio protein structure predictions",

Journal of Structural Biology 134(2-3):186-90, 2001.

[2] Bonneau R, Tsai J, Ruczinski I, Chivian D, Rohl C, Strauss C, Baker D:

"Rosetta in CASP4: progress in ab protein initio structure prediction",

Proteins: Structure, Function and Genetics 45:S5, 2001.

[3] Ruczinski I, Kooperberg C, Bonneau R, Baker D:

"Distributions of beta sheets in proteins with application to

structure prediction",

Proteins: Structure, Function and Genetics (to appear).

[4] Simons KT, Ruczinski I, Kooperberg C, Fox BA, Bystroff C, Baker D:

"Improved recognition of native-like protein structures using a

combination of sequence-dependent and sequence-independent

features of proteins",

Proteins 34(1):82-95, 1999.