|
|
Computational
Biology Branch |
|||||||||||
|
|
Group Members: Teresa Przytycka Collaborators: J.Jeong Piotr Berman reference: Jieun Jeong, Piotr Berman, and Teresa M Przytycka Bringing folding pathways into strand pairing prediction The topology of beta-sheets is defined by the
pattern of hydrogen-bonded strand pairing. Therefore, predicting
hydrogen bonded strand partners is a fundamental step towards predicting $\beta$-sheet
topology. At the same
time, finding the correct partners is very difficult due to long range
interactions involved in strand pairing. Additionally, patterns of aminoacids involved, in
$\beta$-sheet formations are
very general and therefore difficult to use for computational recognition of specific
contacts between strands. In this work, we report a new strand pairing
algorithm. To address above mentioned
difficulties, our algorithm attempts to mimic elements of the folding
process. Namely, in addition to ensuring that the predicted hydrogen bonded
strand pairs satisfy basic global consistency constraints, it takes into
account hypothetical folding pathways. Consistently with this view, introducing hydrogen bonds between a
pair of strands changes the probabilities of forming hydrogen
bonds between other pairs of strand. We demonstrate that this approach
provides an improvement over previously proposed algorithms. We also
compare the performance of this method to that of a global optimization
algorithm that poses the problem as integer linear programming optimization problem
|
||||||||||
