Designing succinct structural alphabets.

ABSTRACT:

Motivation

The 3D structure of a protein sequence can be assembled from the substructures corresponding to small segments of this sequence. For each small sequence segment, there are only a few more likely substructures. We call them the 'structural alphabet' for this segment. Classical approaches such as ROSETTA used sequence profile and secondary structure information, to predict structural fragments. In contrast, we utilize more structural information, such as solvent accessibility and contact capacity, for finding structural fragments.

Results

Integer linear programming technique is applied to derive the best combination of these sequence and structural information items. This approach generates significantly more accurate and succinct structural alphabets with more than

SUBMITTER: Li SC 

PROVIDER: S-EPMC2718643 | biostudies-literature | 2008 Jul

REPOSITORIES: biostudies-literature