Protein 3D Structure Prediction Based on Multi-Level Description

KENTARO ONIZUKA[1] (onizuka@icot.or.jp)
KIYOSHI ASAI[2] (asai@etl.go.jp)
MASATO ISHIKAWA[2] (ishikawa@icot.or.jp)

[1]Institute for New Generation Computer Technology(ICOT)
1-4-28, Mita, Minato-ku, Tokyo, 108 Japan
[2]Electrotechnical Laboratory(ETL)
1-1-4, Umezono, Tsukuba Ibaraki, 305 Japan

Abstract

We propose a novel scheme for protein 3D structure prediction using the Multi-level Description scheme (MLD). In this prediction scheme, a local conformation is not only determined by the primary structure at that region (i.e., primary constraints) but is also constrained by the neighboring or surrounding local conformations (i.e., geometric constraints).

The MLD describes a protein conformation with multiple levels of different scales and degrees of abstraction. This scheme facilitate to model the geometric constraints between the neighboring local conformations by analyzing the frequency of overlapping patterns of the local conformations. The primary constraints are modeled by analyzing the relationship between the primary structure and the local conformation at that region.

The MLD representing a real protein conformation must satisfy most of the constraints above. Thus, a protein conformation can be predicted by searching for the optimal MLD that bset satisfies the constraints. This problems is formulated as a combinatorial optimization problem.