A hierarchical, building-block-based computational scheme for protein structure prediction

C. J. Tsai*, B. Ma, Y. Y. Sham, S. Kumar, H. J. Wolfson, R. Nussinov

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

Protein folding is a hierarchical event in which transiently formed local structural elements asserible to yield the native conformation. We outline the hierarchical building block protein folding model, which is based on two premises. First, while the local building block elements may be unstable, they nevertheless have higher population times than all alternate conformations; second, protein folding progresses through a combinatorial assembly of these elements. In accordance with this model, we describe a building block cutting algorithm, implementing its rationale. Through as automated iterative application to the native structure we obtain an anatomy tree, in terms of protein folding. The anatomy tree automatically yields the most likely folding pathway. In particular, we describe how, by using this algorithm and the building blocks which are obtained, we expect to reduce substantially the computational time involved in simulations of protein folding.

Original languageEnglish
Pages (from-to)513-523
Number of pages11
JournalIBM Journal of Research and Development
Volume45
Issue number3-4
DOIs
StatePublished - 2001
Externally publishedYes

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