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Comparative and Functional Genomics
Volume 4, Issue 4, Pages 397-401
Conference review

Ab Initio Protein Structure Prediction Using Pathway Models

Department of Biology, Rensselaer Polytechnic Institute, Troy 12180, NY, USA

Received 22 May 2003; Revised 30 May 2003; Accepted 2 June 2003

Copyright © 2003 Hindawi Publishing Corporation. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Ab initio prediction is the challenging attempt to predict protein structures based only on sequence information and without using templates. It is often divided into two distinct sub-problems: (a) the scoring function that can distinguish native, or native-like structures, from non-native ones; and (b) the method of searching the conformational space. Currently, there is no reliable scoring function that can always drive a search to the native fold, and there is no general search method that can guarantee a significant sampling of near-natives. Pathway models combine the scoring function and the search. In this short review, we explore some of the ways pathway models are used in folding, in published works since 2001, and present a new pathway model, HMMSTR-CM, that uses a fragment library and a set of nucleation/propagation-based rules. The new method was used for ab initio predictions as part of CASP5. This work was presented at the Winter School in Bioinformatics, Bologna, Italy, 10–14 February 2003.