<p>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.</p> <p>
			<italic>Ab initio</italic> 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 <italic>ab initio</italic>
predictions as part of CASP5. This work was presented at the Winter School in
Bioinformatics, Bologna, Italy, 10–14 February 2003.</p>
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Comp Funct Genomics. 2003 Jul; 4(4):397-401