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Comparative and Functional Genomics - Volume 4 2003, Issue 4, Pages 397-401

Conference review 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.

Abstract

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





Author: Xin Yuan, Yu Shao, and Christopher Bystroff

Source: https://www.hindawi.com/



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