a two-stage approach for improved prediction of residue contact maps两阶段方法改进预测残留接触地图.pdfVIP

BMC Bioinformatics BioMed Central Research article Open Access A two-stage approach for improved prediction of residue contact maps Alessandro Vullo, Ian Walsh and Gianluca Pollastri* Address: School of Computer Science and Informatics, University College Dublin, Belfield, Dublin 4, Ireland Email: Alessandro Vullo - alessandro.vullo@ucd.ie; Ian Walsh - ian.walsh@ucd.ie; Gianluca Pollastri* - gianluca.pollastri@ucd.ie * Corresponding author Published: 30 March 2006 Received: 22 September 2005 Accepted: 30 March 2006 BMC Bioinformatics 2006, 7:180 doi:10.1186/1471-2105-7-180 This article is available from: /1471-2105/7/180 © 2006 Vullo et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Protein topology representations such as residue contact maps are an important intermediate step towards ab initio prediction of protein structure. Although improvements have occurred over the last years, the problem of accurately predicting residue contact maps from primary sequences is still largely unsolved. Among the reasons for this are the unbalanced nature of the problem (with far fewer examples of contacts than non-contacts), the formidable challenge of capturing long-range interactions in the maps, the intrinsic difficulty of mapping one-d