GDFuzz3D: a method for protein 3D structure reconstruction from contact maps, based on a non-Euclidean distance function. (30th June 2015)

• Record Type: Journal Article
• Authors: Pietal, Michal J.; Bujnicki, Janusz M.; Kozlowski, Lukasz P.
• Is Part Of: Bioinformatics. Volume 31:Number 21(2015)
• Page Start: 3499
• Page End: 3505
• Publication Date: 2015-06-30
• Subjects: Bioinformatics -- Periodicals; Genomics -- Data processing -- Periodicals; Computational biology -- Periodicals; 572.80285
• DOI: 10.1093/bioinformatics/btv390
• Languages: English
• ISSNs: 1367-4803

Abstract

Abstract : Motivation: To date, only a few distinct successful approaches have been introduced to reconstruct a protein 3D structure from a map of contacts between its amino acid residues (a 2D contact map). Current algorithms can infer structures from information-rich contact maps that contain a limited fraction of erroneous predictions. However, it is difficult to reconstruct 3D structures from predicted contact maps that usually contain a high fraction of false contacts. Results: We describe a new, multi-step protocol that predicts protein 3D structures from the predicted contact maps. The method is based on a novel distance function acting on a fuzzy residue proximity graph, which predicts a 2D distance map from a 2D predicted contact map. The application of a Multi-Dimensional Scaling algorithm transforms that predicted 2D distance map into a coarse 3D model, which is further refined by typical modeling programs into an all-atom representation. We tested our approach on contact maps predicted de novo by MULTICOM, the top contact map predictor according to CASP10. We show that our method outperforms FT-COMAR, the state-of-the-art method for 3D structure reconstruction from 2D maps. For all predicted 2D contact maps of relatively low sensitivity (60–84%), GDFuzz3D generates more accurate 3D models, with the average improvement of 4.87 Å in terms of RMSD. Availability and implementation: GDFuzz3D server and standalone version are freely available at http://iimcb.genesilico.pl/gdserver/GDFuzz3D/ . Contact: [e-mail] Supplementary information: Supplementary data are available at Bioinformatics online.