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Protein Contact Map Prediction Based on ResNet and DenseNet
Stockholm University, Faculty of Science, Department of Biochemistry and Biophysics. Stockholm University, Science for Life Laboratory (SciLifeLab).
Number of Authors: 42020 (English)In: BioMed Research International, ISSN 2314-6133, E-ISSN 2314-6141, Vol. 2020, article id 7584968Article in journal (Refereed) Published
Abstract [en]

Residue-residue contact prediction has become an increasingly important tool for modeling the three-dimensional structure of a protein when no homologous structure is available. Ultradeep residual neural network (ResNet) has become the most popular method for making contact predictions because it captures the contextual information between residues. In this paper, we propose a novel deep neural network framework for contact prediction which combines ResNet and DenseNet. This framework uses 1D ResNet to process sequential features, and besides PSSM, SS3, and solvent accessibility, we have introduced a new feature, position-specific frequency matrix (PSFM), as an input. Using ResNet's residual module and identity mapping, it can effectively process sequential features after which the outer concatenation function is used for sequential and pairwise features. Prediction accuracy is improved following a final processing step using the dense connection of DenseNet. The prediction accuracy of the protein contact map shows that our method is more effective than other popular methods due to the new network architecture and the added feature input.

Place, publisher, year, edition, pages
2020. Vol. 2020, article id 7584968
National Category
Biological Sciences Bioinformatics (Computational Biology)
Identifiers
URN: urn:nbn:se:su:diva-181870DOI: 10.1155/2020/7584968ISI: 000529176300006PubMedID: 32337273OAI: oai:DiVA.org:su-181870DiVA, id: diva2:1432173
Available from: 2020-05-26 Created: 2020-05-26 Last updated: 2022-03-23Bibliographically approved

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Elofsson, Arne

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