Deeper Profiles and Cascaded Recurrent and Convolutional Neural Networks for state-of-the-art Protein Secondary Structure Prediction
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|Title:||Deeper Profiles and Cascaded Recurrent and Convolutional Neural Networks for state-of-the-art Protein Secondary Structure Prediction||Authors:||Torrisi, Mirko; Kaleel, Manaz; Pollastri, Gianluca||Permanent link:||http://hdl.handle.net/10197/11582||Date:||26-Aug-2019||Online since:||2020-09-22T14:24:36Z||Abstract:||Protein Secondary Structure prediction has been a central topic of research in Bioinformatics for decades. In spite of this, even the most sophisticated ab initio SS predictors are not able to reach the theoretical limit of three-state prediction accuracy (88-90%), while only a few predict more than the 3 traditional Helix, Strand and Coil classes. In this study we present tests on different models trained both on single sequence and evolutionary profile-based inputs and develop a new state-of-the-art system with Porter 5. Porter 5 is composed of ensembles of cascaded Bidirectional Recurrent Neural Networks and Convolutional Neural Networks, incorporates new input encoding techniques and is trained on a large set of protein structures. Porter 5 achieves 84% accuracy (81% SOV) when tested on 3 classes and 73% accuracy (70% SOV) on 8 classes on a large independent set. In our tests Porter 5 is 2% more accurate than its previous version and outperforms or matches the most recent predictors of secondary structure we tested. When Porter 5 is retrained on SCOPe based sets that eliminate homology between training/testing samples we obtain similar results. Porter is available as a web server and standalone program at http://distilldeep.ucd.ie/porter/ alongside all the datasets and alignments.||Funding Details:||Irish Research Council||Type of material:||Journal Article||Publisher:||Springer||Journal:||Scientific Reports||Volume:||9||Issue:||1||Copyright (published version):||2019 the Authors||Keywords:||Protein structure prediction; Secondary structure; Deep learning; Machine learning; Bioinformatics; Structural bioinformatics||DOI:||10.1038/s41598-019-48786-x||Language:||en||Status of Item:||Peer reviewed|
|Appears in Collections:||Computer Science Research Collection|
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