Prediction of polyproline II secondary structure propensity in proteins
|Title:||Prediction of polyproline II secondary structure propensity in proteins||Authors:||O'Brien, Kevin; Mooney, Catherine; Lopez, Cyril; Pollastri, Gianluca; Shields, Denis C.||Permanent link:||http://hdl.handle.net/10197/11764||Date:||15-Jan-2020||Online since:||2020-12-01T15:28:51Z||Abstract:||Background: The polyproline II helix (PPIIH) is an extended protein left-handed secondary structure that usually but not necessarily involves prolines. Short PPIIHs are frequently, but not exclusively, found in disordered protein regions, where they may interact with peptide-binding domains. However, no readily usable software is available to predict this state. Results: We developed PPIIPRED to predict polyproline II helix secondary structure from protein sequences, using bidirectional recurrent neural networks trained on known three-dimensional structures with dihedral angle filtering. The performance of the method was evaluated in an external validation set. In addition to proline, PPIIPRED favours amino acids whose side chains extend from the backbone (Leu, Met, Lys, Arg, Glu, Gln), as well as Ala and Val. Utility for individual residue predictions is restricted by the rarity of the PPIIH feature compared to structurally common features. Conclusion: The software, available at http://bioware.ucd.ie/PPIIPRED, is useful in large-scale studies, such as evolutionary analyses of PPIIH, or computationally reducing large datasets of candidate binding peptides for further experimental validation.||Funding Details:||European Commission Horizon 2020
Science Foundation Ireland
|Type of material:||Journal Article||Publisher:||The Royal Society||Journal:||Royal Society Open Science||Volume:||7||Issue:||1||Copyright (published version):||2020 the Authors||Keywords:||Proproline helix; PPII; Polyproline II helices; Predictor; Protein; Secondary structure||DOI:||10.1098/rsos.191239||Language:||en||Status of Item:||Peer reviewed||ISSN:||2054-5703||This item is made available under a Creative Commons License:||https://creativecommons.org/licenses/by-nc-nd/3.0/ie/|
|Appears in Collections:||Computer Science Research Collection|
Show full item record
If you are a publisher or author and have copyright concerns for any item, please email email@example.com and the item will be withdrawn immediately. The author or person responsible for depositing the article will be contacted within one business day.