Improving Inter-Helix Contact Prediction With Local 2D Topological Information
Date
2023-05-08
Authors
Journal Title
Journal ISSN
Volume Title
Publisher
IEEE/ACM Transactions on Computational Biology and Bioinformatics
Abstract
Inter-helix contact prediction is to identify residue contact across different helices in α-helical integral membrane proteins. Despite the progress made by various computational methods, contact prediction remains as a challenging task, and there is no method to our knowledge that directly tap into the contact map in an alignment free manner. We build 2D contact models from an independent dataset to capture the topological patterns in the neighborhood of a residue pair depending it is a contact or not, and apply the models to the state-of-art method's predictions to extract the features reflecting 2D inter-helix contact patterns. A secondary classifier is trained on such features. Realizing that the achievable improvement is intrinsically hinged on the quality of original predictions, we devise a mechanism to deal with the issue by introducing, 1) partial discretization of original prediction scores to more effectively leverage useful information 2) fuzzy score to assess the quality of the original prediction to help with selecting the residue pairs where improvement is more achievable. The cross-validation results show that the prediction from our method outperforms other methods including the state-of-the-art method (DeepHelicon) by a notable degree even without using the refinement selection scheme. By applying the refinement selection scheme, our method outperforms the state-of-the-art method significantly in these selected sequences.
Description
This article was originally published in IEEE/ACM Transactions on Computational Biology and Bioinformatics. The version of record is available at: https://doi.org/10.1109/TCBB.2023.3274361. © 2023 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works. This article will be embargoed unitl 05/08/2025.
Keywords
Inter-helix contact prediction, Refinement selection, 2D contact model, Fuzzy score, hybrid-cutoffs
Citation
J. Li, A. Sawhney, J. -Y. Lee and L. Liao, "Improving Inter-Helix Contact Prediction With Local 2D Topological Information," in IEEE/ACM Transactions on Computational Biology and Bioinformatics, doi: 10.1109/TCBB.2023.3274361.