Logo image
Back
HIV1-human protein-protein interaction prediction based on interface architecture similarity
Conference proceeding

HIV1-human protein-protein interaction prediction based on interface architecture similarity

Chunyu Zhao, Yizhou Zang, Wei Quan, Xiaohua Hu and Ahmet Sacan
2017 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), v 2017-, pp 97-100
Nov 2017
DOI: https://doi.org/10.1109/BIBM.2017.8217632

Abstract

Benchmark testing Feature extraction HIV-1 Kernel protein interface architecture protein structure alignment protein-protein interaction Proteins Support vector machines Computer Architecture Protein Engineering
In this paper, we computationally predicted the interactions between HIV-1 and human proteins, based on the hypothesis that proteins with similar interface architecture share similar interaction partners. Evolution - aware protein structural alignment method UniAlign was used to calculate the similarity between two protein interface architectures. Using experimentally verified HIV-1, human protein-protein interactions data, we first selected 12 features, including geometric similarity, conversion similarity etc.; then trained a support vector machine (SVM) with Gaussian kernel for the binary classification problem: whether a given protein pairs `interact' or `no interact'. We used the trained and tuned SVM classifier to discover potential novel HIV-1 interacting partners for human proteins. Many predicted interactions had significant literature support, and we modeled the novel 3D interacting complex for HIV-1 envelope gp120 and gp41 proteins. We provided the first structural evidence for those interactions.

Metrics

8 Record Views
3 citations in Web of Science
5 citations in Scopus

Details

Logo image