PreHom-PCLM: protein remote homology detection by combing motifs and protein cubic language model

Author:

Shao Jiangyi1,Zhang Qi1,Yan Ke12,Liu Bin12

Affiliation:

1. School of Computer Science and Technology, Beijing Institute of Technology , Beijing 100081 , China

2. Advanced Research Institute of Multidisciplinary Science, Beijing Institute of Technology , Beijing 100081 , China

Abstract

Abstract Protein remote homology detection is essential for structure prediction, function prediction, disease mechanism understanding, etc. The remote homology relationship depends on multiple protein properties, such as structural information and local sequence patterns. Previous studies have shown the challenges for predicting remote homology relationship by protein features at sequence level (e.g. position-specific score matrix). Protein motifs have been used in structure and function analysis due to their unique sequence patterns and implied structural information. Therefore, designing a usable architecture to fuse multiple protein properties based on motifs is urgently needed to improve protein remote homology detection performance. To make full use of the characteristics of motifs, we employed the language model called the protein cubic language model (PCLM). It combines multiple properties by constructing a motif-based neural network. Based on the PCLM, we proposed a predictor called PreHom-PCLM by extracting and fusing multiple motif features for protein remote homology detection. PreHom-PCLM outperforms the other state-of-the-art methods on the test set and independent test set. Experimental results further prove the effectiveness of multiple features fused by PreHom-PCLM for remote homology detection. Furthermore, the protein features derived from the PreHom-PCLM show strong discriminative power for proteins from different structural classes in the high-dimensional space. Availability and Implementation: http://bliulab.net/PreHom-PCLM.

Funder

National Natural Science Foundation of China

Beijing Institute of Technology Research and Innovation Promoting Project

Publisher

Oxford University Press (OUP)

Subject

Molecular Biology,Information Systems

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