Dataset Information

A deep-learning framework for multi-level peptide-protein interaction prediction.

ABSTRACT: Peptide-protein interactions are involved in various fundamental cellular functions and their identification is crucial for designing efficacious peptide therapeutics. Recently, a number of computational methods have been developed to predict peptide-protein interactions. However, most of the existing prediction approaches heavily depend on high-resolution structure data. Here, we present a deep learning framework for multi-level peptide-protein interaction prediction, called CAMP, including binary peptide-protein interaction prediction and corresponding peptide binding residue identification. Comprehensive evaluation demonstrated that CAMP can successfully capture the binary interactions between peptides and proteins and identify the binding residues along the peptides involved in the interactions. In addition, CAMP outperformed other state-of-the-art methods on binary peptide-protein interaction prediction. CAMP can serve as a useful tool in peptide-protein interaction prediction and identification of important binding residues in the peptides, which can thus facilitate the peptide drug discovery process.

SUBMITTER: Lei Y

PROVIDER: S-EPMC8443569 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature

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A deep-learning framework for multi-level peptide-protein interaction prediction.

Lei Yipin Y Li Shuya S Liu Ziyi Z Wan Fangping F Tian Tingzhong T Li Shao S Zhao Dan D Zeng Jianyang J

Nature communications 20210915 1

Peptide-protein interactions are involved in various fundamental cellular functions and their identification is crucial for designing efficacious peptide therapeutics. Recently, a number of computational methods have been developed to predict peptide-protein interactions. However, most of the existing prediction approaches heavily depend on high-resolution structure data. Here, we present a deep learning framework for multi-level peptide-protein interaction prediction, called CAMP, including bin ...[more]

PMID: 34526500

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Project description:MotivationProteins play pivotal roles in biological systems, and precise prediction of their functions is indispensable for practical applications. Despite the surge in protein sequence data facilitated by high-throughput techniques, unraveling the exact functionalities of proteins still demands considerable time and resources. Currently, numerous methods rely on protein sequences for prediction, while methods targeting protein structures are scarce, often employing convolutional neural networks (CNN) or graph convolutional networks (GCNs) individually.ResultsTo address these challenges, our approach starts from protein structures and proposes a method that combines CNN and GCN into a unified framework called the two-model adaptive weight fusion network (TAWFN) for protein function prediction. First, amino acid contact maps and sequences are extracted from the protein structure. Then, the sequence is used to generate one-hot encoded features and deep semantic features. These features, along with the constructed graph, are fed into the adaptive graph convolutional networks (AGCN) module and the multi-layer convolutional neural network (MCNN) module as needed, resulting in preliminary classification outcomes. Finally, the preliminary classification results are inputted into the adaptive weight computation network, where adaptive weights are calculated to fuse the initial predictions from both networks, yielding the final prediction result. To evaluate the effectiveness of our method, experiments were conducted on the PDBset and AFset datasets. For molecular function, biological process, and cellular component tasks, TAWFN achieved area under the precision-recall curve (AUPR) values of 0.718, 0.385, and 0.488 respectively, with corresponding Fmax scores of 0.762, 0.628, and 0.693, and Smin scores of 0.326, 0.483, and 0.454. The experimental results demonstrate that TAWFN exhibits promising performance, outperforming existing methods.Availability and implementationThe TAWFN source code can be found at: https://github.com/ss0830/TAWFN.

Project description:BackgroundProtein-protein interactions can be seen as a hierarchical process occurring at three related levels: proteins bind by means of specific domains, which in turn form interfaces through patches of residues. Detailed knowledge about which domains and residues are involved in a given interaction has extensive applications to biology, including better understanding of the binding process and more efficient drug/enzyme design. Alas, most current interaction prediction methods do not identify which parts of a protein actually instantiate an interaction. Furthermore, they also fail to leverage the hierarchical nature of the problem, ignoring otherwise useful information available at the lower levels; when they do, they do not generate predictions that are guaranteed to be consistent between levels.ResultsInspired by earlier ideas of Yip et al. (BMC Bioinformatics 10:241, 2009), in the present paper we view the problem as a multi-level learning task, with one task per level (proteins, domains and residues), and propose a machine learning method that collectively infers the binding state of all object pairs. Our method is based on Semantic Based Regularization (SBR), a flexible and theoretically sound machine learning framework that uses First Order Logic constraints to tie the learning tasks together. We introduce a set of biologically motivated rules that enforce consistent predictions between the hierarchy levels.ConclusionsWe study the empirical performance of our method using a standard validation procedure, and compare its performance against the only other existing multi-level prediction technique. We present results showing that our method substantially outperforms the competitor in several experimental settings, indicating that exploiting the hierarchical nature of the problem can lead to better predictions. In addition, our method is also guaranteed to produce interactions that are consistent with respect to the protein-domain-residue hierarchy.

Dataset Information

A deep-learning framework for multi-level peptide-protein interaction prediction.

Publications

A deep-learning framework for multi-level peptide-protein interaction prediction.

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