A novel methodology on distributed representations of proteins using their interacting ligands.

ABSTRACT:

Motivation

The effective representation of proteins is a crucial task that directly affects the performance of many bioinformatics problems. Related proteins usually bind to similar ligands. Chemical characteristics of ligands are known to capture the functional and mechanistic properties of proteins suggesting that a ligand-based approach can be utilized in protein representation. In this study, we propose SMILESVec, a Simplified molecular input line entry system (SMILES)-based method to represent ligands and a novel method to compute similarity of proteins by describing them based on their ligands. The proteins are defined utilizing the word-embeddings of the SMILES strings of their ligands. The performance of the proposed protein description method is evaluated in protein cluste

SUBMITTER: Ozturk H 

PROVIDER: S-EPMC6022674 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature