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PatchSearch: A Fast Computational Method for Off-Target Detection
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DOI：10.1021/acs.jcim.6b00529.png)
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Abstract
En 中文
Many therapeutic molecules are known to bind several proteins, which can be different from the initially targeted, one. Such unexpected-interactions with proteins called off-targets can lead to adverse effects. Potential off-target identification is important to predict to avoid drug side effects or to.discover new targets for existing drugs. We propose a new program named PatcliSearch that implements local nonseqtiential searching for similar binding sites on protein surfaces with a controlled amount of flexibility. It is based on detection of quasi-cliques in product graphs representing all the possible matchings between two compared structures. This method-has been benchniarked on a large diversity of ligands and on five data-sets ranging from 12 to more than 7000 protein structures. The experiments conducted in this study show that the PatchSearch :method could be usefillin the early identification of off-targets. The program and the benchmarks presented in this paper are available as an R package at https://githuli.com/MTiPatchSearch.
Keywords:
PROTEIN-BINDING POCKET
LIGAND-BINDING
DRUG DISCOVERY
SUBGRAPH ISOMORPHISM
SITE SIMILARITY
POLYPHARMACOLOGY
ALGORITHM
PREDICTION
ALIGNMENT
SEQUENCE
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