1Department of Computer Science, 2Department of Biochemistry and Immunology, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha Belo Horizonte - MG, 31270-901, and 3Advanced Campus at Itabira, Universidade Federal de Itajubá, Rua Irmã Ivone Drumond, 200 - Distrito Industrial II Itabira - MG, 35903-087, Brazil
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Motivation:Receptor-ligand interactions are a central phenomenon in most biological systems. They are characterized by molecular recognition, a complex process mainly driven by physicochemical and structural properties of both receptor and ligand. Understanding and predicting these interactions are major steps towards protein ligand prediction, target identification, lead discovery and drug design.Results:We propose a novel graph-based–binding pocket signature called aCSM, which proved to be efficient and effective in handling large-scale protein ligand prediction tasks. We compare our results with those described in the literature and demonstrate that our algorithm overcomes the competitor's techniques. Finally, we predict novel ligands for proteins from Trypanosoma cruzi, the parasite responsible for Chagas disease, and validate them in silico via a docking protocol, showing the applicability of the method in suggesting ligands for pockets in a real-world scenario.Availability and implementation:Datasets and the source code are available at http://www.dcc.ufmg.br/∼dpires/acsm.Contact:email@example.com or firstname.lastname@example.orgSupplementary information:Supplementary data are available at Bioinformatics online.