title: aCSM: noise-free graph-based signatures to large-scale receptor-based ligand prediction.
abstract: BACKGROUND
  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.
  
  
  METHODS
  Datasets and the source code are available at http://www.dcc.ufmg.br/∼dpires/acsm.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors: Department of Computer Science, Universidade Federal de Minas Gerais, Av. Antônio Carlos, 6627, Pampulha Belo Horizonte - MG, 31270-901, Brazil. dpires@dcc.ufmg.br
authors: Douglas E V
authors: DE
authors: Pires
authors: Raquel C
authors: RC
authors: de Melo-Minardi
authors: Carlos H
authors: CH
authors: da Silveira
authors: Frederico F
authors: FF
authors: Campos
authors: Wagner
authors: W
authors: Meira
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D004798:Enzymes / Q000737:chemistry / Q000378:metabolism; D006801:Humans; D008024:Ligands; D008958:Models, Molecular; D008968:Molecular Conformation; D062105:Molecular Docking Simulation; D011485:Protein Binding; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D015800:Protozoan Proteins / Q000737:chemistry / Q000378:metabolism; D014349:Trypanosoma cruzi
chemical_list: D004798:Enzymes; D008024:Ligands; D011506:Proteins; D015800:Protozoan Proteins