title: LIBRA: LIgand Binding site Recognition Application.
abstract: BACKGROUND
  In recent years, structural genomics and ab initio molecular modeling activities are leading to the availability of a large number of structural models of proteins whose biochemical function is not known. The aim of this study was the development of a novel software tool that, given a protein's structural model, predicts the presence and identity of active sites and/or ligand binding sites.
  
  
  RESULTS
  The algorithm implemented by ligand binding site recognition application (LIBRA) is based on a graph theory approach to find the largest subset of similar residues between an input protein and a collection of known functional sites. The algorithm makes use of two predefined databases for active sites and ligand binding sites, respectively, derived from the Catalytic Site Atlas and the Protein Data Bank. Tests indicate that LIBRA is able to identify the correct binding/active site in 90% of the cases analyzed, 90% of which feature the identified site as ranking first. As far as ligand binding site recognition is concerned, LIBRA outperforms other structure-based ligand binding sites detection tools with which it has been compared.
  
  
  METHODS
  The application, developed in Java SE 7 with a Swing GUI embedding a JMol applet, can be run on any OS equipped with a suitable Java Virtual Machine (JVM), and is available at the following URL: http://www.computationalbiology.it/software/LIBRAv1.zip.
authors: Department of Sciences, University of Roma Tre, 00146 Rome, Italy, Department of Science and Technology, Nguyen Tat Thanh University, Ho Chi Minh City, Vietnam and.
authors: Le Viet
authors: le V
authors: Hung
authors: Department of Sciences, University of Roma Tre, 00146 Rome, Italy.
authors: Silvia
authors: S
authors: Caprari
authors: Department of Sciences, University of Roma Tre, 00146 Rome, Italy.
authors: Massimiliano
authors: M
authors: Bizai
authors: Department of Sciences, University of Roma Tre, 00146 Rome, Italy.
authors: Daniele
authors: D
authors: Toti
authors: Department of Sciences, University of Roma Tre, 00146 Rome, Italy, National Institute of Nuclear Physics, Roma Tre Section, 00146 Rome, Italy.
authors: Fabio
authors: F
authors: Polticelli
mesh_terms: D000465:Algorithms; D001665:Binding Sites; D020134:Catalytic Domain; D030562:Databases, Protein; D008024:Ligands; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012984:Software
chemical_list: D008024:Ligands; D011506:Proteins