title: LoopIng: a template-based tool for predicting the structure of protein loops.
abstract: BACKGROUND
  Predicting the structure of protein loops is very challenging, mainly because they are not necessarily subject to strong evolutionary pressure. This implies that, unlike the rest of the protein, standard homology modeling techniques are not very effective in modeling their structure. However, loops are often involved in protein function, hence inferring their structure is important for predicting protein structure as well as function.
  
  
  RESULTS
  We describe a method, LoopIng, based on the Random Forest automated learning technique, which, given a target loop, selects a structural template for it from a database of loop candidates. Compared to the most recently available methods, LoopIng is able to achieve similar accuracy for short loops (4-10 residues) and significant enhancements for long loops (11-20 residues). The quality of the predictions is robust to errors that unavoidably affect the stem regions when these are modeled. The method returns a confidence score for the predicted template loops and has the advantage of being very fast (on average: 1 min/loop).
  
  
  METHODS
  www.biocomputing.it/looping.
  
  
  BACKGROUND
  anna.tramontano@uniroma1.it.
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Physics, Sapienza University, 00185 Rome, Italy and.
authors.forename: Mario Abdel
authors.initials: MA
authors.lastname: Messih
authors.affiliation: Department of Physics, Sapienza University, 00185 Rome, Italy and.
authors.forename: Rosalba
authors.initials: R
authors.lastname: Lepore
authors.affiliation: Department of Physics, Sapienza University, 00185 Rome, Italy and Istituto Pasteur-Fondazione Cenci Bolognetti, Viale Regina Elena 291, 00161 Rome, Italy.
authors.forename: Anna
authors.initials: A
authors.lastname: Tramontano
mesh_terms: D030562:Databases, Protein; D000069550:Machine Learning; D008958:Models, Molecular; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry; D012984:Software
chemical_list: D011506:Proteins