title: ConEVA: a toolbox for comprehensive assessment of protein contacts.
abstract: BACKGROUND
  In recent years, successful contact prediction methods and contact-guided ab initio protein structure prediction methods have highlighted the importance of incorporating contact information into protein structure prediction methods. It is also observed that for almost all globular proteins, the quality of contact prediction dictates the accuracy of structure prediction. Hence, like many existing evaluation measures for evaluating 3D protein models, various measures are currently used to evaluate predicted contacts, with the most popular ones being precision, coverage and distance distribution score (Xd).
  
  
  RESULTS
  We have built a web application and a downloadable tool, ConEVA, for comprehensive assessment and detailed comparison of predicted contacts. Besides implementing existing measures for contact evaluation we have implemented new and useful methods of contact visualization using chord diagrams and comparison using Jaccard similarity computations. For a set (or sets) of predicted contacts, the web application runs even when a native structure is not available, visualizing the contact coverage and similarity between predicted contacts. We applied the tool on various contact prediction data sets and present our findings and insights we obtained from the evaluation of effective contact assessments. ConEVA is publicly available at http://cactus.rnet.missouri.edu/coneva/ .
  
  
  CONCLUSIONS
  ConEVA is useful for a range of contact related analysis and evaluations including predicted contact comparison, investigation of individual protein folding using predicted contacts, and analysis of contacts in a structure of interest.
authors.affiliation: Department of Computer Science, University of Missouri, Columbia, MO, 65211, USA.
authors.forename: Badri
authors.initials: B
authors.lastname: Adhikari
authors.affiliation: Department of Computer Science, University of Missouri, Columbia, MO, 65211, USA.
authors.forename: Jackson
authors.initials: J
authors.lastname: Nowotny
authors.affiliation: Department of Computer Science, University of Missouri, Columbia, MO, 65211, USA.
authors.forename: Debswapna
authors.initials: D
authors.lastname: Bhattacharya
authors.affiliation: Department of Computer Science, University of Missouri, Columbia, MO, 65211, USA.
authors.forename: Jie
authors.initials: J
authors.lastname: Hou
authors.affiliation: Department of Computer Science, University of Missouri, Columbia, MO, 65211, USA. chengji@missouri.edu.|Informatics Institute, University of Missouri, Columbia, MO, 65211, USA. chengji@missouri.edu.|C. Bond Life Science Center, University of Missouri, Columbia, MO, 65211, USA. chengji@missouri.edu.
authors.forename: Jianlin
authors.initials: J
authors.lastname: Cheng
mesh_terms: D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D012984:Software
keywords: Chord diagrams; Contact maps; Contact visualization; Jaccard similarity; Protein contact assessment