title: Assessing Predicted Contacts for Building Protein Three-Dimensional Models.
abstract: Recent successes of contact-guided protein structure prediction methods have revived interest in solving the long-standing problem of ab initio protein structure prediction. With homology modeling failing for many protein sequences that do not have templates, contact-guided structure prediction has shown promise, and consequently, contact prediction has gained a lot of interest recently. Although a few dozen contact prediction tools are already currently available as web servers and downloadables, not enough research has been done towards using existing measures like precision and recall to evaluate these contacts with the goal of building three-dimensional models. Moreover, when we do not have a native structure for a set of predicted contacts, the only analysis we can perform is a simple contact map visualization of the predicted contacts. A wider and more rigorous assessment of the predicted contacts is needed, in order to build tertiary structure models. This chapter discusses instructions and protocols for using tools and applying techniques in order to assess predicted contacts for building three-dimensional models.
authors: Computer Science Department, University of Missouri, Engineering Building West 109, Columbia, MO, 65211, USA.
authors: Badri
authors: B
authors: Adhikari
authors: Computer Science Department, University of Missouri, Engineering Building West 109, Columbia, MO, 65211, USA.
authors: Debswapna
authors: D
authors: Bhattacharya
authors: Computer Science Department, University of Missouri, Engineering Building West 109, Columbia, MO, 65211, USA.
authors: Renzhi
authors: R
authors: Cao
authors: Computer Science Department, University of Missouri, Engineering Building West 109, Columbia, MO, 65211, USA. chengji@missouri.edu.
authors: Jianlin
authors: J
authors: Cheng
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D030562:Databases, Protein; D016571:Neural Networks, Computer; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D020539:Sequence Analysis, Protein; D012984:Software
chemical_list: D011506:Proteins
keywords: Contact-guided ab initio prediction; Protein contact assessment