title: LoopX: A Graphical User Interface-Based Database for Comprehensive Analysis and Comparative Evaluation of Loops from Protein Structures.
abstract: Due to their crucial role in function, folding, and stability, protein loops are being targeted for grafting/designing to create novel or alter existing functionality and improve stability and foldability. With a view to facilitate a thorough analysis and effectual search options for extracting and comparing loops for sequence and structural compatibility, we developed, LoopX a comprehensively compiled library of sequence and conformational features of ∼700,000 loops from protein structures. The database equipped with a graphical user interface is empowered with diverse query tools and search algorithms, with various rendering options to visualize the sequence- and structural-level information along with hydrogen bonding patterns, backbone φ, ψ dihedral angles of both the target and candidate loops. Two new features (i) conservation of the polar/nonpolar environment and (ii) conservation of sequence and conformation of specific residues within the loops have also been incorporated in the search and retrieval of compatible loops for a chosen target loop. Thus, the LoopX server not only serves as a database and visualization tool for sequence and structural analysis of protein loops but also aids in extracting and comparing candidate loops for a given target loop based on user-defined search options.
authors.affiliation: Department of Biological Sciences, Birla Institute of Technology & Science-Pilani , Hyderabad, India .
authors.forename: Rajashekar Varma
authors.initials: RV
authors.lastname: Kadumuri
authors.affiliation: Department of Biological Sciences, Birla Institute of Technology & Science-Pilani , Hyderabad, India .
authors.forename: Ramakrishna
authors.initials: R
authors.lastname: Vadrevu
mesh_terms: D000465:Algorithms; D003196:Computer Graphics; D030562:Databases, Protein; D006801:Humans; D008958:Models, Molecular; D011487:Protein Conformation; D017510:Protein Folding; D011506:Proteins / Q000737:chemistry*; D012984:Software
chemical_list: D011506:Proteins
keywords: data mining; database; loop engineering/grafting; protein loops; web-based GUI