LOOPS: Visual Analysis Tool for Non-Periodic Protein Structures

Abstract

Protein molecules, the basic building blocks of all living organisms, are formed by chain sequences of amino acids. Due to internal forces, these chains are folded into a spatial representation with recurring patterns along the chain, called secondary structures. The basic secondary structures are a-helices and b-sheets, however, the protein function is also determined and influenced by other, non-periodic structural units, such as loops. Playing a pivotal role in the protein folding and dynamics, the loop classification and understanding may be necessary for modeling of shared structure ancestry (homology), protein structure prediction, and protein design. However, their non-repetitive characteristic denies the easy identification of their regularities. Therefore, we present LOOPS, a web-based tool for exploring and analyzing loops in proteins, that offers a high level of interaction with reference to other secondary structures. Displaying the additional information about a loop, such as its conformation, geometry, and multiple b-factors obtained from various methods, LOOPS provides a simple tool for analysis of loops in a protein sequence.