R. Kolodny, L. Guibas, M. Levitt and P. Koehl. Inverse Kinematics in Biology: The Protein Loop Closure Problem. Int. Jour. Robotics Research. (2005) 24, pp. 151-162.
We address an inverse kinematics problem in structural biology: the loop closure problem. We describe a procedure for generating the conformations of candidate loops that fit in a gap in a protein structure framework. Our method concatenates small fragments of protein from small libraries of representative fragments. Our approach has the advantages of ab initio methods since we are able to enumerate all candidate loops in the discrete approximation of the conformational space accessible to the loop, as well as the advantages of database search approach since the use of fragments of known protein structures guarantees that the backbone conformations are physically reasonable.
author = "R. Kolodny and L. Guibas and M. Levitt and P. Koehl",
title = "Inverse Kinematics in Biology: The Protein Loop Closure Problem",
journal = ". Jour. Robotics Research",
volume = 24,
pages = "151-162",
year = 2005