An effective convergence independent loop closure method using Forward-Backward Cyclic Coordinate Descent

Authors:
Kamal Al-Nasr;Jing He
Affiliations:
Department of Computer Science, New Mexico State University, Las Cruces, NM 88003, USA.;Department of Computer Science, New Mexico State University, Las Cruces, NM 88003, USA
Venue:
International Journal of Data Mining and Bioinformatics
Year:
2009

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Abstract

Cyclic Coordinate Descent (CCD) is a popular robotic approach to generate a possible loop that closes the gap between two constrained portions of a protein chain (Canutescu and Dunbrack 2003). In this paper, we describe an effective Forward-Backward CCD (FBCCD) method to connect the two constrained portions of a protein chain without requiring the loop to converge. A test of 30 loops of length 4, 8 and 12 suggests that our method takes fewer number of cycles to produce loops of comparable accuracy and more accurate second portion of the chain, when it is compared to the CCD method.