An effective convergence independent loop closure method using forward-backward cyclic coordinate descent

Kamal Al-Nasr, Jing He

Research output: Contribution to journalArticlepeer-review

12 Scopus citations

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. Copyrigth

Original languageEnglish (US)
Pages (from-to)346-361
Number of pages16
JournalInternational Journal of Data Mining and Bioinformatics
Volume3
Issue number3
DOIs
StatePublished - 2009
Externally publishedYes

ASJC Scopus subject areas

  • Information Systems
  • General Biochemistry, Genetics and Molecular Biology
  • Library and Information Sciences

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