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Cyclic coordinate descent: A robotics algorithm for protein loop closure.

Adrian A Canutescu1, Roland L Dunbrack

  • 1Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, Pennsylvania 19111, USA.

Protein Science : a Publication of the Protein Society
|April 30, 2003
PubMed
Summary
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We present a new algorithm, cyclic coordinate descent (CCD), for protein loop structure prediction. This fast and stable method successfully closes protein loops in 99.79% of cases, aiding in protein structure prediction.

Area of Science:

  • Computational biology
  • Structural bioinformatics
  • Protein structure prediction

Background:

  • Protein structure prediction often requires adjusting segments to connect fixed regions, particularly in loop modeling.
  • Existing algorithms based on inverse Jacobian can be unstable and fail to converge.
  • This problem is analogous to inverse kinematics in robotics, where robot arms adjust to reach targets.

Purpose of the Study:

  • To introduce and evaluate a novel algorithm for protein loop structure prediction.
  • To adapt a robotics technique, cyclic coordinate descent (CCD), for efficient protein loop closure.
  • To provide a stable and fast method for connecting protein segments in structure prediction.

Main Methods:

  • The study adapted the cyclic coordinate descent (CCD) algorithm, originally from robotics.

Related Experiment Videos

  • CCD iteratively adjusts one dihedral angle at a time to minimize distances between backbone atoms.
  • The algorithm moves from the N-terminal to the C-terminal end of the loop, adjusting each dihedral angle sequentially.

    • Main Results:

    • The CCD algorithm demonstrated high success rates, closing loops in 99.79% of a large test set.
    • The method is very fast, with an average loop closure time of 0.037 seconds for loops of length 8.
    • Occasional failures were observed only for short, highly extended loops.

    Conclusions:

    • Cyclic coordinate descent (CCD) is a robust and efficient algorithm for protein loop structure prediction.
    • The algorithm's speed and stability make it suitable for generating numerous trial structures in modeling.
    • CCD offers a reliable solution for a common challenge in both homology and ab initio protein structure prediction.