Cyclic coordinate descent: A robotics algorithm for protein loop closure

By Adrian A. Canutescu, Roland L. Dunbrack. 2003

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In Molecular Biology

Citations in the corpus

The SWISS-MODEL Repository—new features and functionality (2016, methodology): “Briefly, the main improvements are in loop modeling by making use of an optimized database of loops with each candidate loop being placed using the Cyclic Coordinate Descent (CCD) method (23).”
Coordinate descent algorithms (2015, methodology): “Canutescu and Dunbrack [11] describe a cyclic coordinate descent method for determining protein structure, adjusting the dihedral angles in a protein chain so that the atom at the end of the chain comes close to a specified position in space.”
Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules (2011, positive): “The first algorithm uses rounds of fragment insertion to modify the loop conformations where a “chainbreak” term is included in the score function to keep the two cutpoint residues close together, followed by cyclic-coordinate descent (Canutescu and Dunbrack, 2003) to close the chain.”
RosettaAntibodyDesign (RAbD): A general framework for computational antibody design (2017, methodology): “…sampling of CDR structures from this database for antibody design; (3) developed new grafting methods using the cyclic coordinate descent algorithm [71] in Rosetta; (4) implemented an algorithm that utilizes sequence profiles for our CDR clusters for sampling amino acid changes during antibody…”
The Phyre2 web portal for protein modelling, prediction and analysis (2015, methodology): “Click this to download the alignment for importing into any standard multiple-sequence viewer. secondary structure and disorder prediction 17| In the secondary structure and disorder prediction section of the main results page ( Fig.”
Blind prediction performance of RosettaAntibody 3.0: Grafting, relaxation, kinematic loop modeling, and full CDR optimization (2014, methodology): “The classic RosettaAntibody algorithm performs de novo CDR H3 modeling by inserting small fragments of residues from known structures followed by loop closure using the cyclic coordinate descent (CCD)64,65 algo-rithm.”
Modeling and docking antibody structures with Rosetta (2017, methodology): “The graft points are then adjusted using cycles of minimization, random torsional sampling and cyclic coordinate descent 28,29 of the two stem residues to prevent unphysical bond lengths and angles from being incorporated into the model.”
RosettaScripts: A Scripting Language Interface to the Rosetta Macromolecular Modeling Suite (2011, background): “Two loop-remodeling strategies are currently supported: fragment insertion[21] followed by cyclic coordinate descent[22], and kinematic loop closure[23], which vary in how torsion-angle sampling is conducted.”
Improvements to Robotics-Inspired Conformational Sampling in Rosetta (2013, methodology): “In all but one of our benchmark cases, whenever CCD identifies sub-Angstrom models, NGK samples these sub-Angstrom conformations as well (Figure 5).”
RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design (2011, methodology): “We noted that the correlation with RMSD to native was only observed when KIC was applied after structural refinement with CCD.”