Sub-angstrom accuracy in protein loop reconstruction by robotics-inspired conformational sampling

By Daniel J. Mandell, E. Coutsias, T. Kortemme. 2009

967 citations recorded by the source corpus.

Subfields: Biomedical Engineering, Infectious Diseases

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In Biomedical Engineering

In Infectious Diseases

Citations in the corpus

Scientific Benchmarks for Guiding Macromolecular Energy Function Improvement (2013, positive): “We used the benchmark set of 45 12-residue loops as described in Mandell et al. (2009).”
The Rosetta all-atom energy function for macromolecular modeling and design (2017, background): “…after full repacking [50] ∆∆ G Prediction Prediction of free energy changes upon mutation [97] Loop Modeling Prediction of loop conformations [98] High-resolution refinement Discrimination of native-like decoys upon refinement of ab initio protein models [99] Docking Prediction of…”
Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules (2011, positive): “The second type uses an algorithm called kinematic closure (KIC; Coutsias et al., 2004; Mandell et al., 2009).”
Essentials of de novo protein design: Methods and applications (2018, positive): “The recent implementation of a generalized form of KIC, known as GenKIC , allows the ability to work with any covalently linked chain of atoms and bias the sampling of the N -6 degrees of freedom to predefined structural requirements.”
Sub‐angstrom modeling of complexes between flexible peptides and globular proteins (2010, positive): “…of both the peptide and the receptor, using the extensive set of Rosetta backbone sampling tools, such as backrub-like movements,50 loop modeling51,52 and backbone fragments library,40 which were recently shown to cover the space of peptide backbones by Vanhee et al .53 As an illustrative example…”
RosettaRemodel: A Generalized Framework for Flexible Backbone Protein Design (2011, positive): “We noted that the correlation with RMSD to native was only observed when KIC was applied after structural refinement with CCD.”
A Web Resource for Standardized Benchmark Datasets, Metrics, and Rosetta Protocols for Macromolecular Modeling and Design (2015, neutral): “%) than for standard KIC (6.4”
Coupling Protein Side-Chain and Backbone Flexibility Improves the Re-design of Protein-Ligand Specificity (2015, positive): “Active site loops whose lengths could be changed without disrupting protein stability could be identified prior to design, and moves that add or remove residues in these loops could be made using robotics-inspired loop modeling techniques such as kinematic closure [39].”