Rotamer libraries in the 21st century.

By Roland L. Dunbrack. 2002

639 citations recorded by the source corpus.

Subfields: Molecular Biology, Organic Chemistry

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Citations in the corpus

Scientific Benchmarks for Guiding Macromolecular Energy Function Improvement (2013, methodology): “Rotamers are sampled from Roland Dunbrack’s backbone-dependent rotamer library from 2002 (Dunbrack, 2002), with extra samples taken at (cid:6) s for both w 1 and w 2 .”
MolProbity’s Ultimate Rotamer-Library Distributions for Model Validation (2016, background): “The mean for the bond angles (Equation (4)) and the r for both v and bond angles (Equation (3)) are calculated straightforwardly from the measures of each example in the filtered Top8000.”
UCSF Chimera, MODELLER, and IMP: an Integrated Modeling System (2011, methodology): “…2009), SAXS proﬁle ﬁtting by IMP FoXS (Forster et al., 2008; Schneidman-Duhovny et al., 2010), and evaluation of sidechain conformations from backbone-dependent and backbone-independent rotamer libraries (Dunbrack, 2002; Lovell et al., 2000) into the UCSF Chi-mera molecular visualization package.”
Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences (2015, methodology): “Individual states optimize rotamer placement using a simulated annealing Monte Carlo search, sampling from a predefined rotamer library [17,18].”
A smoothed backbone-dependent rotamer library for proteins derived from adaptive kernel density estimates and regressions (2011, positive): “3 10! grid of the backbone dihedral angles f and c (Dunbrack, 2002; Dunbrack and Cohen, 1997).”
A Generic Program for Multistate Protein Design (2011, methodology): “Backbone-dependent rotamer building: Rosetta uses the 2002 version of Dunbrack’s backbone dependent rotamer library [61].”
SCWRL and MolIDE: computer programs for side-chain conformation prediction and homology modeling (2008, methodology): “0 uses the 2002 version of the backbone-dependent rotamer librar”
GalaxyRefine: protein structure refinement driven by side-chain repacking (2013, background): “GalaxyRefine first rebuilds all side-chains by placing the highest-probability rotamers (18), starting from the core and then extending to the surface layer by layer.”
Recent developments in phasing and structure refinement for macromolecular crystallography (2009, background): “Stereochemical validation such as rotamer [57] and Ramachandran [58] criteria has benefited from great increases in high-resolution data, B-factor filtering at the residue level, and evaluation as multidimensional distributions.”
A general-purpose protein design framework based on mining sequence–structure relationships in known protein structures (2018, background): “(11), or loop geometries with associated sequence preferences (39-41).”
Perturbing the energy landscape for improved packing during computational protein design (2020, methodology): “In these simulations, the side chains are modeled using a set of commonly observed discrete conformations, referred to as rotamers, and the protein backbone is often held fixed while the sequence is optimized.(3) As a consequence of these approximations, amino acid combinations that could be favorab”
Improvements to Robotics-Inspired Conformational Sampling in Rosetta (2013, methodology): “To ensure that no information from native rotamers was used, all starting structures were repacked using a fixed backbone protocol that performs simultaneous rotamer placement (using only a standard rotamer library expanded by one standard deviation around the side chain x1 and x2 torsion angles [44”