Improved prediction of protein side-chain conformations with SCWRL 4

By Georgii G. Krivov, Maxim V. Shapovalov, Roland L. Dunbrack. 2009

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Citations in the corpus

lDDT: a local superposition-free score for comparing protein structures and models using distance difference tests (2013, methodology): “For each domain, side-chain coordinates were removed and then rebuilt using the SCWRL software package (with default parameters) (Krivov et al., 2009).”
The SWISS-MODEL Repository—new features and functionality (2016, methodology): “Sidechain modeling is inspired by the work of the Dunbrack lab and uses the 2010 backbone dependent rotamer library (24).”
Sequence co-evolution gives 3D contacts and structures of protein complexes (2014, methodology): “Therefore, where possible we used complexes that had a solved 3D structure of the unbound monomer, namely GcsH/GcsT, CyoA, FimC, DhaL, AtpE, PtqA/PtqB, RS10 and HK/RR, and in all other cases the side chains of the monomers were randomized either by using SCWRL461 or restrained minimization with Schr”
Prediction of amino acid side chain conformation using a deep neural network (2017, methodology): “many computational methods have been developed to solve the fundamental problem of side chain prediction(5, 6).”
Deep convolutional networks for quality assessment of protein folds (2018, methodology): “To make the structural data more consistent we optimize the side chains of all decoy structures using SCWRL4 [26].”
COFACTOR: an accurate comparative algorithm for structure-based protein function annotation (2012, methodology): “The side chains of ligand binding residues are further optimized using Scwrl4 (21).”
Improving the physical realism and structural accuracy of protein models by a two-step atomic-level energy minimization. (2011, background): “Among the five external programs, PULCHRA, Modeller, and REMO, which directly build full-atom models from Ca traces, have worse physical qualities than Rosetta and Scwrl, which start from the main-chain models by ModRefiner, partly because ModRefiner provides better initial models for these two prog”