Backbone flexibility in computational protein design.

By Daniel J. Mandell, Tanja Kortemme. 2009

111 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences (2015, background): “Single state design protocols have successfully incorporated backbone movement, allowing the introduction of mutations that would have been unfavorable on the original backbone [1,8,27].”
Computationally Designed Bispecific Antibodies Using Negative State Repertoires (2016, background): “Most protocols then allow the backbone to relax in response to the new sequence and may iterate between sequence design and backbone movement (Mandell and Kortemme, 2009).”
Atomic-Accuracy Prediction of Protein Loop Structures through an RNA-Inspired Ansatz (2012, background): “Finally, efforts to design protein interfaces and enzyme active sites often encounter sampling bottlenecks due to the difficulty of simultaneously optimizing side-chain identity, sidechain conformation, and new backbones [3].”
Predicting the Tolerated Sequences for Proteins and Protein Interfaces Using RosettaBackrub Flexible Backbone Design (2011, background): “Developing and, importantly, adequately testing flexible backbone protein design approaches has been a long-standing problem ( [17] and references therein).”
A de novo protein binding pair by computational design and directed evolution (2011, methodology): “Our initial efforts using this approach did not lead to models containing interaction density comparable to that observed in natural protein interfaces, even after incorporation of methodology that included sampling intramolecular backbone degrees of freedom (Mandell and Kortemme, 2009a).”
Energy functions in de novo protein design: current challenges and future prospects. (2013, background): “Unfortunately, efficient sampling of the conformational space of flexible proteins has not been resolved, although progress has been made (78).”
A general-purpose protein design framework based on mining sequence–structure relationships in known protein structures (2018, background): “Backbone flexibility techniques have been proposed to address the issue that while rotamer-based methods are effectively modeling the ground state, a pre-specified template may not represent such a state for any designed sequence (9, 69).”
Methods in Enzymology: “Flexible backbone sampling methods to model and design protein alternative conformations” (2013, unknown): “However, it is clear that both side-chain and backbone flexibility are necessary to describe and design protein conformational heterogeneity (Friedland, Linares, Smith, & Kortemme, 2008; Mandell & Kortemme, 2009).”