De Novo Computational Design of Retro-Aldol Enzymes

By Lin Jiang, Eric A. Althoff, Fernando R. Clemente, Lindsey Doyle, Daniela Röthlisberger, A. Zanghellini, Jasmine L. Gallaher, Jamie L. Betker, F. Tanaka, C. Barbas and 4 more. 2008

1,138 citations recorded by the source corpus.

Subfields: Molecular Biology, Pharmacology

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Citations in the corpus

ProDCoNN: Protein design using a convolutional neural network (2019, background): “Another problem with wide applications is to design proteins with new functions, such as enzyme design.(3,4,7,12) The design will usually start from a known structure, which will be kept in the process, and modify part of the sequence to achieve a new function.”
Computational Protein Design with Deep Learning Neural Networks (2018, methodology): “The training set was collected from PDB29 using the following criteria: (1) the structure is determined with x-ray crystallography, (2) the resolution is better than 2 Å, (3) the chain Top 1 Top 2 Top 3 Top 5 Top 10”
Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules (2011, positive): “…et al. , 2005; Das et al. , 2007; Raman et al. , 2009; Simons et al. , 1997) enzdes Design a protein active site to catalyze a chemical reaction ( Jiang et al. , 2008; Rothlisberger et al. , 2008; Zanghellini et al. , 2006) FixedBBProteinDesign Redesign the amino acids on a ﬁxed protein backbone…”
Diffusion probabilistic modeling of protein backbones in 3D for the motif-scaffolding problem (2022, neutral): “[21] Lin Jiang, Eric A Althoff, Fernando R Clemente, Lindsey Doyle, Daniela Rothlisberger, Alexandre Zanghellini, Jasmine L Gallaher, Jamie L Betker, Fujie Tanaka, Carlos F Barbas III, Donald Hilvert, Kendal N Houk, Barry L.”
Energy-based models for atomic-resolution protein conformations (2020, background): “…from data, which, in combination with physically motivated force Published as a conference paper at ICLR 2020 ﬁelds, have contributed to the feasibility of de novo design of protein structures and functions (Kuhlman et al., 2003; Ambroggio & Kuhlman, 2006; Jiang et al., 2008; King et al., 2014).”
Achievements and Challenges in Computational Protein Design. (2017, methodology): “The retro-aldolase CPD strategy is described over 12 pages in the supplementary material of the publication highlighting the many aspects that must be addressed [71].”
De Novo Enzyme Design Using Rosetta3 (2011, background): “Though it has been shown to be capable of designing active enzymes in three cases [1,2,3], in each case the best designed proteins only had very modest activity, while many of the designs tested had no activity at all.”