Design of a Novel Globular Protein Fold with Atomic-Level Accuracy
By Brian Kuhlman, G. Dantas, G. Ireton, Gabriele Varani, Barry L. Stoddard, David Baker. 2003
821 citations recorded by the source corpus.
Subfields: Materials Chemistry, Molecular Biology
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Materials Chemistry
- David Baker
- Jeffrey J. Gray
- Tanja Kortemme
- Jens Meiler
- Yang Zhang
- Xingjie Pan
- I. Samish
- Robin Pearce
In Molecular Biology
- David Baker
- Tanja Kortemme
- Jeffrey J. Gray
- Jens Meiler
- I. Samish
- Yang Zhang
- Xingjie Pan
- Po-Ssu Huang
Citations in the corpus
- Generating functional protein variants with variational autoencoders (2020, background): “Recent progress has also been made in the rational design of proteins 43 with artificial folds from scratch [7, 8, 9].”
- Scientific Benchmarks for Guiding Macromolecular Energy Function Improvement (2013, methodology): “For example, protocols in the molecular modeling program Rosetta for ligand docking (Meiler & Baker, 2003), protein design (Kuhlman et al., 2003), and loop modeling (Wang, Bradley, & Baker, 2007) share a common energy function, which allowed Murphy, Bolduc, Gallaher, Stoddard, and Baker (2009) to…”
- 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).”
- Protein engineering by highly parallel screening of computationally designed variants (2016, methodology): “method (8), a simulated annealing procedure that samples alternative amino acid side chainswhose configurations are specified by theDunbrack rotamer library (23).”
- A general-purpose protein design framework based on mining sequence–structure relationships in known protein structures (2018, background): “ε = 20 max(N,N], 1) (27) where, N and N] are the observed and expected counts (of whatever quantity is being modeled), respectively.”
- Alteration of enzyme specificity by computational loop remodeling and design (2009, methodology): “Computational design algorithms that iterate between sequence design and backbone optimization using structure-prediction methods have been used to design previously unobserved protein fold and loop conformations (2, 14), but have not yet been applied to achieving functional changes such as alterati”