Computational design of receptor and sensor proteins with novel functions

By L. Looger, M. Dwyer, J. J. Smith, H. Hellinga. Nature, 2003

685 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/28c1862d6c7ebdc2cab38e71175c5692554ef884

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Citations in the corpus

RNA synthetic biology (2006, background): “Future benefits from synthetic biology, in addition to those mentioned above, may include new classes of therapeutics, novel protein”
Synthetic biology - putting engineering into biology (2006, background): “to build completely new active sites into proteins (Dwyer, et al., 2004) or to redesign binding specificities of proteins ( Looger, et al., 2003 ).”
The protein folding problem. (2008, background): “Novel proteins are now designed as variants of existing proteins (43,94,99,145,173,243), or from broadened alphabets of nonnatural amino acids (226), or de novo (129) (Figure 2).”
Improved side‐chain modeling for protein–protein docking (2005, positive): “This is the approach taken by Looger and Hellinga (Looger et al. 2003) in their groundbreaking ligand binding site design, which involved up to 5000 rotamers at each designed position, and by Xiang and Honig (2001), who achieved excellent side-chain packing results with a rotamer library with over 7”
Computational redesign of protein-protein interaction specificity (2004, methodology): “These rotamer search–based methods have been applied to the design of new protein-small molecul”
Potential energy functions for protein design. (2007, background): “For example, the LJ radii can be scaled down [21], the repulsive component of the LJ energy can be scaled down [13] or the LJ function can be linearly extrapolated below a cutoff distance [12].”
Environmentally controlled invasion of cancer cells by engineered bacteria. (2006, background): “Recently, Hellinga and co-workers computationally designed maltose binding protein variants that bind various unnatural ligands, including TNT.8 In addition, Buskirk et al. linked small molecules to translation by designing RNA aptamers that bind tetramethylrosamine and activate gene expression.9 To”
Protein Design by Sampling an Undirected Graphical Model of Residue Constraints (2009, background): “Protein engineering seeks to produce amino acid sequences with desired characteristics, such as specified structure [1] or function [4].”