Probing the role of packing specificity in protein design.

By B. Dahiyat, Stephen L. Mayo. 1997

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Citations in the corpus

Learning inverse folding from millions of predicted structures (2022, background): “…studied the packing of amino acid side chains to fill the interior space of predetermined backbone structures, either for a fixed backbone conformation (Street & Mayo, 1999; Dahiyat & Mayo, 1997; De-Grado et al., 1991), or with flexibility in the backbone conformation (Harbury et al., 1998).”
The Rosetta all-atom energy function for macromolecular modeling and design (2017, background): “72,73 To alleviate this problem, we weaken the repulsive component by replacing the 1/𝑑 ’,”
Energy functions in de novo protein design: current challenges and future prospects. (2013, background): “This result points out an area for future improvement by introducing explicit (18, 49, 110) or implicit (116) scoring methods for hydrophobic patches.”
De novo protein design: towards fully automated sequence selection. (1997, methodology): “Solvent exposed residues on the surface of a protein are designed using a hydrogen-bond potential and secondary structure propensities in addition to a van der Waals potential (Dahiyat & Mayo, 1997a).”
High-resolution structural validation of the computational redesign of human U1A protein. (2006, background): “Remarkable progress has recently been made after a decade of steady progress in this field (Dahiyat and Mayo, 1997; Harbury et al., 1998; Havranek and Harbury, 2003; Kaplan and DeGrado, 2004; Mooers et al., 2003; Pokala and Handel, 2001; Shifman and Mayo, 2003), as demonstrated, for example, by the ”
Automated design of specificity in molecular recognition (2003, methodology): “Lennard-Jones interaction energies were calculated with radii scale”
A de novo designed protein–protein interface (2007, methodology): “…selection process performed on interfacial positions including the potential energy function and parameters for solvation, hydrogen bonding, and van der Waals interactions are essentially the same as described previously (Dahiyat and Mayo 1996, 1997a,b; Dahiyat et al. 1997; Gordon et al. 1999).”
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].”
Protein design: a perspective from simple tractable models (1998, methodology): “Interesting methods to account for sidechain stereochemistry in sequence selections have been developed [6,88,89] that use the dead-end elimination theorem or Monte-Carlo design, which takes into account the degrees of freedom of the sidechains [90].”
Emergence of Protein Fold Families through Rational Design (2006, background): “A small deviation of the sidechain from the average dihedral angles might result in a different energy [28,45].”