Automated design of specificity in molecular recognition

By James J. Havranek, Pehr Harbury. 2003

327 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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Citations in the corpus

Protein sequence design by conformational landscape optimization (2021, background): “Multistate design (10 – 12) can be carried out to maximize the energy gap between the desired conformation and other specified conformations, but the latter must be known in advance and be relatively few in number for such calculations to be tractable.”
Emerging themes in the computational design of novel enzymes and protein–protein interfaces (2013, background): “A crucial early insight was that both the energy function and sampling techniques used should be general and independent of the particular design or modeling problem [2–4].”
A de novo designed protein–protein interface (2007, methodology): “…to generate calmodulin variants with enhanced binding specificity (Shifman and Mayo 2002, 2003); Bolon et al. (2005) re-engineered a protein homodimer into a heterodimer; Havranek and Harbury (2003) 3Present address: Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.”
Design of Protein Multi-specificity Using an Independent Sequence Search Reduces the Barrier to Low Energy Sequences (2015, background): “MSD has been successful in engineering proteins when both including [6,7,10,12] and ignoring [9,13,38] these negative design states.”
Computational reprogramming of homing endonuclease specificity at multiple adjacent base pairs (2010, methodology): “Using a genetic algorithm (19), a population of randomized amino acid identities at positions in contact with the substituted nucleotide positions was evolved in silico by enriching for combinations that maximized the discrimination between the target and alternative DNA sites.”
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 ”
Rewiring the specificity of two-component signal transduction systems. (2008, unknown): “There have been some recent successes, such as the redesign of colicin-immunity protein interactions (Kortemme et al., 2004) and coiled-coil dimerization (Havranek and Harbury, 2003), but these studies have relied heavily on structural data.”
Reconfigurable asymmetric protein assemblies through implicit negative design (2021, unknown): “Explicit negative-design methods favor one state by considering the effect of amino acid substitutions on the free energies of both states ( 15 – 17 ).”
Achievements and Challenges in Computational Protein Design. (2017, background): “In 2003 Havernek and Harbury approached molecular recognition by entwining positive- and negative-design using a multi-state framework for engineering specificity in GCN4-based coiled-coils [40].”
An efficient algorithm for multistate protein design based on FASTER (2009, background): “3, 11–14 However, single-state design is not necessarily sufficient when design objectives require the explicit consideration of multiple states at once.(15)”