ArticleProtein science : a publication of the Protein Society2009
Motif-directed flexible backbone design of functional interactions.
Article in Protein science : a publication of the Protein Society, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Prioritizing neuroactive ligands using motif-guided virtual discovery and zebrafish profiling.npj drug discovery · 2026Article
- Prioritizing Neuroactive Ligands Using Motif-Guided Virtual Discovery and Zebrafish Profiling.bioRxiv : the preprint server for biology · 2026Article
- Toward a Computational NMR Procedure for Modeling Dipeptide Side-Chain Conformation.Journal of chemical information and modeling · 2021Article
- EMRinger: side chain-directed model and map validation for 3D cryo-electron microscopy.Nature methods · 2015Article
- Structure-based modeling of protein: DNA specificity.Briefings in functional genomics · 2015Review
- Motif-directed redesign of enzyme specificity.Protein science : a publication of the Protein Society · 2014Article
- Reprogramming homing endonuclease specificity through computational design and directed evolution.Nucleic acids research · 2014Article
- Proteins comparison through probabilistic optimal structure local alignment.Frontiers in genetics · 2014Article
- Improved modeling of side-chain--base interactions and plasticity in protein--DNA interface design.Journal of molecular biology · 2012Article
- Increasing sequence diversity with flexible backbone protein design: the complete redesign of a protein hydrophobic core.Structure (London, England : 1993) · 2012Article
- The power of hard-sphere models: explaining side-chain dihedral angle distributions of Thr and Val.Biophysical journal · 2012Article
- Increased Diels-Alderase activity through backbone remodeling guided by Foldit players.Nature biotechnology · 2012Article
- Hotspot-centric de novo design of protein binders.Journal of molecular biology · 2011Article
- Successful targeting and disruption of an integrated reporter lentivirus using the engineered homing endonuclease Y2 I-AniI.PloS one · 2011Article
- RosettaScripts: a scripting language interface to the Rosetta macromolecular modeling suite.PloS one · 2011Article
- Article
- De novo enzyme design using Rosetta3.PloS one · 2011Article
- Specificity in computational protein design.The Journal of biological chemistry · 2010Review
- Conformational diversity and computational enzyme design.Current opinion in chemical biology · 2010Review
- Computer-aided design of functional protein interactions.Nature chemical biology · 2009Review
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2 authors.
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Abstract
Computational protein design relies on a number of approximations to efficiently search the huge sequence space available to proteins. The fixed backbone and rotamer approximations in particular are important for formulating protein design as a discrete combinatorial optimization problem. However, the resulting coarse-grained sampling of possible side-chain terminal positions is problematic for the design of protein function, which depends on precise positioning of side-chain atoms. Although backbone flexibility can greatly increase the conformation freedom of side-chain functional groups, it is not obvious which backbone movements will generate the critical constellation of atoms responsible for protein function. Here, we report an automated method for identifying protein backbone movements that can give rise to any specified set of desired side-chain atomic placements and interactions, using protein-DNA interfaces as a model system. We use a library of previously observed protein-DNA interactions (motifs) and a rotamer-based description of side-chain conformation freedom to identify placements for the protein backbone that can give rise to a favorable side-chain interaction with DNA. We describe a tree-search algorithm for identifying those combinations of interactions from the library that can be realized with minimal perturbation of the protein backbone. We compare the efficiency of this method with the alternative approach of building and screening alternate backbone conformations.
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