ReviewBiochemical Society transactions2013
Using anchoring motifs for the computational design of protein-protein interactions.
Review in Biochemical Society transactions, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
7 citing papers in PubMed.
- Artificial intelligence in bioinformatics: a survey.Briefings in bioinformatics · 2025Review
- Design of target specific peptide inhibitors using generative deep learning and molecular dynamics simulations.Nature communications · 2024Article
- Tertiary motifs as building blocks for the design of protein-binding peptides.Protein science : a publication of the Protein Society · 2022Article
- Comparing side chain packing in soluble proteins, protein-protein interfaces, and transmembrane proteins.Proteins · 2018Article
- Article
- Rational design of TNFα binding proteins based on the de novo designed protein DS119.Protein science : a publication of the Protein Society · 2016Article
- Design and fine-tuning redox potentials of metalloproteins involved in electron transfer in bioenergetics.Biochimica et biophysica acta · 2016Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
The computer-based design of PPIs (protein-protein interactions) is a challenging problem because large desolvation and entropic penalties must be overcome by the creation of favourable hydrophobic and polar contacts at the target interface. Indeed, many computationally designed interactions fail to form when tested in the laboratory. In the present article, we highlight strategies our laboratory has been pursuing to make interface design more tractable. Our general approach has been to make use of structural motifs found in native proteins that are predisposed to interact with a particular binding geometry, and then further bolster these anchor points with favourable hydrophobic contacts. We describe the use of three different anchor points, i.e. β-strand pairing, metal binding and the docking of α-helix into a groove, to successfully design new interfaces. In several cases, high-resolution crystal structures show that the design models closely match the experimental structure. In addition, we have tested the use of buried hydrogen-bond networks as a source of affinity and specificity at interfaces. In these cases, the designed complexes did not form, highlighting the challenges associated with designing buried polar interactions.
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Registered trials
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