ArticlePloS one2011
Anchored design of protein-protein interfaces.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
What it found
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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
39 citing papers in PubMed.
- PALB2 and 53BP1 govern post-resection homologous recombination DNA repair.Molecular cell · 2025Article
- AbFlex: designing antibody complementarity determining regions with flexible CDR definition.Bioinformatics (Oxford, England) · 2024Article
- Pyruvate dehydrogenase operates as an intramolecular nitroxyl generator during macrophage metabolic reprogramming.Nature communications · 2023Article
- Rational peptide design for inhibition of the KIX-MLL interaction.Scientific reports · 2023Article
- Crystal structure of LGR ligand α2/β5 fromProceedings of the National Academy of Sciences of the United States of America · 2023Article
- Simulation of Energy-Resolved Mass Spectrometry Distributions from Surface-Induced Dissociation.Analytical chemistry · 2022Article
- Surface-induced Dissociation Mass Spectrometry as a Structural Biology Tool.Chemical reviews · 2022Review
- A TCR mimic monoclonal antibody reactive with the "public" phospho-neoantigen pIRS2/HLA-A*02:01 complex.JCI insight · 2022Article
- Hallucinating structure-conditioned antibody libraries for target-specific binders.Frontiers in immunology · 2022Article
- The Collagen Receptor Discoidin Domain Receptor 1b Enhances Integrin β1-Mediated Cell Migration by Interacting With Talin and Promoting Rac1 Activation.Frontiers in cell and developmental biology · 2022Article
- Tetracycline as an inhibitor to the SARS-CoV-2.Journal of cellular biochemistry · 2021Article
- Protein structure analysis of the interactions between SARS-CoV-2 spike protein and the human ACE2 receptor: from conformational changes to novel neutralizing antibodies.Cellular and molecular life sciences : CMLS · 2021Article
- Review
- Article
- Predicting Protein Complex Structure from Surface-Induced Dissociation Mass Spectrometry Data.ACS central science · 2019Article
- Role of antibody heavy and light chain interface residues in affinity maturation of binding to HIV envelope glycoprotein.Molecular systems design & engineering · 2019Article
- Relative interfacial cleavage energetics of protein complexes revealed by surface collisions.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Tertiary Structural Motif Sequence Statistics Enable Facile Prediction and Design of Peptides that Bind Anti-apoptotic Bfl-1 and Mcl-1.Structure (London, England : 1993) · 2019Article
- In Silico Engineering of Synthetic Binding Proteins from Random Amino Acid Sequences.iScience · 2019Article
- Discovery of novel helix binding sites at protein-protein interfaces.Computational and structural biotechnology journal · 2019Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
backgroundFew existing protein-protein interface design methods allow for extensive backbone rearrangements during the design process. There is also a dichotomy between redesign methods, which take advantage of the native interface, and de novo methods, which produce novel binders. METHODOLOGY: Here, we propose a new method for designing novel protein reagents that combines advantages of redesign and de novo methods and allows for extensive backbone motion. This method requires a bound structure of a target and one of its natural binding partners. A key interaction in this interface, the anchor, is computationally grafted out of the partner and into a surface loop on the design scaffold. The design scaffold's surface is then redesigned with backbone flexibility to create a new binding partner for the target. Careful choice of a scaffold will bring experimentally desirable characteristics into the new complex. The use of an anchor both expedites the design process and ensures that binding proceeds against a known location on the target. The use of surface loops on the scaffold allows for flexible-backbone redesign to properly search conformational space. CONCLUSIONS AND SIGNIFICANCE: This protocol was implemented within the Rosetta3 software suite. To demonstrate and evaluate this protocol, we have developed a benchmarking set of structures from the PDB with loop-mediated interfaces. This protocol can recover the correct loop-mediated interface in 15 out of 16 tested structures, using only a single residue as an anchor.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.