ArticleJournal of molecular biology2011
Hotspot-centric de novo design of protein binders.
Article in Journal of molecular biology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
27 citing papers in PubMed.
- Antibody Hotspot-CentricACS medicinal chemistry letters · 2026Article
- Surf2Spot: a surface-informed geometry-aware model for predicting partner-independent binder and nanobody design hotspots.Briefings in bioinformatics · 2026Article
- Article
- Article
- Using Short Molecular Dynamics Simulations to Determine the Important Features of Interactions in Antibody-Protein Complexes.Proteins · 2025Article
- AI Prediction of Structural Stability of Nanoproteins Based on Structures and Residue Properties by Mean Pooled Dual Graph Convolutional Network.Interdisciplinary sciences, computational life sciences · 2025Article
- Targeting Ras-binding domain of ELMO1 by computational nanobody design.Communications biology · 2023Article
- Analysis of conformational stability of interacting residues in protein binding interfaces.Protein engineering, design & selection : PEDS · 2023Article
- Deep learning of protein sequence design of protein-protein interactions.Bioinformatics (Oxford, England) · 2023Article
- Massively parallel, computationally guided design of a proenzyme.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- MutDock: A computational docking approach for fixed-backbone protein scaffold design.Frontiers in molecular biosciences · 2022Article
- De Novo Design of Peptidic Positive Allosteric Modulators Targeting TRPV1 with Analgesic Effects.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2021Article
- Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design.Biochemistry · 2021Review
- Computational design and experimental optimization of protein binders with prospects for biomedical applications.Protein engineering, design & selection : PEDS · 2021Review
- Computational design of structured loops for new protein functions.Biological chemistry · 2019Review
- Recent advances in automated protein design and its future challenges.Expert opinion on drug discovery · 2018Review
- RosettaAntibodyDesign (RAbD): A general framework for computational antibody design.PLoS computational biology · 2018Article
- Computational design of an epitope-specific Keap1 binding antibody using hotspot residues grafting and CDR loop swapping.Scientific reports · 2017Article
- Two common structural motifs for TCR recognition by staphylococcal enterotoxins.Scientific reports · 2016Article
- AbDesign: An algorithm for combinatorial backbone design guided by natural conformations and sequences.Proteins · 2015Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
Protein-protein interactions play critical roles in biology, and computational design of interactions could be useful in a range of applications. We describe in detail a general approach to de novo design of protein interactions based on computed, energetically optimized interaction hotspots, which was recently used to produce high-affinity binders of influenza hemagglutinin. We present several alternative approaches to identify and build the key hotspot interactions within both core secondary structural elements and variable loop regions and evaluate the method's performance in natural-interface recapitulation. We show that the method generates binding surfaces that are more conformationally restricted than previous design methods, reducing opportunities for off-target interactions.
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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.