ArticleNature chemical biology2014
Comprehensive analysis of loops at protein-protein interfaces for macrocycle design.
Article in Nature chemical biology, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 101 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
101 citing papers in PubMed.
- Learning Protein-Protein Binding Free Energies from Interface Graphs and Physicochemical Descriptors.ACS physical chemistry Au · 2026Article
- Organometallic Chemistry Approach to Peptide Tricycles.Bioconjugate chemistry · 2026Article
- Design of permeability-optimized target-binding macrocyclesChemical science · 2026Article
- Bridging Heterocycle-Mediated Hydrogen Bonding Facilitates Permeability of Polar Macrobicycles.Journal of the American Chemical Society · 2026Article
- CyclicMPNN: Stable Cyclic Peptide Sequence Generation.bioRxiv : the preprint server for biology · 2026Article
- Using generative AI to transform peptide hits into small molecule leads.Beilstein journal of organic chemistry · 2026Article
- Switching the strict substrate specificities of the β-ketoacyl-acyl carrier protein synthases, FabH and BioZ.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Small-Molecule Trk Agonists: Where Do We Go from Here?Journal of medicinal chemistry · 2025Review
- Selective Modulation of Trk Receptors byACS chemical neuroscience · 2025Article
- From Concepts to Inhibitors: A Blueprint for Targeting Protein-Protein Interactions.Chemical reviews · 2025Review
- π-Turns in Peptides: A Crystal-State Literature Survey.Journal of peptide science : an official publication of the European Peptide Society · 2025Review
- Cyclic peptide structure prediction and design using AlphaFold2.Nature communications · 2025Article
- An mRNA Display Approach for Covalent Targeting of aJournal of the American Chemical Society · 2025Article
- Advancements in Loop Cyclization Approaches for Enhanced Peptide Therapeutics for Targeting Protein-Protein Interactions.The Journal of organic chemistry · 2025Article
- Physicochemical, functional, and evolutionary characteristics of protein loop regions in human andBiophysics and physicobiology · 2025Article
- Tackling Undruggable Targets with Designer Peptidomimetics and Synthetic Biologics.Chemical reviews · 2024Review
- Selection of Nucleotide-Encoded Mass Libraries of Macrocyclic Peptides for Inaccessible Drug Targets.Chemical reviews · 2024Review
- An mRNA Display Approach for Covalent Targeting of abioRxiv : the preprint server for biology · 2024Article
- Selective, Intrinsically Fluorescent Trk Modulating Probes.ACS chemical neuroscience · 2024Article
- Molecular Mechanism of pH-Induced Protrusion Configuration Switching in Piscine Betanodavirus Implies a Novel Antiviral Strategy.ACS infectious diseases · 2024Article
41 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Inhibiting protein-protein interactions (PPIs) with synthetic molecules remains a frontier of chemical biology. Many PPIs have been successfully targeted by mimicking α-helices at interfaces, but most PPIs are mediated by nonhelical, nonstrand peptide loops. We sought to comprehensively identify and analyze these loop-mediated PPIs by writing and implementing LoopFinder, a customizable program that can identify loop-mediated PPIs within all of the protein-protein complexes in the Protein Data Bank. Comprehensive analysis of the entire set of 25,005 interface loops revealed common structural motifs and unique features that distinguish loop-mediated PPIs from other PPIs. 'Hot loops', named in analogy to protein hot spots, were identified as loops with favorable properties for mimicry using synthetic molecules. The hot loops and their binding partners represent new and promising PPIs for the development of macrocycle and constrained peptide inhibitors.
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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.