ArticleMethods in molecular biology (Clifton, N.J.)2017
Identifying Loop-Mediated Protein-Protein Interactions Using LoopFinder.
Article in Methods in molecular biology (Clifton, N.J.), 2017. 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.
- Small-Molecule Trk Agonists: Where Do We Go from Here?Journal of medicinal chemistry · 2025Review
- Selective Modulation of Trk Receptors byACS chemical neuroscience · 2025Article
- Selective, Intrinsically Fluorescent Trk Modulating Probes.ACS chemical neuroscience · 2024Article
- Computational Prediction of Cyclic Peptide Structural Ensembles and Application to the Design of Keap1 Binders.Journal of chemical information and modeling · 2023Article
- Computational Design of Structured and Functional Peptide Macrocycles.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Understanding and designing head-to-tail cyclic peptides.Biopolymers · 2018Review
- Essential multimeric enzymes in kinetoplastid parasites: A host of potentially druggable protein-protein interactions.PLoS neglected tropical diseases · 2017Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Peptides are an increasingly useful class of molecules, finding unique applications as chemical probes and potential drugs. They are particularly adept at inhibiting protein-protein interactions, which are often difficult to target using small molecules. The identification and rational design of protein-binding epitopes remains a bottleneck in the development of bioactive peptides. One fruitful strategy has been using structured scaffolds to present essential hot spot residues involved in protein-protein recognition, and this process has been greatly advanced by computational tools that can identify hot spot residues. Here we discuss LoopFinder, a program that uses structures from the Protein Data Bank to comprehensively search for protein-protein interactions that are mediated by nonhelical, nonsheet loop structures. We developed LoopFinder to identify these "hot loops" and to assist in the design of cyclic peptides that mimic these important structures. In this article, we provide all key files, outline step-by-step methods for users to conduct independent LoopFinder searches, and provide guidance on additional potential applications for the LoopFinder program.
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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.