ArticlePLoS computational biology2019
Protein-protein binding supersites.
Article in PLoS computational biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 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
12 citing papers in PubMed, 22 citations in OpenAlex.
- Development of the TSR-based computational method to investigate spike and monoclonal antibody interactions.Frontiers in chemistry · 2025Article
- Computational prediction of multiple antigen epitopes.Bioinformatics (Oxford, England) · 2024Article
- Computational Methods to Predict Conformational B-Cell Epitopes.Biomolecules · 2024Review
- Assessing the functional impact of protein binding site definition.Protein science : a publication of the Protein Society · 2024Article
- Optimal selection of suitable templates in protein interface prediction.Bioinformatics (Oxford, England) · 2023Article
- Integrated structure-based protein interface prediction.BMC bioinformatics · 2022Article
- Modeling of protein complexes in CASP14 with emphasis on the interaction interface prediction.Proteins · 2021Article
- Residue-based pharmacophore approaches to study protein-protein interactions.Current opinion in structural biology · 2021Review
- Classification and prediction of protein-protein interaction interface using machine learning algorithm.Scientific reports · 2021Article
- Challenges in protein docking.Current opinion in structural biology · 2020Review
- Computational structure modeling for diverse categories of macromolecular interactions.Current opinion in structural biology · 2020Review
- HMI-PRED: A Web Server for Structural Prediction of Host-Microbe Interactions Based on Interface Mimicry.Journal of molecular biology · 2020Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
The lack of a deep understanding of how proteins interact remains an important roadblock in advancing efforts to identify binding partners and uncover the corresponding regulatory mechanisms of the functions they mediate. Understanding protein-protein interactions is also essential for designing specific chemical modifications to develop new reagents and therapeutics. We explored the hypothesis of whether protein interaction sites serve as generic biding sites for non-cognate protein ligands, just as it has been observed for small-molecule-binding sites in the past. Using extensive computational docking experiments on a test set of 241 protein complexes, we found that indeed there is a strong preference for non-cognate ligands to bind to the cognate binding site of a receptor. This observation appears to be robust to variations in docking programs, types of non-cognate protein probes, sizes of binding patches, relative sizes of binding patches and full-length proteins, and the exploration of obligate and non-obligate complexes. The accuracy of the docking scoring function appears to play a role in defining the correct site. The frequency of interaction of unrelated probes recognizing the binding interface was utilized in a simple prediction algorithm that showed accuracy competitive with other state of the art methods.
Indexed as
Identifiers
What OpenQuestion holds
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.