ArticlePLoS computational biology2013
Exploring Protein-Peptide Binding Specificity through Computational Peptide Screening.
Article in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 40 citations in OpenAlex.
- Peptide-Based Strategies for Targeted Tumor Treatment and Imaging.Pharmaceutics · 2021Review
- Noncanonical Sequences Involving NHERF1 Interaction with NPT2A Govern Hormone-Regulated Phosphate Transport: Binding Outside the Box.International journal of molecular sciences · 2021Review
- Computational Design of PDZ-Peptide Binding.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Adaptive landscape flattening allows the design of both enzyme: Substrate binding and catalytic power.PLoS computational biology · 2020Article
- A comprehensive ensemble model for comparing the allosteric effect of ordered and disordered proteins.PLoS computational biology · 2018Article
- Large-scale docking predicts that sORF-encoded peptides may function through protein-peptide interactions in Arabidopsis thaliana.PloS one · 2018Article
- Computer-aided design of amino acid-based therapeutics: a review.Drug design, development and therapy · 2018Review
- Unraveling the Roots of Selectivity of Peptide Affinity Reagents for Structurally Similar Ribosomal Inactivating Protein Derivatives.Molecules (Basel, Switzerland) · 2016Article
- PepComposer: computational design of peptides binding to a given protein surface.Nucleic acids research · 2016Article
- Binding cavities and druggability of intrinsically disordered proteins.Protein science : a publication of the Protein Society · 2015Article
- Advantages of proteins being disordered.Protein science : a publication of the Protein Society · 2014Review
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The binding of short disordered peptide stretches to globular protein domains is important for a wide range of cellular processes, including signal transduction, protein transport, and immune response. The often promiscuous nature of these interactions and the conformational flexibility of the peptide chain, sometimes even when bound, make the binding specificity of this type of protein interaction a challenge to understand. Here we develop and test a Monte Carlo-based procedure for calculating protein-peptide binding thermodynamics for many sequences in a single run. The method explores both peptide sequence and conformational space simultaneously by simulating a joint probability distribution which, in particular, makes searching through peptide sequence space computationally efficient. To test our method, we apply it to 3 different peptide-binding protein domains and test its ability to capture the experimentally determined specificity profiles. Insight into the molecular underpinnings of the observed specificities is obtained by analyzing the peptide conformational ensembles of a large number of binding-competent sequences. We also explore the possibility of using our method to discover new peptide-binding pockets on protein structures.
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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.