ArticleStructure (London, England : 1993)2011
Structural and dynamic determinants of protein-peptide recognition.
Article in Structure (London, England : 1993), 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 53 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.
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Who cites it
53 citing papers in PubMed, 96 citations in OpenAlex.
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- In Silico Structure-Guided Design of Peptide Candidates Targeting γ-Secretase Subunit Assembly.Proteins · 2026Article
- Structure-Guided Design of an Interface-Derived Inhibitor Peptide Against Spodoptera frugiperda Digestive Trypsins.Archives of insect biochemistry and physiology · 2026Article
- Peptide-based drug design using generative AI.Chemical communications (Cambridge, England) · 2026Review
- Differential Self-Assembly Behaviors and Proteolytic Stability of Bicyclic Peptides Compared to Monocyclic Peptides.Chemistry, an Asian journal · 2026Article
- DiffPepDock: Efficient protein-peptide docking and binder screening via SE(3)-equivariant diffusion.Protein science : a publication of the Protein Society · 2025Article
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- Sensory plasticity caused by up-down regulation encodes the information of short-term learning and memory.iScience · 2025Article
- Design and Development of Natural-Product-Derived Nanoassemblies and Their Interactions with Alpha Synuclein.Biomimetics (Basel, Switzerland) · 2025Article
- Leveraging Therapeutic Proteins and Peptides fromInternational journal of molecular sciences · 2024Article
- Current Computational Methods for Protein-peptide Complex Structure Prediction.Current medicinal chemistry · 2024Review
- Assessing Genetic Algorithm-Based Docking Protocols for Prediction of Heparin Oligosaccharide Binding Geometries onto Proteins.Biomolecules · 2023Article
- Peptidomimetics in cancer targeting.Molecular medicine (Cambridge, Mass.) · 2022Review
- Binding site identification of G protein-coupled receptors through a 3D Zernike polynomials-based method: application to C. elegans olfactory receptors.Journal of computer-aided molecular design · 2022Article
- Anchor extension: a structure-guided approach to design cyclic peptides targeting enzyme active sites.Nature communications · 2021Article
- Two 20-Residue-Long Peptides Derived fromInternational journal of molecular sciences · 2021Article
- Protein-Protein Binding as a Two-Step Mechanism: Preselection of Encounter Poses during the Binding of BPTI and Trypsin.Biophysical journal · 2020Article
- Machine learning and AI-based approaches for bioactive ligand discovery and GPCR-ligand recognition.Methods (San Diego, Calif.) · 2020Review
- Experimentally-driven protein structure modeling.Journal of proteomics · 2020Review
Corrections and comments
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Authors and funding
5 authors at 2 institutions in 1 country.
Funding
Abstract
Protein-peptide interactions play important roles in many cellular processes, including signal transduction, trafficking, and immune recognition. Protein conformational changes upon binding, an ill-defined peptide binding surface, and the large number of peptide degrees of freedom make the prediction of protein-peptide interactions particularly challenging. To address these challenges, we perform rapid molecular dynamics simulations in order to examine the energetic and dynamic aspects of protein-peptide binding. We find that, in most cases, we recapitulate the native binding sites and native-like poses of protein-peptide complexes. Inclusion of electrostatic interactions in simulations significantly improves the prediction accuracy. Our results also highlight the importance of protein conformational flexibility, especially side-chain movement, which allows the peptide to optimize its conformation. Our findings not only demonstrate the importance of sufficient sampling of the protein and peptide conformations, but also reveal the possible effects of electrostatics and conformational flexibility on peptide recognition.
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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.