ArticleNucleic acids research2016
PepComposer: computational design of peptides binding to a given protein surface.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- DiffPepDock: Efficient protein-peptide docking and binder screening via SE(3)-equivariant diffusion.Protein science : a publication of the Protein Society · 2025Article
- A Computational Perspective to Intermolecular Interactions and the Role of the Solvent on Regulating Protein Properties.Chemical reviews · 2025Review
- Molecular Modelling in Bioactive Peptide Discovery and Characterisation.Biomolecules · 2025Review
- A New Advanced Approach: Design and Screening of Affinity Peptide Ligands Using Computer Simulation Techniques.Current topics in medicinal chemistry · 2024Review
- Computational approaches for the design of modulators targeting protein-protein interactions.Expert opinion on drug discovery · 2023Review
- Computer- and NMR-Aided Design of Small-Molecule Inhibitors of the Hub1 Protein.Molecules (Basel, Switzerland) · 2022Article
- Protocol for iterative optimization of modified peptides bound to protein targets.Journal of computer-aided molecular design · 2022Article
- Tertiary motifs as building blocks for the design of protein-binding peptides.Protein science : a publication of the Protein Society · 2022Article
- Predicting Protein-Peptide Complex Structures by Accounting for Peptide Flexibility and the Physicochemical Environment.Journal of chemical information and modeling · 2022Article
- Harnessing protein folding neural networks for peptide-protein docking.Nature communications · 2022Article
- Modelling peptide-protein complexes: docking, simulations and machine learning.QRB discovery · 2022Article
- Computational Evolution Protocol for Peptide Design.Methods in molecular biology (Clifton, N.J.) · 2022Article
- The Effects of Tetrapeptides Designed to Fit the Androgen Binding Site of ZIP9 on Myogenic and Osteogenic Cells.Biology · 2021Article
- Toward Development of a Label-Free Detection Technique for Microfluidic Fluorometric Peptide-Based Biosensor Systems.Micromachines · 2021Article
- Structural Characterization of Receptor-Receptor Interactions in the Allosteric Modulation of G Protein-Coupled Receptor (GPCR) Dimers.International journal of molecular sciences · 2021Review
- Computational Modeling as a Tool to Investigate PPI: From Drug Design to Tissue Engineering.Frontiers in molecular biosciences · 2021Review
- In-Silico Evidence for a Two Receptor Based Strategy of SARS-CoV-2.Frontiers in molecular biosciences · 2021Article
- Review
- Article
- A novel strategy for molecular interfaces optimization: The case of Ferritin-Transferrin receptor interaction.Computational and structural biotechnology journal · 2020Article
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
There is a wide interest in designing peptides able to bind to a specific region of a protein with the aim of interfering with a known interaction or as starting point for the design of inhibitors. Here we describe PepComposer, a new pipeline for the computational design of peptides binding to a given protein surface. PepComposer only requires the target protein structure and an approximate definition of the binding site as input. We first retrieve a set of peptide backbone scaffolds from monomeric proteins that harbor the same backbone arrangement as the binding site of the protein of interest. Next, we design optimal sequences for the identified peptide scaffolds. The method is fully automatic and available as a web server at http://biocomputing.it/pepcomposer/webserver.
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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.