ArticlePloS one2011
Rosetta FlexPepDock ab-initio: simultaneous folding, docking and refinement of peptides onto their receptors.
Article in PloS one, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 164 papers.
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Who cites it
164 citing papers in PubMed.
- Peptide Aptamers: Innovative Design and Applications in Pathogen Detection.Chembiochem : a European journal of chemical biology · 2026Review
- Strategic Template Filtering Accelerates Fragment-Based Peptide Docking.Journal of chemical information and modeling · 2026Article
- Computational Analysis of Antimicrobial Peptides Targeting Agglutinin-Like Protein 3 (Als3) and β-Glucan Synthase in Denture-Associated Candidiasis.International dental journal · 2026Article
- ProteinDock: A physics-informed layer to improve protein-protein docking reliability.bioRxiv : the preprint server for biology · 2026Article
- Venom-Derived Enzyme Inhibitors as Anticancer Agents: Structure-Activity Relationships, Molecular Targets and Mechanistic Insights.Molecules (Basel, Switzerland) · 2026Review
- Article
- Peptide-protein docking: from physics-based models to generative intelligence.Chemical communications (Cambridge, England) · 2026Review
- Open-Source Molecular Docking and AI-Augmented Structure-Based Drug Design: Current Workflows, Challenges, and Opportunities.International journal of molecular sciences · 2026Review
- Discovery of Peptide-Based Tubulin Inhibitors Through Structure-Guided Design.Pharmaceutics · 2026Article
- A Review of Current Computational Tools for Peptide-Protein Docking.Journal of computational chemistry · 2026Review
- PepScorer::RMSD: An Improved Machine Learning Scoring Function for Protein-Peptide Docking.International journal of molecular sciences · 2026Article
- First inhibitor of a bacterial two-partner secretion system.bioRxiv : the preprint server for biology · 2026Article
- Bioactive peptides targeting dyslipidemia and atherosclerosis: from computational discovery and data bottlenecks to precision medicine translation.Frontiers in molecular biosciences · 2026Review
- Pseudokinases can catalyse peptide cyclization through thioether crosslinking.Nature chemistry · 2026Article
- Lab to codes: multimodel advanced AI-driven pipelines to drive antimicrobial peptide design for the post-antibiotic era.Frontiers in cellular and infection microbiology · 2026Review
- Identification of a novel MIPEP splice variant with altered substrate-binding properties.Biochemistry and biophysics reports · 2025Article
- A hybrid evolutionary and structural method for AI-guided peptide inhibitor design using AlphaFold and Rosetta.Scientific reports · 2025Article
- Docking in the Dark: Insights into Protein-Protein and Protein-Ligand Blind Docking.Pharmaceuticals (Basel, Switzerland) · 2025Review
- DiffPepDock: Efficient protein-peptide docking and binder screening via SE(3)-equivariant diffusion.Protein science : a publication of the Protein Society · 2025Article
- Competitive binding of actin and SH3 domains at proline-rich regions of Las17/WASP regulates actin polymerisation.Communications biology · 2025Article
104 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Flexible peptides that fold upon binding to another protein molecule mediate a large number of regulatory interactions in the living cell and may provide highly specific recognition modules. We present Rosetta FlexPepDock ab-initio, a protocol for simultaneous docking and de-novo folding of peptides, starting from an approximate specification of the peptide binding site. Using the Rosetta fragments library and a coarse-grained structural representation of the peptide and the receptor, FlexPepDock ab-initio samples efficiently and simultaneously the space of possible peptide backbone conformations and rigid-body orientations over the receptor surface of a given binding site. The subsequent all-atom refinement of the coarse-grained models includes full side-chain modeling of both the receptor and the peptide, resulting in high-resolution models in which key side-chain interactions are recapitulated. The protocol was applied to a benchmark in which peptides were modeled over receptors in either their bound backbone conformations or in their free, unbound form. Near-native peptide conformations were identified in 18/26 of the bound cases and 7/14 of the unbound cases. The protocol performs well on peptides from various classes of secondary structures, including coiled peptides with unusual turns and kinks. The results presented here significantly extend the scope of state-of-the-art methods for high-resolution peptide modeling, which can now be applied to a wide variety of peptide-protein interactions where no prior information about the peptide backbone conformation is available, enabling detailed structure-based studies and manipulation of those interactions.
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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.