ArticlePloS one2013
A unified conformational selection and induced fit approach to protein-peptide docking.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 90 papers, 1 of them a synthesis that pooled it.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
90 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Immunoinformatics prediction of potential B-cell and T-cell epitopes as effective vaccine candidates for eliciting immunogenic responses against Epstein-Barr virus.Biomedical journal · 2021Pooled it
- SPPIDER-seq: sequence-based partner-aware predictor of protein-protein interaction sites.Bioinformatics (Oxford, England) · 2026Article
- SPPIDER-seq: Sequence-based partner-aware predictor of protein-protein interaction sites.bioRxiv : the preprint server for biology · 2026Article
- Peptide-protein docking: from physics-based models to generative intelligence.Chemical communications (Cambridge, England) · 2026Review
- Harnessing deep statistical potential for biophysical scoring of protein-peptide interactions.Acta pharmacologica Sinica · 2026Article
- 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
- 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
- Probing Biomolecular Interactions with Paramagnetic Nuclear Magnetic Resonance Spectroscopy.Chembiochem : a European journal of chemical biology · 2025Review
- Efficient Refinement of Complex Structures of Flexible Histone Peptides Using Post-Docking Molecular Dynamics Protocols.International journal of molecular sciences · 2024Article
- Challenges of Protein-Protein Docking of the Membrane Proteins.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Current Computational Methods for Protein-peptide Complex Structure Prediction.Current medicinal chemistry · 2024Review
- A New Advanced Approach: Design and Screening of Affinity Peptide Ligands Using Computer Simulation Techniques.Current topics in medicinal chemistry · 2024Review
- Exploring binding positions and backbone conformations of peptide ligands of proteins with a backbone-centred statistical energy function.Journal of computer-aided molecular design · 2023Article
- Molecular docking in organic, inorganic, and hybrid systems: a tutorial review.Monatshefte fur chemie · 2023Review
- Article
- Atomic resolution protein allostery from the multi-state structure of a PDZ domain.Nature communications · 2022Article
- Structural insights into the pSer/pThr dependent regulation of the SHP2 tyrosine phosphatase in insulin and CD28 signaling.Nature communications · 2022Article
- Cyclization and Docking Protocol for Cyclic Peptide-Protein Modeling Using HADDOCK2.4.Journal of chemical theory and computation · 2022Article
30 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
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Protein-peptide interactions are vital for the cell. They mediate, inhibit or serve as structural components in nearly 40% of all macromolecular interactions, and are often associated with diseases, making them interesting leads for protein drug design. In recent years, large-scale technologies have enabled exhaustive studies on the peptide recognition preferences for a number of peptide-binding domain families. Yet, the paucity of data regarding their molecular binding mechanisms together with their inherent flexibility makes the structural prediction of protein-peptide interactions very challenging. This leaves flexible docking as one of the few amenable computational techniques to model these complexes. We present here an ensemble, flexible protein-peptide docking protocol that combines conformational selection and induced fit mechanisms. Starting from an ensemble of three peptide conformations (extended, a-helix, polyproline-II), flexible docking with HADDOCK generates 79.4% of high quality models for bound/unbound and 69.4% for unbound/unbound docking when tested against the largest protein-peptide complexes benchmark dataset available to date. Conformational selection at the rigid-body docking stage successfully recovers the most relevant conformation for a given protein-peptide complex and the subsequent flexible refinement further improves the interface by up to 4.5 Å interface RMSD. Cluster-based scoring of the models results in a selection of near-native solutions in the top three for ∼75% of the successfully predicted cases. This unified conformational selection and induced fit approach to protein-peptide docking should open the route to the modeling of challenging systems such as disorder-order transitions taking place upon binding, significantly expanding the applicability limit of biomolecular interaction modeling by docking.
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.