ArticleCancer research2017
DINC 2.0: A New Protein-Peptide Docking Webserver Using an Incremental Approach.
Article in Cancer research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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
46 citing papers in PubMed.
- A Review of Current Computational Tools for Peptide-Protein Docking.Journal of computational chemistry · 2026Review
- A Computational Perspective to Intermolecular Interactions and the Role of the Solvent on Regulating Protein Properties.Chemical reviews · 2025Review
- DINC-ensemble: A web server for docking large ligands incrementally to an ensemble of receptor conformations.Journal of molecular biology · 2025Article
- Molecular Modelling in Bioactive Peptide Discovery and Characterisation.Biomolecules · 2025Review
- Identification of a Clade-Specific HLA-C*03:02 CTL Epitope GY9 Derived from the HIV-1 p17 Matrix Protein.International journal of molecular sciences · 2024Article
- Therapeutic peptides for coronary artery diseases: in silico methods and current perspectives.Amino acids · 2024Review
- APE-Gen2.0: Expanding Rapid Class I Peptide-Major Histocompatibility Complex Modeling to Post-Translational Modifications and Noncanonical Peptide Geometries.Journal of chemical information and modeling · 2024Article
- Virtual Screening of Peptide Libraries: The Search for Peptide-Based Therapeutics Using Computational Tools.International journal of molecular sciences · 2024Review
- Design of Cyclic Peptides Targeting Protein-Protein Interactions Using AlphaFold.International journal of molecular sciences · 2023Article
- Modeling of MT. P495, an mRNA-based vaccine against the phosphate-binding protein PstS1 of Mycobacterium tuberculosis.Molecular diversity · 2023Article
- Loss of PI3Kα Mediates Protection From Myocardial Ischemia-Reperfusion Injury Linked to Preserved Mitochondrial Function.Journal of the American Heart Association · 2023Article
- Albumin/Thiacalix[4]arene Nanoparticles as Potential Therapeutic Systems: Role of the Macrocycle for Stabilization of Monomeric Protein and Self-Assembly with Ciprofloxacin.International journal of molecular sciences · 2022Article
- Molecular mechanism of interaction between fatty acid delta 6 desaturase and acyl-CoA by computational prediction.AMB Express · 2022Article
- Computational Tools and Strategies to Develop Peptide-Based Inhibitors of Protein-Protein Interactions.Methods in molecular biology (Clifton, N.J.) · 2022Review
- Modelling peptide-protein complexes: docking, simulations and machine learning.QRB discovery · 2022Article
- Drug and Anti-Viral Peptide Design to Inhibit the Monkeypox Virus by Restricting A36R Protein.Bioinformatics and biology insights · 2022Article
- ADMET profiling and molecular docking of potential antimicrobial peptides previously isolated from African catfish,Frontiers in molecular biosciences · 2022Article
- Structural Prediction of Peptide-MHC Binding Modes.Methods in molecular biology (Clifton, N.J.) · 2022Review
- T-cell epitope-based vaccine designing against Orthohantavirus: a causative agent of deadly cardio-pulmonary disease.Network modeling and analysis in health informatics and bioinformatics · 2022Article
- Graph representation learning for structural proteomics.Emerging topics in life sciences · 2021Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors.
Funding
Abstract
Molecular docking is a standard computational approach to predict binding modes of protein-ligand complexes by exploring alternative orientations and conformations of the ligand (i.e., by exploring ligand flexibility). Docking tools are largely used for virtual screening of small drug-like molecules, but their accuracy and efficiency greatly decays for ligands with more than 10 flexible bonds. This prevents a broader use of these tools to dock larger ligands, such as peptides, which are molecules of growing interest in cancer research. To overcome this limitation, our group has previously proposed a meta-docking strategy, called DINC, to predict binding modes of large ligands. By incrementally docking overlapping fragments of a ligand, DINC allowed predicting binding modes of peptide-based inhibitors of transcription factors involved in cancer. Here, we describe DINC 2.0, a revamped version of the DINC webserver with enhanced capabilities and a more user-friendly interface. DINC 2.0 allows docking ligands that were previously too challenging for DINC, such as peptides with more than 25 flexible bonds. The webserver is freely accessible at http://dinc.kavrakilab.org, together with additional documentation and video tutorials. Our team will provide continuous support for this tool and is working on extending its applicability to other challenging fields, such as personalized immunotherapy against cancer.
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.