ArticleMolecules (Basel, Switzerland)2021
Improving Blind Docking in DOCK6 through an Automated Preliminary Fragment Probing Strategy.
Article in Molecules (Basel, Switzerland), 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 33 citations in OpenAlex.
- Can Cavity Prediction Algorithms Help in Docking Experiments?Journal of computational chemistry · 2026Article
- Docking in the Dark: Insights into Protein-Protein and Protein-Ligand Blind Docking.Pharmaceuticals (Basel, Switzerland) · 2025Review
- CoBdock-2: enhancing blind docking performance through hybrid feature selection combining ensemble and multimodel feature selection approaches.Journal of computer-aided molecular design · 2025Article
- Mechanism of action of Coptidis Rhizome in treating periodontitis based on network pharmacology and in vitro validation.BMC oral health · 2024Article
- Virtual Screening of Peptide Libraries: The Search for Peptide-Based Therapeutics Using Computational Tools.International journal of molecular sciences · 2024Review
- Cobdock: an accurate and practical machine learning-based consensus blind docking method.Journal of cheminformatics · 2024Article
- Synthesis of Pyrrolo[3,4-Pharmaceuticals (Basel, Switzerland) · 2023Article
- Pharmacophore-Aided Virtual Screening and Molecular Dynamics Simulation Identifies TrkB Agonists for Treatment ofBioinformatics and biology insights · 2023Article
- Interaction of the new inhibitor paxlovid (PF-07321332) and ivermectin with the monomer of the main protease SARS-CoV-2: A volumetric study based on molecular dynamics, elastic networks, classical thermodynamics and SPT.Computational biology and chemistry · 2022Article
- Concatenation of molecular docking and molecular simulation of BACE-1, γ-secretase targeted ligands: in pursuit of Alzheimer's treatment.Annals of medicine · 2021Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Probing protein surfaces to accurately predict the binding site and conformation of a small molecule is a challenge currently addressed through mainly two different approaches: blind docking and cavity detection-guided docking. Although cavity detection-guided blind docking has yielded high success rates, it is less practical when a large number of molecules must be screened against many detected binding sites. On the other hand, blind docking allows for simultaneous search of the whole protein surface, which however entails the loss of accuracy and speed. To bridge this gap, in this study, we developed and tested BLinDPyPr, an automated pipeline which uses FTMap and DOCK6 to perform a hybrid blind docking strategy. Through our algorithm, FTMap docked probe clusters are converted into DOCK6 spheres for determining binding regions. Because these spheres are solely derived from FTMap probes, their locations are contained in and specific to multiple potential binding pockets, which become the regions that are simultaneously probed and chosen by the search algorithm based on the properties of each candidate ligand. This method yields pose prediction results (45.2-54.3% success rates) comparable to those of site-specific docking with the classic DOCK6 workflow (49.7-54.3%) and is half as time-consuming as the conventional blind docking method with DOCK6.
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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.