ArticleJournal of molecular graphics & modelling2021
dockECR: Open consensus docking and ranking protocol for virtual screening of small molecules.
Article in Journal of molecular graphics & modelling, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed, 26 citations in OpenAlex.
- DockM8: an all-in-one open-source platform for consensus virtual screening in drug design.Journal of cheminformatics · 2026Article
- Data driven selection of consensus docking pipelines for structure based hit identification.npj drug discovery · 2026Article
- Structure-guided compound prioritization strategy for virtual screening identifies putative binders for the nuclear receptor LRH-1.bioRxiv : the preprint server for biology · 2026Article
- Discovery of Novel PTP1B Inhibitors by High-throughput Virtual Screening.Current computer-aided drug design · 2026Article
- In search of novel PD1 inhibitor from natural products by high-throughput virtual screening and molecular dynamics simulation.PloS one · 2026Article
- Article
- Discovery of novel HBV core protein inhibitors by high throughput virtual screening.Scientific reports · 2025Article
- TREM-1 as a Potential Coreceptor in Norovirus Pathogenesis: Insights from Transcriptomic Analysis and Molecular Docking.ACS omega · 2025Article
- Identification of novel cyclin-dependent kinase 4/6 inhibitors from marine natural products.PloS one · 2025Article
- Consensus scoring-guided virtual screening identifies potent anti-saprolegniasis compounds targeting a P450 fusion protein.Frontiers in microbiology · 2025Article
- Consensus holistic virtual screening for drug discovery: a novel machine learning model approach.Journal of cheminformatics · 2024Article
- Molecular modelling studies and in vitro enzymatic assays identified A 4-(nitrobenzyl)guanidine derivative as inhibitor of SARS-CoV-2 Mpro.Scientific reports · 2024Article
- In Search of Novel SGLT2 Inhibitors by High-throughput Virtual Screening.Current drug discovery technologies · 2024Article
- Large-Scale Docking in the Cloud.Journal of chemical information and modeling · 2023Article
- Comprehensive Survey of Consensus Docking for High-Throughput Virtual Screening.Molecules (Basel, Switzerland) · 2022Review
- Drugsniffer: An Open Source Workflow for Virtually Screening Billions of Molecules for Binding Affinity to Protein Targets.Frontiers in pharmacology · 2022Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The development of open computational pipelines to accelerate the discovery of treatments for emerging diseases allows finding novel solutions in shorter periods of time. Consensus molecular docking is one of these approaches, and its main purpose is to increase the detection of real actives within virtual screening campaigns. Here we present dockECR, an open consensus docking and ranking protocol that implements the exponential consensus ranking method to prioritize molecular candidates. The protocol uses four open source molecular docking programs: AutoDock Vina, Smina, LeDock and rDock, to rank the molecules. In addition, we introduce a scoring strategy based on the average RMSD obtained from comparing the best poses from each single program to complement the consensus ranking with information about the predicted poses. The protocol was benchmarked using 15 relevant protein targets with known actives and decoys, and applied using the main protease of the SARS-CoV-2 virus. For the application, different crystal structures of the protease, and frames obtained from molecular dynamics simulations were used to dock a library of 79 molecules derived from previously co-crystallized fragments. The ranking obtained with dockECR was used to prioritize eight candidates, which were evaluated in terms of the interactions generated with key residues from the protease. The protocol can be implemented in any virtual screening campaign involving proteins as molecular targets. The dockECR code is publicly available at: https://github.com/rochoa85/dockECR.
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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.