ArticleJournal of computer-aided molecular design2012
Docking and scoring with ICM: the benchmarking results and strategies for improvement.
Article in Journal of computer-aided molecular design, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 168 papers.
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Who cites it
168 citing papers in PubMed.
- Beyond the flat screen: evaluating virtual reality as a complementary tool for molecular docking in drug discovery.Journal of computer-aided molecular design · 2026Review
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- Machine learning-assisted screening of natural product database for the identification of novel chalcone-based derivative as a potent DHODH inhibitor in cancer therapy.Discover oncology · 2026Article
- 2-Butanone 4-glucopyranoside 6'-O-gallate isolated from Memecylon scutellatum exhibits anti-inflammatory activity via modulation of the NF-κB and MAPK signaling pathways in LPS-stimulated RAW 264.7 macrophages.Inflammopharmacology · 2026Article
- A Polypharmacology-Driven Approach to Alzheimer's Disease and Tauopathies: Rational Design, Synthesis and Characterization of Amino-Pyrazole-Based Multikinase (GSK-3β/FYN-α/DYRK1A) Inhibitors.Journal of medicinal chemistry · 2026Article
- Pharmacological proximities in the GPCR family discovered using contact-informed amino-acid and binding pocket similarities.bioRxiv : the preprint server for biology · 2026Article
- Discovery of novel peptidomimetics against HSP90-HOP interactions towards improved cancer therapeutics using machine learning strategies.Frontiers in bioinformatics · 2026Article
- Multi-target computational pipeline for discovery of pan-influenza neuraminidase inhibitors.Frontiers in pharmacology · 2026Article
- Novel GPU Engines for Virtual Screening of Giga-Sized Libraries Identify Inhibitors of Challenging Targets.Journal of chemical information and modeling · 2025Article
- A novel chemoreactive calcilytic for the potential treatment of autosomal dominant hypocalcemia.Acta pharmaceutica Sinica. B · 2025Article
- Exploration of Fluorinated Pyrazolidine-3,5-Diones for Positron Emission Tomography Imaging of the P2YChemMedChem · 2025Article
- Noncanonical roles of chemokine regions in CCR9 activation revealed by structural modeling and mutational mapping.Nature communications · 2025Article
- Activity of STAMP inhibitors inBlood neoplasia · 2025Article
- Potent β-lactam-based tyrosyl-DNA phosphodiesterase 1 inhibitors identified by a virtual screen.Scientific reports · 2025Article
- NAMPT and NNMT released via extracellular vesicles and as soluble mediators are distinguished traits of BRAF inhibitor resistance of melanoma cells impacting on the tumor microenvironment.Cell communication and signaling : CCS · 2025Article
- Discovery of an autoinhibited conformation in mesotrypsin reveals a strategy for selective serine protease inhibition.Science advances · 2025Article
- Deciphering the language of mingling lipids and proteins.Current opinion in structural biology · 2025Review
- Generating 3D Binding Molecules Using Shape-Conditioned Diffusion Models with Guidance.Nature machine intelligence · 2025Article
108 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors.
Funding
Abstract
Flexible docking and scoring using the internal coordinate mechanics software (ICM) was benchmarked for ligand binding mode prediction against the 85 co-crystal structures in the modified Astex data set. The ICM virtual ligand screening was tested against the 40 DUD target benchmarks and 11-target WOMBAT sets. The self-docking accuracy was evaluated for the top 1 and top 3 scoring poses at each ligand binding site with near native conformations below 2 Å RMSD found in 91 and 95% of the predictions, respectively. The virtual ligand screening using single rigid pocket conformations provided the median area under the ROC curves equal to 69.4 with 22.0% true positives recovered at 2% false positive rate. Significant improvements up to ROC AUC = 82.2 and ROC((2%)) = 45.2 were achieved following our best practices for flexible pocket refinement and out-of-pocket binding rescore. The virtual screening can be further improved by considering multiple conformations of the target.
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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.