ArticleJournal of chemical information and modeling2020
CANDOCK: Chemical Atomic Network-Based Hierarchical Flexible Docking Algorithm Using Generalized Statistical Potentials.
Article in Journal of chemical information and modeling, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
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Who cites it
33 citing papers in PubMed, 57 citations in OpenAlex.
- Combining cutting edge computational and experimental methods for targeting KRAS mutations in non-small cell lung cancer.Expert opinion on drug discovery · 2026Review
- Multiscale analysis and optimal glioma therapeutic candidate discovery using the CANDO platform.Journal of cheminformatics · 2026Article
- Strategies for robust, accurate, and generalizable benchmarking of drug discovery platforms.Bioinformatics (Oxford, England) · 2025Article
- Strategies for robust, accurate, and generalizable benchmarking of drug discovery platforms.bioRxiv : the preprint server for biology · 2025Article
- Identification of potential human targets for epigallocatechin gallate through a novel protein binding site screening approach.Journal of molecular modeling · 2025Article
- Ten quick tips to perform meaningful and reproducible molecular docking calculations.PLoS computational biology · 2025Article
- Uncovering the molecular targets of phytocannabinoids: mechanistic insights from inverse molecular docking fingerprint approaches.Frontiers in pharmacology · 2025Article
- Advances and Challenges in Molecular Docking Applied to Neglected Tropical Diseases.Current medicinal chemistry · 2025Review
- Alkynyl nicotinamides show antileukemic activity in drug-resistant acute myeloid leukemia.The Journal of clinical investigation · 2024Article
- Modeling Molecular Mechanisms of Pirfenidone Interaction with Kinases.bioRxiv : the preprint server for biology · 2024Article
- A Monocarbonyl Curcuminoid Derivative Inhibits the Activity of Human Glutathione Transferase A4-4 and Chemosensitizes Glioblastoma Cells to Temozolomide.Pharmaceuticals (Basel, Switzerland) · 2024Article
- Identification of Coumarin-Chalcone and Coumarin-Pyrazoline Derivatives as Novel Anti-Drug design, development and therapy · 2024Article
- Novel coumarin-6-sulfonamide-chalcone hybrids as glutathione transferase P1-1 inhibitors.PloS one · 2024Article
- Article
- Monocarbonyl Curcumin Analogues as Potent Inhibitors against Human Glutathione Transferase P1-1.Antioxidants (Basel, Switzerland) · 2022Article
- Inverse Molecular Docking Elucidating the Anticarcinogenic Potential of the Hop Natural Product Xanthohumol and Its Metabolites.Foods (Basel, Switzerland) · 2022Article
- Evaluating the performance of drug-repurposing technologies.Drug discovery today · 2022Review
- Mechanistic Insights into Biological Activities of Polyphenolic Compounds from Rosemary Obtained by Inverse Molecular Docking.Foods (Basel, Switzerland) · 2021Article
- A synthetic small molecule stalls pre-mRNA splicing by promoting an early-stage U2AF2-RNA complex.Cell chemical biology · 2021Article
- Multiscale Virtual Screening Optimization for Shotgun Drug Repurposing Using the CANDO Platform.Molecules (Basel, Switzerland) · 2021Article
Corrections and comments
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Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
Abstract
Small-molecule docking has proven to be invaluable for drug design and discovery. However, existing docking methods have several limitations such as improper treatment of the interactions of essential components in the chemical environment of the binding pocket (e.g., cofactors, metal ions, etc.), incomplete sampling of chemically relevant ligand conformational space, and the inability to consistently correlate docking scores of the best binding pose with experimental binding affinities. We present CANDOCK, a novel docking algorithm, that utilizes a hierarchical approach to reconstruct ligands from an atomic grid using graph theory and generalized statistical potential functions to sample biologically relevant ligand conformations. Our algorithm accounts for protein flexibility, solvent, metal ions, and cofactor interactions in the binding pocket that are traditionally ignored by current methods. We evaluate the algorithm on the PDBbind, Astex, and PINC proteins to show its ability to reproduce the binding mode of the ligands that is independent of the initial ligand conformation in these benchmarks. Finally, we identify the best selector and ranker potential functions such that the statistical score of the best selected docked pose correlates with the experimental binding affinities of the ligands for any given protein target. Our results indicate that CANDOCK is a generalized flexible docking method that addresses several limitations of current docking methods by considering all interactions in the chemical environment of a binding pocket for correlating the best-docked pose with biological activity. CANDOCK along with all structures and scripts used for benchmarking is available at https://github.com/chopralab/candock_benchmark.
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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.