ArticleJournal of computational chemistry2019
AutoGridFR: Improvements on AutoDock Affinity Maps and Associated Software Tools.
Article in Journal of computational chemistry, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 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
32 citing papers in PubMed.
- Experimental, Genomic, and Structural Evidence Supporting Putative PET-Hydrolases in Thermophilic Bacteria Isolated From Hot Springs in Cajamarca, Peru.MicrobiologyOpen · 2026Article
- In Silico Structure-Guided Design of Peptide Candidates Targeting γ-Secretase Subunit Assembly.Proteins · 2026Article
- Mechanistic Insights into PET-MPs-Aggravated Ischemic Stroke via Integrated Computational-Experimental Approaches.Environmental science & technology · 2026Article
- Unnatural amino acid compounds as potent multi-target inhibitors of aldose reductase, α-glucosidase, and α-amylase: integrated in vitro, SAR, and molecular dynamics insights.Naunyn-Schmiedeberg's archives of pharmacology · 2026Article
- Dual Inhibition of COX-2/5-LOX Through Novel Hybrids of NSAIDs and Peptides: Insights from Molecular Dynamics Simulation and Per-Residue Decomposition.ChemistryOpen · 2026Article
- Structural modeling and docking analysis of canonical and novel resistance-associated missense mutations in Sudanese Escherichia coli.Scientific reports · 2026Article
- PepScorer::RMSD: An Improved Machine Learning Scoring Function for Protein-Peptide Docking.International journal of molecular sciences · 2026Article
- Bacteriocin-transport-inspired oral peptide-probiotic delivery ameliorates IBD complications via autophagy and gut homeostasis.Science advances · 2026Article
- A novel Ru(II) complex with pyrene-1-carbaldehyde hydrazone: structural, electronic, theoretical, and biological studies.Frontiers in chemistry · 2026Article
- Investigating the Antioxidant, Pro-Inflammatory Enzyme Inhibitory, Neuroprotective, and Antineuroinflammatory Bioactives ofACS omega · 2025Article
- Mucus-derived glycans are inhibitory signals for Salmonella Typhimurium SPI-1-mediated invasion.Cell reports · 2025Article
- In Silico Design and Computational Elucidation of Hypothetical Resveratrol-Curcumin Hybrids as Potential Cancer Pathway Modulators.Pharmaceuticals (Basel, Switzerland) · 2025Article
- Locusts adopt IPScience advances · 2025Article
- Article
- Molecular docking and biological evaluation of a novel IWS1 inhibitor for the treatment of human retroperitoneal liposarcoma.Scientific reports · 2025Article
- Cartilage targeting cationic peptide carriers display deep cartilage penetration and retention in a rabbit model of post-traumatic osteoarthritis.Osteoarthritis and cartilage · 2025Article
- Article
- Ru(II) Complexes with 3,4-Dimethylphenylhydrazine: Exploring In Vitro Anticancer Activity and Protein Affinities.Biomolecules · 2025Article
- Different fluorescent labels report distinct components of spHCN channel voltage sensor movement.The Journal of general physiology · 2024Article
- Discovery of New Dual-Target Agents Against PPAR-γ and α-Glucosidase Enzymes with Molecular Modeling Methods: Molecular Docking, Molecular Dynamic Simulations, and MM/PBSA Analysis.The protein journal · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
Precomputed affinity maps are used by AutoDock to efficiently describe rigid biomolecules called receptors in automated docking. These maps greatly speed up the docking process and allow users to experiment with the forcefield. Here, we present AutoGridFR (AGFR): a software tool facilitating the calculation of these maps. We describe a new version of the AutoSite algorithm that improves the description of binding pockets automatically detected on receptors, and an algorithm for adding affinity gradients which help search methods optimize solution using fewer evaluations of the scoring functions. AGFR supports the calculation of maps for various advanced docking techniques such as covalent docking, hydrated docking, and docking with flexible receptor sidechains. Maps are stored in a single file along with metadata supporting data provenance, reproducibility, and facilitating their management. Finally, maps can be calculated from the command line or through a modern graphical user interface which also supports their visualization. © 2019 Wiley Periodicals, Inc.
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.