ArticleJournal of chemical information and modeling2013
Lessons learned in empirical scoring with smina from the CSAR 2011 benchmarking exercise.
Article in Journal of chemical information and modeling, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 528 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
528 citing papers in PubMed.
- GDEE: A Structure-Based Platform for Gene Discovery and Enzyme Engineering.Journal of chemical information and modeling · 2026Article
- Synthesis, SAR Analysis, and Antifungal Potency against Plant Pathogenic Fungi of New Azidopyrazoles.ACS omega · 2026Article
- DockM8: an all-in-one open-source platform for consensus virtual screening in drug design.Journal of cheminformatics · 2026Article
- Enhanced Line Search Improves Robustness and Efficiency of Pose Sampling in Protein-Ligand Docking.Journal of chemical theory and computation · 2026Article
- Data driven selection of consensus docking pipelines for structure based hit identification.npj drug discovery · 2026Article
- 4-Ethyl phenyl sulfate binding to human serum albumin.Protein science : a publication of the Protein Society · 2026Article
- Evaluating molecular docking for binding affinity predictions: a systematic analysis of key parameters and the utility of AlphaFold2 structures for the Schrödinger dataset.Journal of computer-aided molecular design · 2026Article
- Computational Investigation of Cinnamon Phytochemicals Targeting Key Cancer Signaling Pathways: Molecular Docking, ADMET and Molecular Dynamics Simulations Analysis.Current issues in molecular biology · 2026Article
- EasyDock 1.3: An Automated Pipeline for Molecular Docking.Journal of chemical information and modeling · 2026Article
- In Silico Isomerization Produces Apt Negative Data for VHTS Validation.Journal of chemical information and modeling · 2026Article
- USP20-mediated PGAM1 stabilization promotes glycolysis and confers osimertinib resistance in non-small cell lung carcinoma.Oncogene · 2026Article
- Bridging between Structure-Based and Data-Driven Affinity Prediction.Journal of chemical information and modeling · 2026Article
- Benchmarking Docking Protocols on Predicting Alternative Binding Modes.Journal of chemical information and modeling · 2026Article
- QSAR-ML- and Metadynamics-Guided Design of Symmetrical Bis-Indanones to Overcome Mutational Anchor Loss in Acetylcholinesterase.Pharmaceuticals (Basel, Switzerland) · 2026Article
- Assessing Fluoroacetate Defluorination Potential across Diverse Enzymes Using Quantum Chemistry.The journal of physical chemistry. B · 2026Article
- A versatile yeast platform for N-demethylation of therapeutic alkaloids.Journal of biological engineering · 2026Article
- Enhancing virtual screening of cystathionine β-synthase inhibitors: benchmarking target-specific machine-learning scoring functions against state-of-the-art AI docking and co-folding approaches.Journal of cheminformatics · 2026Article
- SynergisticiScience · 2026Article
- Reversing the Fold: Polyanionic Macrocycle Dissolves αA66-80 Crystallin Peptide Aggregates.Biomacromolecules · 2026Article
- Exploiting the T790M Gatekeeper: A Theoretical Blueprint for Non-Covalent Inhibition of inPharmaceutics · 2026Article
468 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
We describe a general methodology for designing an empirical scoring function and provide smina, a version of AutoDock Vina specially optimized to support high-throughput scoring and user-specified custom scoring functions. Using our general method, the unique capabilities of smina, a set of default interaction terms from AutoDock Vina, and the CSAR (Community Structure-Activity Resource) 2010 data set, we created a custom scoring function and evaluated it in the context of the CSAR 2011 benchmarking exercise. We find that our custom scoring function does a better job sampling low RMSD poses when crossdocking compared to the default AutoDock Vina scoring function. The design and application of our method and scoring function reveal several insights into possible improvements and the remaining challenges when scoring and ranking putative ligands.
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.