ReviewCurrent topics in medicinal chemistry2009
Docking screens: right for the right reasons?
Review in Current topics in medicinal chemistry, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 48 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
48 citing papers in PubMed.
- Bioactive Peptides from Andean Crops: Lactic Acid Bacteria Fermentation, Complementary Proteolysis, and Biological Activities.Foods (Basel, Switzerland) · 2026Review
- Evaluating generalization in protein-ligand cofolding methods.Nature structural & molecular biology · 2026Article
- Cholinesterase Inhibitory Activity of Alkylated Quinobenzothiazinium Salts.Molecules (Basel, Switzerland) · 2026Article
- Binding Free Energies without Alchemy.ArXiv · 2026Article
- Unfreezing structural biology for drug discovery.Nature chemical biology · 2026Review
- Solvent-Site Prediction for Fragment Docking and Its Implication on Fragment-Based Drug Discovery.Journal of chemical information and modeling · 2025Article
- An MD View of Ligand Binding.Molecules (Basel, Switzerland) · 2025Article
- Structure-guided discovery of Otopetrin 1 inhibitors reveals druggable binding sites at the intrasubunit interface.Nature communications · 2025Article
- Building shape-focused pharmacophore models for effective docking screening.Journal of cheminformatics · 2024Article
- Development of Potential Multi-Target Inhibitors for Human Cholinesterases and Beta-Secretase 1: A Computational Approach.Pharmaceuticals (Basel, Switzerland) · 2023Article
- Exploring Pyrrolo-Fused Heterocycles as Promising Anticancer Agents: An Integrated Synthetic, Biological, and Computational Approach.Pharmaceuticals (Basel, Switzerland) · 2023Article
- Structure-based discovery of conformationally selective inhibitors of the serotonin transporter.Cell · 2023Article
- Towards Arginase Inhibition: Hybrid SAR Protocol for Property Mapping of ChlorinatedInternational journal of molecular sciences · 2023Article
- Allosteric modulators of solute carrier function: a theoretical framework.Frontiers in physiology · 2023Article
- Computational and Biological Evaluation ofPharmaceuticals (Basel, Switzerland) · 2022Article
- Structural similarities between SARS-CoV2 3CLFrontiers in chemistry · 2022Article
- A practical guide to large-scale docking.Nature protocols · 2021Review
- Hepatitis C virus drugs that inhibit SARS-CoV-2 papain-like protease synergize with remdesivir to suppress viral replication in cell culture.Cell reports · 2021Article
- Two Decades of 4D-QSAR: A Dying Art or Staging a Comeback?International journal of molecular sciences · 2021Review
- Synthesis and Hybrid SAR Property Modeling of Novel Cholinesterase Inhibitors.International journal of molecular sciences · 2021Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
Abstract
Whereas docking screens have emerged as the most practical way to use protein structure for ligand discovery, an inconsistent track record raises questions about how well docking actually works. In its favor, a growing number of publications report the successful discovery of new ligands, often supported by experimental affinity data and controls for artifacts. Few reports, however, actually test the underlying structural hypotheses that docking makes. To be successful and not just lucky, prospective docking must not only rank a true ligand among the top scoring compounds, it must also correctly orient the ligand so the score it receives is biophysically sound. If the correct binding pose is not predicted, a skeptic might well infer that the discovery was serendipitous. Surveying over 15 years of the docking literature, we were surprised to discover how rarely sufficient evidence is presented to establish whether docking actually worked for the right reasons. The paucity of experimental tests of theoretically predicted poses undermines confidence in a technique that has otherwise become widely accepted. Of course, solving a crystal structure is not always possible, and even when it is, it can be a lot of work, and is not readily accessible to all groups. Even when a structure can be determined, investigators may prefer to gloss over an erroneous structural prediction to better focus on their discovery. Still, the absence of a direct test of theory by experiment is a loss for method developers seeking to understand and improve docking methods. We hope this review will motivate investigators to solve structures and compare them with their predictions whenever possible, to advance the field.
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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.