ArticleJournal of computer-aided molecular design2012
Surflex-Dock: Docking benchmarks and real-world application.
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 102 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
102 citing papers in PubMed.
- Pose Reproduction, Cross Docking, Database Enrichment, and Reverse Docking Benchmarks for DOCK6, Vina, and AutoDock 4 with Emphasis on Approved Drugs.Journal of chemical information and modeling · 2026Article
- A brief guideline for the studies of structure-function relationship of ion channels using AlphaFold3.Fundamental research · 2026Review
- Refining the Study of Endophytic Fungi: Best Practices in Antibacterial Research.Current microbiology · 2026Review
- Recent advances in drug repositioning and rediscovery for different therapeutic activities utilizing updated technological approaches.Molecular diversity · 2026Review
- Lab to codes: multimodel advanced AI-driven pipelines to drive antimicrobial peptide design for the post-antibiotic era.Frontiers in cellular and infection microbiology · 2026Review
- Topological deep learning for enhancing peptide-protein complex prediction.Communications chemistry · 2025Article
- Molecular Docking and Target-Specific Binding Profiles of Benzosuberane-Based Compounds.ChemMedChem · 2025Review
- The covalent docking software landscape: features and applications in drug design.Briefings in bioinformatics · 2025Review
- Token-Mol 1.0: tokenized drug design with large language models.Nature communications · 2025Article
- Article
- Jiawei Duhuo Jisheng Mixture Mitigates Osteoarthritis Progression in Rabbits by Inhibiting Inflammation: A Network Pharmacology and Experimental Approach.Combinatorial chemistry & high throughput screening · 2025Article
- Structure-based identification of HNF4α agonists: Rosmarinic acid as a promising candidate for NAFLD treatment.Computational and structural biotechnology journal · 2025Article
- Pheromone-Binding Protein 1 Performs a Dual Function for Intra- and Intersexual Signaling in a Moth.International journal of molecular sciences · 2024Article
- Identification of novel PD-1/PD-L1 small molecule inhibitors: virtual screening, synthesis andJournal of enzyme inhibition and medicinal chemistry · 2024Article
- Structure-based pose prediction: Non-cognate docking extended to macrocyclic ligands.Journal of computer-aided molecular design · 2024Article
- Targeting ERK-MYD88 interaction leads to ERK dysregulation and immunogenic cancer cell death.Nature communications · 2024Article
- Recent advances in the area of plant-based anti-cancer drug discovery using computational approaches.Molecular diversity · 2024Review
- Resistance and virulence genes characteristic of a South Asia Clade (I) Candida auris strain isolated from blood in Beijing.Clinics (Sao Paulo, Brazil) · 2024Article
- Phytochemistry and Cytotoxic Activity ofACS omega · 2023Article
- Computer-Assisted Design of Peptide-Based Radiotracers.International journal of molecular sciences · 2023Review
42 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
2 authors.
Funding
Abstract
Benchmarks for molecular docking have historically focused on re-docking the cognate ligand of a well-determined protein-ligand complex to measure geometric pose prediction accuracy, and measurement of virtual screening performance has been focused on increasingly large and diverse sets of target protein structures, cognate ligands, and various types of decoy sets. Here, pose prediction is reported on the Astex Diverse set of 85 protein ligand complexes, and virtual screening performance is reported on the DUD set of 40 protein targets. In both cases, prepared structures of targets and ligands were provided by symposium organizers. The re-prepared data sets yielded results not significantly different than previous reports of Surflex-Dock on the two benchmarks. Minor changes to protein coordinates resulting from complex pre-optimization had large effects on observed performance, highlighting the limitations of cognate ligand re-docking for pose prediction assessment. Docking protocols developed for cross-docking, which address protein flexibility and produce discrete families of predicted poses, produced substantially better performance for pose prediction. Performance on virtual screening performance was shown to benefit by employing and combining multiple screening methods: docking, 2D molecular similarity, and 3D molecular similarity. In addition, use of multiple protein conformations significantly improved screening enrichment.
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.