ArticleJournal of computer-aided molecular design2016
D3R grand challenge 2015: Evaluation of protein-ligand pose and affinity predictions.
Article in Journal of computer-aided molecular design, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 124 papers.
What it found
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Who cites it
124 citing papers in PubMed, 221 citations in OpenAlex.
- Article
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- Large-Scale Collaborative Assessment of Binding Free Energy Calculations for Drug Discovery Using OpenFE.Journal of chemical information and modeling · 2026Article
- More protein-ligand data are needed for AlphaFold-like models to enable drug discovery.Current opinion in structural biology · 2026Review
- Evaluating generalization in protein-ligand cofolding methods.Nature structural & molecular biology · 2026Article
- A Diffusion-Based Time-Frequency Dual-Stream Contrastive Learning Model for Multivariate Time Series Anomaly Detection.Entropy (Basel, Switzerland) · 2026Article
- Discovery of potential RSV fusion protein inhibitors from benzimidazole derivatives using QSAR, molecular docking, and ADMET evaluation methods.Molecular diversity · 2026Article
- The Open Molecular Software Foundation (OMSF) and the Growing Role of Open Source Software in Molecular Modeling.Journal of chemical information and modeling · 2026Review
- A fully automated benchmarking suite to compare macromolecular complexes.Nature methods · 2026Review
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- CACHE Challenge #2: Targeting the RNA Site of the SARS-CoV-2 Helicase Nsp13.Journal of chemical information and modeling · 2025Article
- Computation of Protein-Ligand Binding Free Energies with a Quantum Mechanics-Based Mining Minima Algorithm.Journal of chemical theory and computation · 2025Article
- ABCG2: A Milestone Charge Model for Accurate Solvation Free Energy Calculation.Journal of chemical theory and computation · 2025Article
- The Need for Continuing Blinded Pose- and Activity Prediction Benchmarks.Journal of chemical information and modeling · 2025Review
- Rationalizing protein-ligand interactions via the effective fragment potential method and structural data from classical molecular dynamics.The Journal of chemical physics · 2025Article
- AIntibody: an experimentally validated in silico antibody discovery design challenge.Nature biotechnology · 2024Article
- Prediction of Threonine-Tyrosine Kinase Receptor-Ligand Unbinding Kinetics with Multiscale Milestoning and Metadynamics.The journal of physical chemistry letters · 2024Article
- Advances in machine-learning approaches to RNA-targeted drug design.Artificial intelligence chemistry · 2024Article
- Docking strategies for predicting protein-ligand interactions and their application to structure-based drug design.Communications in information and systems · 2024Article
64 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
15 authors at 4 institutions in 1 country.
Funding
Abstract
The Drug Design Data Resource (D3R) ran Grand Challenge 2015 between September 2015 and February 2016. Two targets served as the framework to test community docking and scoring methods: (1) HSP90, donated by AbbVie and the Community Structure Activity Resource (CSAR), and (2) MAP4K4, donated by Genentech. The challenges for both target datasets were conducted in two stages, with the first stage testing pose predictions and the capacity to rank compounds by affinity with minimal structural data; and the second stage testing methods for ranking compounds with knowledge of at least a subset of the ligand-protein poses. An additional sub-challenge provided small groups of chemically similar HSP90 compounds amenable to alchemical calculations of relative binding free energy. Unlike previous blinded Challenges, we did not provide cognate receptors or receptors prepared with hydrogens and likewise did not require a specified crystal structure to be used for pose or affinity prediction in Stage 1. Given the freedom to select from over 200 crystal structures of HSP90 in the PDB, participants employed workflows that tested not only core docking and scoring technologies, but also methods for addressing water-mediated ligand-protein interactions, binding pocket flexibility, and the optimal selection of protein structures for use in docking calculations. Nearly 40 participating groups submitted over 350 prediction sets for Grand Challenge 2015. This overview describes the datasets and the organization of the challenge components, summarizes the results across all submitted predictions, and considers broad conclusions that may be drawn from this collaborative community endeavor.
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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.