ArticleJournal of computer-aided molecular design2022
SAMPL7 protein-ligand challenge: A community-wide evaluation of computational methods against fragment screening and pose-prediction.
Article in Journal of computer-aided molecular design, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 24 citations in OpenAlex.
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- Predicting Chromatographic Retention Times from Quantum-Chemical Solvation Free Energies: A Pilot Study of Oxysterols.The journal of physical chemistry. A · 2026Article
- A Computational Community Blind Challenge on Pan-Coronavirus Drug Discovery Data.Journal of chemical information and modeling · 2026Article
- Developments and challenges in hit progression within fragment-based drug discovery.Nature communications · 2026Review
- Article
- Binding-Site Purification of Actives (B-SPA) Enables Efficient Large-Scale Progression of Fragment Hits by Combining Multi-Step Array Synthesis With HT Crystallography.Angewandte Chemie (International ed. in English) · 2025Article
- The Need for Continuing Blinded Pose- and Activity Prediction Benchmarks.Journal of chemical information and modeling · 2025Review
- Thermal Titration Molecular Dynamics: The Revenge of the Fragments.Journal of chemical information and modeling · 2025Article
- Fighting Antimicrobial Resistance: Insights on How theJournal of chemical information and modeling · 2023Article
- An Imbalance in the Force: The Need for Standardized Benchmarks for Molecular Simulation.Journal of chemical information and modeling · 2023Review
- ChemFlow─From 2D Chemical Libraries to Protein-Ligand Binding Free Energies.Journal of chemical information and modeling · 2023Article
- Investigating RNA-protein recognition mechanisms through supervised molecular dynamics (SuMD) simulations.NAR genomics and bioinformatics · 2022Article
- MEDIATE - Molecular DockIng at homE: Turning collaborative simulations into therapeutic solutions.Expert opinion on drug discoveryArticle
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Authors and funding
7 authors at 4 institutions in 2 countries.
Funding
Abstract
A novel crystallographic fragment screening data set was generated and used in the SAMPL7 challenge for protein-ligands. The SAMPL challenges prospectively assess the predictive power of methods involved in computer-aided drug design. Application of various methods to fragment molecules are now widely used in the search for new drugs. However, there is little in the way of systematic validation specifically for fragment-based approaches. We have performed a large crystallographic high-throughput fragment screen against the therapeutically relevant second bromodomain of the Pleckstrin-homology domain interacting protein (PHIP2) that revealed 52 different fragments bound across 4 distinct sites, 47 of which were bound to the pharmacologically relevant acetylated lysine (Kac) binding site. These data were used to assess computational screening, binding pose prediction and follow-up enumeration. All submissions performed randomly for screening. Pose prediction success rates (defined as less than 2 Å root mean squared deviation against heavy atom crystal positions) ranged between 0 and 25% and only a very few follow-up compounds were deemed viable candidates from a medicinal-chemistry perspective based on a common molecular descriptors analysis. The tight deadlines imposed during the challenge led to a small number of submissions suggesting that the accuracy of rapidly responsive workflows remains limited. In addition, the application of these methods to reproduce crystallographic fragment data still appears to be very challenging. The results show that there is room for improvement in the development of computational tools particularly when applied to fragment-based drug design.
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