Diverse, high-quality test set for the validation of protein-ligand docking performance.

By M. Hartshorn, Marcel L. Verdonk, G. Chessari, S. Brewerton, Wijnand T. M. Mooij, Paul N. Mortenson, Christopher W. Murray. 2007

619 citations recorded by the source corpus.

Subfields: Computational Theory and Mathematics, Materials Chemistry, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Computational Theory and Mathematics

1. Yang Zhang
2. Stefano Forli
3. Elizabeth Yuriev
4. Paul A. Ramsland
5. Arthur J. Olson
6. Garrett M. Morris
7. David S. Goodsell
8. Michel F. Sanner

In Materials Chemistry

1. Ambrish Roy
2. Yang Zhang
3. Stefano Forli
4. N. V. Dokholyan
5. Elizabeth Yuriev
6. Paul A. Ramsland
7. Garrett M. Morris
8. Shuangye Yin

In Molecular Biology

1. Yang Zhang
2. Ambrish Roy
3. Stefano Forli
4. Elizabeth Yuriev
5. Paul A. Ramsland
6. Arthur J. Olson
7. Garrett M. Morris
8. Jianyi Yang

Citations in the corpus

• P2Rank: machine learning based tool for rapid and accurate prediction of ligand binding sites from protein structure (2018, background): “• ASTEX—Astex Diverse set [78] is a collection of 85 proteins that was introduced as a benchmarking dataset for molecular docking methods.”
• Structure-based drug discovery and protein targets in the CNS. (2011, methodology): “…have been performed which show that the computational methods are relatively good (>70% within 2 Å root mean squared deviation e RMSD e between actual and predicted pose, Hartshorn et al., 2007) for re-docking of compounds back into the previously determined structure of a proteineligand complex.”
• Recognizing protein-ligand binding sites by global structural alignment and local geometry refinement (2012, background): “Ligand-Binding Pocket Predictions The ability of the algorithms to identify ligand-binding pocket is tested on 501 benchmarking proteins, collected from three previous experiments (Dessailly et al., 2008; Hartshorn et al., 2007; Perola et al., 2004), which harbor 582 ligands.”
• Challenges and advances in computational docking: 2009 in review (2011, methodology): “(89) have used three scoring functions associated with GOLD (49,50) (Chem-Score, GoldScore, ASP) and the Astex Diverse Set to test two alternative proposals.”
• rDock: A Fast, Versatile and Open Source Program for Docking Ligands to Proteins and Nucleic Acids (2014, methodology): “The CCDCAstex Diverse Set of 85 diverse protein-ligand complexes was selected for comparing binding mode prediction [21].”
• Protein-ligand docking in the new millennium--a retrospective of 10 years in the field. (2013, methodology): “The ASTEX Diverse Set [191] is a docking validation set, derived from the Protein Data Bank, that contains 85 diverse, relevant protein-ligand complexes.”