SuperStar: a knowledge-based approach for identifying interaction sites in proteins.

By Marcel L. Verdonk, Jason C. Cole, Robin Taylor. 1999

Subfields: Evaluation & Benchmarks

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In Evaluation & Benchmarks

1. Gerhard Klebe
2. Gregory A. Ross
3. Philip C. Biggin
4. Garrett M. Morris
5. Holger Gohlke

Citations in the corpus

• A Role for Fragment-Based Drug Design in Developing Novel Lead Compounds for Central Nervous System Targets (2015, methodology): “This information is translated into a scatterplot, to be used to predict how fragments will interact with the binding site of the target protein (27).”
• Virtual ligand screening: strategies, perspectives and limitations (2006, methodology): “These methods are either based on thoroughly parameterized force fields [62] or on well-selected empirical information (SuperStar [63] , DrugScore [64] ; Figure 4 ).”
• A new test set for validating predictions of protein–ligand interaction (2002, background): “Most protein classes have 1 to 4 entries; classes with more representatives are (in the clean set of 224 entries): dihydrofolate reductase (5); carbonic anhydrase II (5); neuraminidases (5); trypsin (7); thrombin ( and ) (9); hiv-1 protease (10).”
• New software for searching the Cambridge Structural Database and visualizing crystal structures. (2002, methodology): “SuperStar therefore exempli®es a program that answers a speci®c question of relevance to drug design and does so by manipulating data derived ultimately and solely from a crystallographic database.”
• Knowledge-based scoring function to predict protein-ligand interactions. (2000, background): “This in¯uence was ®rst recognized by Verdonk et al. (1999) during the development of SuperStar.”
• Rapid and Accurate Prediction and Scoring of Water Molecules in Protein Binding Sites (2012, methodology): “SuperStar is another knowledge-based method that combines structural data from the Protein Data Bank [55] and the Cambridge Structural Database [56] (CSD) to predict chemical propensity maps within protein cavities [57].”
• Protein-ligand docking in the new millennium--a retrospective of 10 years in the field. (2013, methodology): “Other less recent approaches such as AQUARIUS [103], CS-Map [104], MCSS [105], SuperStar [106] and most notably GRID[107] have also been described in the literature to identify potential water binding sites.”