A comparison of the pharmacophore identification programs: Catalyst, DISCO and GASP.
Three commercially available pharmacophore generation programs, Catalyst/HipHop, DISCO and GASP, were compared on their ability to generate known pharmacophores deduced from protein-ligand complexes extracted from the Protein Data Bank. Five different protein families were included Thrombin, Cyclin Dependent Kinase 2, Dihydrofolate Reductase, HIV Reverse Transcriptase and Thermolysin. Target pharmacophores were defined through visual analysis of the data sets. The pharmacophore models produced were evaluated qualitatively through visual inspection and according to their ability to generate the target pharmacophores. Our results show that GASP and Catalyst outperformed DISCO at reproducing the five target pharmacophores.
Patel
Yogendra
Y
Krebs Institute for Biomolecular Research and Department of Information Studies, University of Sheffield, Western Bank, Sheffield S10 2TN, United Kingdom.
Gillet
Valerie J
VJ
Bravi
Gianpaolo
G
Leach
Andrew R
AR
D000465:Algorithms; D042846:CDC2-CDC28 Kinases; D051357:Cyclin-Dependent Kinase 2; D018844:Cyclin-Dependent Kinases / Q000187:drug effects / Q000378:metabolism; D030562:Databases, Protein; D015195:Drug Design; D054303:HIV Reverse Transcriptase / Q000187:drug effects / Q000378:metabolism; D006801:Humans; D066298:In Vitro Techniques; D008024:Ligands; D008956:Models, Chemical; D008958:Models, Molecular; D015394:Molecular Structure; D017346:Protein Serine-Threonine Kinases / Q000187:drug effects / Q000378:metabolism; D011506:Proteins / Q000187:drug effects* / Q000378:metabolism*; D012984:Software; D013762:Tetrahydrofolate Dehydrogenase / Q000187:drug effects / Q000378:metabolism; D013820:Thermolysin / Q000187:drug effects / Q000378:metabolism; D013917:Thrombin / Q000187:drug effects / Q000378:metabolism
D008024:Ligands; D011506:Proteins; D013762:Tetrahydrofolate Dehydrogenase; D017346:Protein Serine-Threonine Kinases; D042846:CDC2-CDC28 Kinases; C495894:CDK2 protein, human; D051357:Cyclin-Dependent Kinase 2; D018844:Cyclin-Dependent Kinases; D054303:HIV Reverse Transcriptase; D013917:Thrombin; D013820:Thermolysin