title: pROC-Chemotype Plots Enhance the Interpretability of Benchmarking Results in Structure-Based Virtual Screening.
abstract: Recently, we have reported a systematic comparison of molecular preparation protocols (using MOE or Maestro) in combination with two docking tools (GOLD or Glide), employing our DEKOIS 2.0 benchmark sets. Herein, we demonstrate how comparable settings of data preparation protocols can affect the profile and AUC of pROC curves based on variations in chemotype enrichment. We show how the recognition of different classes of chemotypes can affect the docking performance, particularly in the early enrichment, and monitor changes in this recognition behavior based on score normalization and rescoring strategies. For this, we have developed "pROC-Chemotype", which is an automated protocol that matches and visualizes ligand chemotype information together with potency classes in the pROC profiles obtained by docking. This tool enhances the understanding of the influence of chemotype recognition in early enrichment, but also reveals trends of impaired recognition of chemotype classes at the end of the score-ordered rank. Identifying such issues helps to devise score-normalization strategies to overcome this potential bias in an intuitive manner. Furthermore, strong perturbations in chemotype ranking between different methods can help to identify the underlying reasons (e.g., changes in the protonation/tautomerization state). It also assists in the selection of appropriate scoring functions that are capable to retrieve more potent and diverse hits. In summary, we demonstrate how this new tool can be utilized to identify and highlight chemotype-specific behavior, e.g., in dataset preparation. This can help to overcome some chemistry-related bias in virtual screening campaigns. pROC-Chemotype is made freely available at www.dekois.com.
authors.affiliation: Laboratory for Molecular Design and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen , Auf der Morgenstelle 8, 72076 Tübingen, Germany.
authors.forename: Tamer M
authors.initials: TM
authors.lastname: Ibrahim
authors.affiliation: Laboratory for Molecular Design and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen , Auf der Morgenstelle 8, 72076 Tübingen, Germany.
authors.forename: Matthias R
authors.initials: MR
authors.lastname: Bauer
authors.affiliation: Center for Bioinformatics Tübingen (ZBIT), Eberhard Karls University Tübingen , Sand 1, 72076 Tübingen, Germany.
authors.forename: Alexander
authors.initials: A
authors.lastname: Dörr
authors.affiliation: Laboratory for Molecular Design and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen , Auf der Morgenstelle 8, 72076 Tübingen, Germany.
authors.forename: Erdem
authors.initials: E
authors.lastname: Veyisoglu
authors.affiliation: Laboratory for Molecular Design and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmaceutical Sciences, Eberhard Karls Universität Tübingen , Auf der Morgenstelle 8, 72076 Tübingen, Germany.|Center for Bioinformatics Tübingen (ZBIT), Eberhard Karls University Tübingen , Sand 1, 72076 Tübingen, Germany.
authors.forename: Frank M
authors.initials: FM
authors.lastname: Boeckler
mesh_terms: D019540:Area Under Curve; D015195:Drug Design; D005493:Folic Acid Antagonists / Q000737:chemistry / Q000494:pharmacology*; D006801:Humans; D008024:Ligands; D062105:Molecular Docking Simulation; D011485:Protein Binding; D011799:Quinazolines / Q000737:chemistry / Q000494:pharmacology; D012372:ROC Curve; D013762:Tetrahydrofolate Dehydrogenase / Q000378:metabolism*
chemical_list: D005493:Folic Acid Antagonists; D008024:Ligands; D011799:Quinazolines; D013762:Tetrahydrofolate Dehydrogenase