title: ChemGPS-NP(Web): chemical space navigation online.
abstract: Internet has become a central source for information, tools, and services facilitating the work for medicinal chemists and drug discoverers worldwide. In this paper we introduce a web-based public tool, ChemGPS-NP(Web) (http://chemgps.bmc.uu.se), for comprehensive chemical space navigation and exploration in terms of global mapping onto a consistent, eight dimensional map over structure derived physico-chemical characteristics. ChemGPS-NP(Web) can assist in compound selection and prioritization; property description and interpretation; cluster analysis and neighbourhood mapping; as well as comparison and characterization of large compound datasets. By using ChemGPS-NP(Web), researchers can analyze and compare chemical libraries in a consistent manner. In this study it is demonstrated how ChemGPS-NP(Web) can assist in interpreting results from two large datasets tested for activity in biological assays for pyruvate kinase and Bcl-2 family related protein interactions, respectively. Furthermore, a more than 30-year-old suggestion of "chemical similarity" between the natural pigments betalains and muscaflavins is tested.
authors.affiliation: Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, BMC Box 574, 75123 Uppsala, Sweden. josefin.rosen@fkog.uu.se
authors.forename: Josefin
authors.initials: J
authors.lastname: Rosén
authors.forename: Anders
authors.initials: A
authors.lastname: Lövgren
authors.forename: Thierry
authors.initials: T
authors.lastname: Kogej
authors.forename: Sorel
authors.initials: S
authors.lastname: Muresan
authors.forename: Johan
authors.initials: J
authors.lastname: Gottfries
authors.forename: Anders
authors.initials: A
authors.lastname: Backlund
mesh_terms: D000970:Antineoplastic Agents / Q000737:chemistry / Q000494:pharmacology; D051017:Apoptosis Regulatory Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism; D000072224:Bcl-2-Like Protein 11; D050858:Betalains / Q000737:chemistry; D019295:Computational Biology / Q000379:methods*; D016208:Databases, Factual; D055808:Drug Discovery / Q000379:methods*; D004791:Enzyme Inhibitors / Q000737:chemistry; D005415:Flavins / Q000737:chemistry; D006801:Humans; D020407:Internet; D008565:Membrane Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D011485:Protein Binding / Q000187:drug effects; D011518:Proto-Oncogene Proteins / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism; D019253:Proto-Oncogene Proteins c-bcl-2 / Q000037:antagonists & inhibitors / Q000737:chemistry / Q000378:metabolism; D011770:Pyruvate Kinase / Q000037:antagonists & inhibitors; D012984:Software; D012985:Software Design; D014584:User-Computer Interface
chemical_list: D000970:Antineoplastic Agents; D051017:Apoptosis Regulatory Proteins; C000606775:BCL2L11 protein, human; D000072224:Bcl-2-Like Protein 11; D004791:Enzyme Inhibitors; D005415:Flavins; D008565:Membrane Proteins; D011518:Proto-Oncogene Proteins; D019253:Proto-Oncogene Proteins c-bcl-2; D050858:Betalains; D011770:Pyruvate Kinase