Enrichment of ligands for the serotonin receptor using the Shape Signatures approach. Nagarajan, K., Zauhar, R., & Welsh, W. J J.~Chem.~Inf.~Model., 45(1):49--57, Department of Pharmacology, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, New Jersey 08854, USA., 2005. doi abstract bibtex Shape Signatures, a new 3-dimensional molecular comparison method, has been adapted to rank ligands of the serotonin receptors. A set of 825 agonists and 400 antagonists together with approximately 10,000 randomly chosen compounds from the NCI database were used in this study. Both 1D and 2D Shape Signature databases were created, and enrichment studies were carried out. Results from these studies reveal that the 1D Shape Signature approach is highly efficient in separating agonists from a mixture of molecules which includes compounds randomly selected from the NCI database taken as inactives. It is also equally effective at separating agonists and antagonists from a pool of active ligands for the serotonin receptor. Parallel enrichment studies using 2D shape signatures showed high selectivity with more restricted coverage due to the high specificity of 2D signatures. The influence of conformational variation of the shape signature on enrichment was explored by docking a subset of ligands into the crystal structure of serotonin N-acetyltransferase. Enrichment studies on the resulting "docked" conformations produced only slightly improved results compared with the CORINA-generated conformations.
@article{Nagarajan:2005fk,
Abstract = {Shape Signatures, a new 3-dimensional molecular comparison method, has been adapted to rank ligands of the serotonin receptors. A set of 825 agonists and 400 antagonists together with approximately 10,000 randomly chosen compounds from the NCI database were used in this study. Both 1D and 2D Shape Signature databases were created, and enrichment studies were carried out. Results from these studies reveal that the 1D Shape Signature approach is highly efficient in separating agonists from a mixture of molecules which includes compounds randomly selected from the NCI database taken as inactives. It is also equally effective at separating agonists and antagonists from a pool of active ligands for the serotonin receptor. Parallel enrichment studies using 2D shape signatures showed high selectivity with more restricted coverage due to the high specificity of 2D signatures. The influence of conformational variation of the shape signature on enrichment was explored by docking a subset of ligands into the crystal structure of serotonin N-acetyltransferase. Enrichment studies on the resulting "docked" conformations produced only slightly improved results compared with the CORINA-generated conformations.},
Address = {Department of Pharmacology, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, 675 Hoes Lane, Piscataway, New Jersey 08854, USA.},
Au = {Nagarajan, K and Zauhar, R and Welsh, WJ},
Author = {Nagarajan, Karthigeyan and Zauhar, Randy and Welsh, William J},
Da = {20050125},
Date-Added = {2007-12-11 17:01:03 -0500},
Date-Modified = {2007-12-11 17:01:03 -0500},
Dcom = {20050225},
Doi = {10.1021/ci049746x},
Edat = {2005/01/26 09:00},
Issn = {1549-9596 (Print)},
Jid = {101230060},
Journal = {J.~Chem.~Inf.~Model.},
Jt = {Journal of chemical information and modeling},
Keywords = {serotonin antagonist shape signature conformation},
Language = {eng},
Mhda = {2005/02/26 09:00},
Number = {1},
Own = {NLM},
Pages = {49--57},
Pl = {United States},
Pmid = {15667128},
Pst = {ppublish},
Pt = {Journal Article},
Pubm = {Print},
Rn = {0 (Ligands); 0 (Serotonin Agonists); 0 (Serotonin Antagonists)},
Sb = {IM},
So = {J.~Chem.~Inf.~Model.. 2005 Jan-Feb;45(1):49-57.},
Stat = {MEDLINE},
Title = {Enrichment of ligands for the serotonin receptor using the Shape Signatures approach.},
Volume = {45},
Year = {2005},
Bdsk-Url-1 = {http://dx.doi.org/10.1021/ci049746x}}
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