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return kwic search for molecular out of >500 occurrences
333489 occurrences (No.56 in the rank) during 5 years in the PubMed. [no cache] 500 found

380) Most pharmacophore discovery programs face difficulties in conformational flexibility, molecular alignment, pharmacophore features sampling, and feature selection to score models if the data-set constitutes diverse ligands.

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PMID:24735019 DOI:10.1080/07391102.2014.908142

2015 Journal of biomolecular structure & dynamics

* Development of pharmacophore similarity-based quantitative activity hypothesis and its applicability domain: applied on a diverse data-set of HIV-1 integrase inhibitors.

- Quantitative pharmacophore hypothesis combines the 3D spatial arrangement of pharmacophore features with biological activities of the ligand data-set and predicts the activities of geometrically and/or pharmacophoric similar ligands. Most pharmacophore discovery programs face difficulties in conformational flexibility, molecular alignment, pharmacophore features sampling, and feature selection to score models if the data-set constitutes diverse ligands. Towards this focus, we describe a ligand-based computational procedure to introduce flexibility in aligning the small molecules and generating a pharmacophore hypothesis without geometrical constraints to define pharmacophore space, enriched with chemical features necessary to elucidate common pharmacophore hypotheses (CPHs). Maximal common substructure (MCS)-based alignment method was adopted to guide the alignment of carbon molecules, deciphered the MCS atom connectivity to cluster molecules in bins and subsequently, calculated the pharmacophore similarity matrix with the bin-specific reference molecules. After alignment, the carbon molecules were enriched with original atoms in their respective positions and conventional pharmacophore features were perceived. Distance-based pharmacophoric descriptors were enumerated by computing the interdistance between perceived features and MCS-aligned 'centroid' position. The descriptor set and biological activities were used to develop support vector machine models to predict the activities of the external test set. Finally, fitness score was estimated based on pharmacophore similarity with its bin-specific reference molecules to recognize the best and poor alignments and, also with each reference molecule to predict outliers of the quantitative hypothesis model. We applied this procedure to a diverse data-set of 40 HIV-1 integrase inhibitors and discussed its effectiveness with the reported CPH model.

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(1)52 mechanisms	(19)5 docking	(37)3 recognition	(55)2 heparin
(2)26 weight	(20)5 information	(38)3 serotyping	(56)2 identification
(3)18 data	(21)5 methods	(39)3 sieve	(57)2 knowledge
(4)18 mechanism	(22)5 modeling	(40)3 structure	(58)2 mass
(5)16 dynamics	(23)5 phylogenetic	(41)3 techniques	(59)2 mechanisms,
(6)15 and	(24)5 targets	(42)3 variance	(60)2 or
(7)10 analysis	(25)4 diagnosis	(43)2 Dynamics	(61)2 oxygen
(8)10 basis	(26)4 interactions	(44)2 approach	(62)2 perspectives
(9)8 characterization	(27)4 level	(45)2 biological	(63)2 phenotypic
(10)7 epidemiology	(28)4 level,	(46)2 classification	(64)2 phylogenies
(11)7 genetic	(29)4 responses	(47)2 clock	(65)2 probes
(12)7 imaging	(30)4 target	(48)2 dating	(66)2 profiles
(13)6 biology	(31)3 evolution	(49)2 details	(67)2 subtype
(14)6 changes	(32)3 features	(50)2 diffusion	(68)2 therapies
(15)6 markers	(33)3 levels	(51)2 effects	(69)2 underpinnings
(16)6 pathways	(34)3 marker	(52)2 events
(17)5 analyses	(35)3 medicine	(53)2 evidence
(18)5 characteristics	(36)3 orbital	(54)2 genetics

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--- WordNet output for molecular --- =>分子の Overview of adj molecular The adj molecular has 2 senses (first 1 from tagged texts) 1. (6) molecular -- (relating to or produced by or consisting of molecules; "molecular structure"; "molecular oxygen"; "molecular weight is the sum of all the atoms in a molecule") 2. molecular -- (relating to simple or elementary organization; "proceed by more and more detailed analysis to the molecular facts of perception"--G.A. Miller) --- WordNet end ---