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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. [cache]

119) AutoDock 4.2 was used to dock nine hybrid compounds to four DNA duplexes, while monitoring of conformational changes of four best hybrid-DNA complexes during 2 ns was performed by Amber9 molecular dynamics package.

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PMID:24580066 DOI:10.1080/07391102.2014.887480

2015 Journal of biomolecular structure & dynamics

* The binding modes of cationic porphyrin-anthraquinone hybrids to DNA duplexes: in silico study.

- Cationic porphyrin-anthraquinone hybrids bearing peripheral substituents, either pyridine, imidazole, or pyrazole rings have been investigated for their binding mode to DNA duplexes. The four kinds of DNA duplexes were used, which represent intercalation and groove binding modes. AutoDock 4.2 was used to dock nine hybrid compounds to four DNA duplexes, while monitoring of conformational changes of four best hybrid-DNA complexes during 2 ns was performed by Amber9 molecular dynamics package. The binding energy calculation of best four complexes was then carried out using MMPBSA method. The hybrid compounds interacted to DNA duplexes through intercalation and groove binding modes. The minor groove binding of DNA was energetically preferred by cationic porphyrin hybrids due to favorable electrostatic and van der Waals interactions. Both electrostatic and van der Waals contributions were able to distinguish the binding mode of porphyrin hybrid to DNA duplexes.

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[frequency of next (right) word to molecular]

(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 ---