ELIZA

return kwic search for used to out of >500 occurrences
298981 occurrences (No.78 in the rank) during 5 years in the PubMed. [cache]

356) The mechanism of a protein's function, which used to be explained by the ideas of 'lock and key' has evolved today as the concept of 'induced fit' as well as the 'population shift' models.

--- ABSTRACT ---

PMID:24433438 DOI:10.1080/07391102.2013.873002

2015 Journal of biomolecular structure & dynamics

* Adaptability in protein structures: structural dynamics and implications in ligand design.

- The basic framework of understanding the mechanisms of protein functions is achieved from the knowledge of their structures which can model the molecular recognition. Recent advancement in the structural biology has revealed that in spite of the availability of the structural data, it is nontrivial to predict the mechanism of the molecular recognition which progresses via situation-dependent structural adaptation. The mutual selectivity of protein-protein and protein-ligand interactions often depends on the modulations of conformations empowered by their inherent flexibility, which in turn regulates the function. The mechanism of a protein's function, which used to be explained by the ideas of 'lock and key' has evolved today as the concept of 'induced fit' as well as the 'population shift' models. It is felt that the 'dynamics' is an essential feature to take into account for understanding the mechanism of protein's function. The design principles of therapeutic molecules suffer from the problems of plasticity of the receptors whose binding conformations are accurately not predictable from the prior knowledge of a template structure. On the other hand, flexibility of the receptors provides the opportunity to improve the binding affinity of a ligand by suitable substitution that will maximize the binding by modulating the receptors surface. In this paper, we discuss with example how the protein's flexibility is correlated with its functions in various systems, revealing the importance of its understanding and for making applications. We also highlight the methodological challenges to investigate it computationally and to account for the flexible nature of the molecules in drug design.

--- ABSTRACT END ---

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[frequency of next (right) word to used to]

(1)28 assess	(20)5 design	(39)3 establish	(58)2 find
(2)28 identify	(21)5 increase	(40)3 observe	(59)2 fit
(3)23 evaluate	(22)5 inform	(41)3 prevent	(60)2 form
(4)20 study	(23)5 obtain	(42)3 solve	(61)2 further
(5)17 estimate	(24)5 quantify	(43)3 validate	(62)2 gain
(6)17 measure	(25)5 reconstruct	(44)2 accurately	(63)2 help
(7)16 determine	(26)4 calculate	(45)2 address	(64)2 improve
(8)16 examine	(27)4 characterize	(46)2 amplify	(65)2 make
(9)12 explore	(28)4 confirm	(47)2 avoid	(66)2 match
(10)10 treat	(29)4 construct	(48)2 be	(67)2 optimize
(11)9 analyze	(30)4 illustrate	(49)2 conduct	(68)2 perform
(12)8 develop	(31)4 reduce	(50)2 create	(69)2 prepare
(13)8 investigate	(32)4 screen	(51)2 demonstrate	(70)2 produce
(14)8 predict	(33)4 simulate	(52)2 derive	(71)2 promote
(15)7 collect	(34)4 verify	(53)2 describe	(72)2 recruit
(16)7 compare	(35)3 classify	(54)2 distinguish	(73)2 represent
(17)7 test	(36)3 compute	(55)2 explain	(74)2 select
(18)6 analyse	(37)3 control	(56)2 extrapolate
(19)6 detect	(38)3 define	(57)2 facilitate

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--- WordNet output for used --- =>1.〜に慣れて, 2.用いられた, 中古の Overview of verb use The verb use has 6 senses (first 3 from tagged texts) 1. (603) use, utilize, utilise, apply, employ -- (put into service; make work or employ for a particular purpose or for its inherent or natural purpose; "use your head!"; "we only use Spanish at home"; "I can't use this tool"; "Apply a magnetic field here"; "This thinking was applied to many projects"; "How do you utilize this tool?"; "I apply this rule to get good results"; "use the plastic bags to store the food"; "He doesn't know how to use a computer") 2. (12) use, habituate -- (take or consume (regularly or habitually); "She uses drugs rarely") 3. (8) use, expend -- (use up, consume fully; "The legislature expended its time on school questions") 4. use -- (seek or achieve an end by using to one's advantage; "She uses her influential friends to get jobs"; "The president's wife used her good connections") 5. practice, apply, use -- (avail oneself to; "apply a principle"; "practice a religion"; "use care when going down the stairs"; "use your common sense"; "practice non-violent resistance") 6. use -- (habitually do something (use only in the past tense); "She used to call her mother every week but now she calls only occasionally"; "I used to get sick when I ate in that dining hall"; "They used to vacation in the Bahamas") Overview of adj used The adj used has 3 senses (first 3 from tagged texts) 1. (4) used -- (employed in accomplishing something; "the principle of surprise is the most used and misused of all the principles of war"- H.H.Arnold & I.C.Eaker) 2. (1) exploited, ill-used, put-upon, used, victimized, victimised -- (of persons; taken advantage of; "after going out of his way to help his friend get the job he felt not appreciated but used") 3. (1) secondhand, used -- (previously used or owned by another; "bought a secondhand (or used) car") --- WordNet end ---