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Flashcards in ch3717 Deck (48)
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1
Q

force field

A

functional form and parameters set to describe the potential energy of a molecular system

2
Q

Ep of system

A

energy of a system is considered to have due to the positions of its components in space

3
Q

simple force field

A
bond stretching
angle bending
torsion
electrostatic
van der Waals
4
Q

bonded terms

A

bond stretching
angle bending
torsions

5
Q

non-bonded terms

A

electrostatic interactions

van der Waals

6
Q

electrostatic interactions

A

non-uniform charge distribution in a molecule, represented by fractional point charges

7
Q

van der waals

A

attraction due to dispersion
repulsion due to exchange replusion
Lennard-jones potential

8
Q

Lennard-jones potential

A

sigma - where passes through 0 on x
e - well depth
equilibrium distance when = minimum

9
Q

deficiencies in point charge model

A

lack of polarisability as charges not affected by the local electrostatic environment

10
Q

polarizability

A

modification in the charge distribution in an atom due to an applied electric field

11
Q

water models

A

set parameters used fro models water or aqueous soltions

12
Q

water molecules rigid

A

fixed bond length, angle and torsion

only account for non-bonded interactions

13
Q

3-site. model

A

charges on atom

14
Q

4-site model

A

charges on atom and one charge away from o

15
Q

5-site model

A

2 lone pairs with. charge

16
Q

6-site model

A

2 lon e pairs and charge away from o

17
Q

more accurate models of water

A

intramolecular flexibly

including polarizability

18
Q

potential energy surface

A

energy of the molecular system as a function of the nuclear coordinates

19
Q

potential energy surface

A

maxima - eclipsed
minima - staggered
transition state

20
Q

energy minimisatuon

A

minimum energy ofd a paerticujkar molecule

calculate energy at particular bond length, change bond length and measure new energy

21
Q

molecular dynamics

A

form of computer simulation where the atoms and molecules are allowed tov interact with eachothetr for a period of time

22
Q

phase space

A

define the state of a molecular system containing N atoms, 6N values are required 3 coordinates x,y,z and 3 momentum components px,py,pz per atom

23
Q

calculate tranjectory

A

have energy function
differentiate -dv/dx = force
newtons 2nd law to give a = f / m
integration of equations of motion give v and x
gives trajectory describing how x,v,a of particle vary with time

24
Q

particles experience a constant force

A

charged partible through uniform electric field

force on particle is not constant

25
Q

running an md simulation

A
establish initial configuration of system
assign initial velocities
calculated the force on each atom
and new positions of atoms
equilibrium phase
production phase
26
Q

md used to

A

stimulate a reaction

calculate thermodynamic properties

27
Q

ensemble

A

collection of points in phase space, a collection of the mictrostates in the trajectory

28
Q

calculate thermodynamic properties

A

statistical mechanics

macroscopic property calculated as an average over a corresponding microscopic property

29
Q

microanonical ensemble

A

thermally isolated system - constant E, N, volume

30
Q

canonical ensemble

A

system exchanges energy with heat bath. temp constant, n and volume

31
Q

lead compound

A

molecule with pharmacological or biological activity can be used as a starting point for chemical. modicifaqtion to enhance its potency and selectivity

32
Q

agonist

A

enhance or normal activity as natural substrate

33
Q

antagonist

A

inhibits the effect of natural ligand

34
Q

inverse agonist

A

creates opposite of natural ligand

35
Q

drug activity

A

molecular binding of one molecule to the pocket (binding site) of anothwe

36
Q

docking

A

predict structure and stability of complex, formed by 2 interacting molecules ligand and protein

37
Q

search alogorithm

A

generation of plausible strujcutres

38
Q

scoring function

A

how strong it binds

calculate likelihood that the pose represents a favourable binding interaqction

39
Q

a good scoring function is

A

selective - distinguish between correct t and incorrect structures
efficient - fast

40
Q

search algorithms

A

protein and ligand rigid bodies (6 degrees of freedom)
ligand flexible
both flexible

41
Q

QSAR

A

quantitive structural activity analysis

method that relates numerical properties of a drug molecule to its biological acitivty

42
Q

receptor flexability

A

bond lengths/angles do not affect there shape of molecule much - torsions

43
Q

qsar

A

v = f (p)

44
Q

pharmacophores

A

set of structural featured that is common to a series of active molecules, recognised by receptors and are responsible for drug activity

45
Q

pharmacophores - structural featrurws

A

h bond donors and acceptors, charged groups, aromaticity, hydrophobic groups

46
Q

3d pharmacophore

A

includes spatial relationship between pharmacophoric groups. relationships expressed as distances, torsio ns and angles

47
Q

pharmacophoric mapping

A

can determine 3d pharmacophoerws for a series of comppununs

assumes all active compounds bind in similar way

48
Q

de novo ligand design

A

design of new molecules