Vicky Choi Department of Computer Science Duke University
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Vicky ChoiDepartment of Computer Science Duke University
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Outline
Local Improvement Basic Idea Details of Each Step Current Results Work in Progress
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Protein Docking Problem (bound case)
.5))(,(&maximized))(,(
s.t.motionrigidafind
},1:),{(},1:),{( Given
BABumpisBAScore
misbBnjraA iijj
““local”
local”
(a,r) (b,s)
5.1Score:
(a,r) (b,s)
Bump:
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Local Improvement
A
B
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Basic Idea
:
Goal Tentative 1.Compute
)},s{(b B)} ,s{(cC iiii
minimized is )(
:),,(tchingWeightedMa .22
iiii cbw
CBw
.5))(',Bump(
s.t. ' :n ResolutioCollision.3
BA
?),())(',( Does BAScoreBAScore
A BA C B
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1.Compute Tentative Goal
}:),{(
,),(eachFor
DsbaAraA
Bsb
iiai
ii
0),(
]1,0[ ))(,(),(:)( 0
ii
iiiiii
cABump
ttbAScorecAScoretbc
[0,1] t)()( iiii bAtbtb
) if0(0
}{min),(
iii
iaiArai
Aww
srcawia
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2. Weighted Matching
minimized is )(
:),,(tchingWeightedMa 2
i
iii cbw
CBw
)()()( wwBBCBRB
w
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3. Collision Resolution
521
0
10
,,,
0.) )()(,(
then,minLet
bump.ut witho
anslationlargest tr thebelet
),(),( eachfor
0),()(consider
,0))(,( If
:0))(,( Suppose
TTT
BCTBRABump
tT
t
BRsb
tBCtBR
BRABump
BABump
B
imi
i
Bii
B
B
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3. Collision Resolution (Cont.)
40 ,4
),(: R
: vary and uFix
axis rotation thealong directedr unit vectoa is
rotation, theof magnitude theis where),(:
:0))(,( If
kku
u
uR
BRABump
kkk
B
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Example 1: 1BRS (patches)
Native Input Correspondence Rotation Rotation + Translation Collision Resolution[304, 2] [26, 0] [466, 0] [44, 0] [342, 35] [122, 5]
RMSD=3.29 RMSD=1.83
[44, 0] [491, 0] [25, 0] [319, 10] [248, 5]RMSD=3.21 RMSD=0.69
[Score, Bump]
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Example 2: 1BRSNative Input Correspondence Rotation Rotation + Translation Collision Resolution[309, 2] [10, 0] [313, 0] [22, 1] [171, 17] [29, 3]
RMSD=5.10 [17, 0] [151, 15] [35, 3][17, 0] [356, 0] [19, 0] [184, 25] [63, 5]
RMSD=5.01 RMSD=4.27
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Example 3: 1BRS (non-docking site)Input Correspondence Rotation Rotation + Translation Collision Resolution
[13, 0] [226, 0] [5, 0] [193, 64] [23, 4]
[5, 0] [272, 0] [1, 0] [230, 71] [64, 5]
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Example 4: 1CHONative Input Correspondence Rotation Rotation + Translation Collision Resolution[254, 1] [13, 0] [390, 0] [25, 1] [191, 20] [122, 5]
RMSD=4.44 [14,0] (1) [97, 3] [21, 0](t=0.214)[17, 0] [432, 0] [67, 4] [342, 38] [78,4]RMSD=3.21 [17, 0] (0) [117, 2] [231, 5]
RMSD=1.58
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Work in Progress
A. varying neighborhood distance “D”;B. choosing the weights;C. trying jittering motions: C1. alternating between rotation and translation in pieces; C2. using a damping factor and iterating;D. adding hydrogens into the models.
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Protein Docking Group @Duke
Pankaj K. AgarwalSergei BespamiatnykhVicky ChoiHerbert EdelsbrunnerAbhijit GuriaJohannes RudolphYusu Wang
VMD – Visual Molecular Dynamics: http://www.ks.uiuc.edu/Research/vmd