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Parallel Programming for Bioinformatics

CUDA

Software Project:Protein-protein docking by simulated annealing

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A CUDA software project

Write a CUDA program to perform simulated annealingcalculations on a CUDA enabled graphics adapter

Parts of the program

read in pdb-structures of two proteins (C++)

perform simulated annealing on CUDA card

randomly change rotation vector

randomly change translation vector

evaluate new energy

accept new position based on Metropolis criterion

output of docked structures (C++)

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Simulated annealing part

Start with a given temprature t

Perform n steps at same temperature level

For each step

change randomly in small steps

translation

orientation

of smaller protein

evaluate energy between both molecules

if better than best known, store orientation and energy as new best

accept as new position according to Metropolis criterion

Decrease temperature by factorf= 0.9 Stop algorithm if no improvement of best overall energy for last

x steps

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Changing translation and rotation

Use Gaussian distributed numbers

Create one number for each degree of freedom

x, y, z, s, vx, vy, vz

Add random number to each variable independently

normalize new quaternion vector

Apply transformation to original coordinates

rotation

translation

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Orientation of moving molecule

Orientation

described by quaternion q = [s, vx, vy, vz]=[s, v]

Quaternion

represents rotation ofs radians about axis [vx, vy, vz]

Creating quaternion

create random number for each entry in q

normalize quaternion such that |q| = 1

Changing quaternions

q = q0 x q1 = [s0s1v0 * v1, s0v1 + s1v0 + v0 x v1]

Calculating rotation matrix R

+

+

+

=

22

22

22

2212222

2222122

2222221

yxxzyyzx

xzyzxzyx

yzxzyxzy

vvsvvvsvvv

svvvvvsvvv

svvvsvvvvv

R

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Interaction energy

The total energy of a conformation is given by the sum over allEij with ibeing atoms of moving protein andjbeing atoms ofreceptor protein

( )

+

+=13375.3

90836.1exp26067.11

51471.0

83634.2exp1

355472303382.0

2x

x

.Eij

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Random number generator

unsi gned z1, z2, z3, z4;f l oat Hybr i dTaus( ){

r et ur n 2. 3283064365387e- 10 * (TausSt ep( z1, 13, 19, 12, 4294967294UL) ^TausSt ep( z2, 2, 25, 4, 4294967288UL) ^TausSt ep( z3, 3, 11, 17, 4294967280UL) ^LCGSt ep( z4, 1664525, 1013904223UL)

) ;}

unsi gned TausSt ep( unsi gned &z, i nt S1, i nt S2, i nt S3,unsi gned M)

{unsi gned b = ( ( z

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First steps in software project

Write a simple(!) CUDA program to perform simulatedannealing in global memory

Parse two pdb structures and store positions in two arrays off l oat 3

Perform annealing on CPU

Use the GSL for random number creation on the CPU

Write a CUDA kernel for

changing atom positions

evaluating energy