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Parallel constrained minimization for interactive protein modeling

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1 Author(s)
Surles, M.C. ; Supercomput. Center, Gen. Atomics, San Diego, CA, USA

A coarse-grain parallel algorithm for nonlinear constrained minimization allows interactive modeling of electrostatic interactions in proteins. The constrained minimization problem is the basis of a graphical protein modeling system called Sculpt. While a user interactively changes a protein structure or explores protein-drug interaction, Sculpt maintains protein properties such as bond lengths and non-bonded atom separation. Between screen updates, Sculpt finds a focal energy minimum that satisfies constraints specifying ideal bond lengths and angles. This paper shows a parallel algorithm that models electrostatic interactions in 3500-atom proteins at two updates per second on an eight-processor SGI Challenge, a 7.2-times improvement over the sequential algorithm. These results are demonstrated through applications of Sculpt in biochemistry and drug design.<>

Published in:

System Sciences, 1994. Proceedings of the Twenty-Seventh Hawaii International Conference on  (Volume:5 )

Date of Conference:

4-7 Jan. 1994