Pirooz Vakili

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Our approach to protein-protein docking includes three main steps. First, we run PIPER, a rigid body docking program based on the Fast Fourier Transform (FFT) correlation approach, extended to use pairwise interactions potentials. Second, the 1000 best energy conformations are clustered, and the 30 largest clusters are retained for refinement. Third, the(More)
In this paper we propose a new approach to parallel and distributed simulation of discrete event systems. Most parallel and distributed discrete event simulation algorithms are concerned with the simulation of one “large” discrete event system. In this case the computational intensity is due to the size and complexity of the simulated system. In(More)
In planning and managing production systems, manufacturers have two main strategies for responding to uncertainty: they build inventory to hedge against periods in which the production capacity is not suÆcient to satisfy demand, or they temporarily increase the production capacity by \purchasing" extra capacity. We consider the problem of minimizing the(More)
Virtually all docking methods include some local continuous minimization of an energy/scoring function in order to remove steric clashes and obtain more reliable energy values. In this paper, we describe an efficient rigid-body optimization algorithm that, compared to the most widely used algorithms, converges approximately an order of magnitude faster to(More)
Similarly to protein folding, the association of two proteins is driven by a free energy funnel, determined by favorable interactions in some neighborhood of the native state. We describe a docking method based on stochastic global minimization of funnel-shaped energy functions in the space of rigid body motions (SE(3)) while accounting for flexibility of(More)
An outstanding challenge has been to understand the mechanism whereby proteins associate. We report here the results of exhaustively sampling the conformational space in protein-protein association using a physics-based energy function. The agreement between experimental intermolecular paramagnetic relaxation enhancement (PRE) data and the PRE profiles(More)
This paper introduces a new stochastic global optimization method targeting protein-protein docking problems, an important class of problems in computational structural biology. The method is based on finding general convex quadratic underestimators to the binding energy function that is funnel-like. Finding the optimum underestimator requires solving a(More)
The paper introduces a new global optimization method that is targeted to solve molecular docking problems, an important class of problems in computational biology. The search method is based on finding general convex quadratic underestimators to the binding energy function that is funnellike. Finding the optimum underestimator requires solving a(More)