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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)
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)
The technique of control variates requires that the user identify a set of variates that are correlated with the estimation variable and whose means are known to the user. We relax the known mean requirement and instead assume the means are to be estimated. We argue that this strategy can be beneficial in parametric studies, analyze the properties of(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)
We discuss the simulation of M replications of a uniformizable Markov chain simultaneously and in parallel (the so-called parallel replicated approach). Distributed implementation on a number of processors and parallel SIMD implementation on massively parallel computers are described. We investigate various ways of inducing correlation across replications(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)
We discuss a way of simulating M replications of a uniformizable Markov chain simultaneously and in parallel (the so-called parallel replication approach), Simulation is performed to estimate the expectation of some cumulative reward over a finite deterministic time horizon. Distributed implementation on a number of processors and parallel SIMD(More)