Probability-based model of protein-protein interactions on biological timescales 英文参考文献.docVIP

Algorithms for Molecular Biology BioMedCentral Research Open Access Probability-based model of protein-protein interactions on biological timescales Alexander L Tournier*, Paul W Fitzjohn and Paul A Bates* Address: Biomolecular Modelling Laboratory, Cancer Research UK London Research Institute, 44 Lincolns Inn Fields, London WC2A 3PX, UK Email: Alexander L Tournier* - Alexander.tournier@.uk; Paul W Fitzjohn - paul.fitzjohn@.uk; Paul A Bates* - paul.bates@.uk * Corresponding authors Published: 11 December 2006 Received: 25 September 2006 Accepted: 11 December 2006 Algorithms for Molecular Biology 2006, 1:25 doi:10.1186/1748-7188-1-25 This article is available from: /content/1/1/25 ? 2006 Tournier et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Abstract Background: Simulation methods can assist in describing and understanding complex networks of interacting proteins, providing fresh insights into the function and regulation of biological systems. Recent studies have investigated such processes by explicitly modelling the diffusion and interactions of individual molecules. In these approaches, two entities are considered to have interacted if they come within a set cutoff distance of each other. Results: In this study, a new model of bimolecular interactions is presented that uses a simple, probability-based description of the reaction process. This description is well-suited to simulations on timescales relevant to biological systems (from seconds to hours), and provides an alternative to the previous description given by Smoluchowski. In the present approach (TFB) the diffusion process is explicitly taken into account in generating the probability that two freely