A Process Calculus for Molecular Interaction Maps
نویسندگان
چکیده
We present the MIM calculus, a modeling formalism with a strong biological basis, which provides biologically-meaningful operators for representing the interaction capabilities of molecular species. The operators of the calculus are inspired by the reaction symbols used in Molecular Interaction Maps (MIMs), a diagrammatic notation used by biologists. Models of the calculus can be easily derived from MIM diagrams, for which an unambiguous and executable interpretation is thus obtained. We give a formal definition of the syntax and semantics of the MIM calculus, and we study properties of the formalism. A case study is also presented to show the use of the calculus for modeling biomolecular networks.
منابع مشابه
A Calculus for Molecular Interaction Maps
Molecular Interaction Maps are a graphical formalism used by biologists to describe complex interactions between molecules. We provide a formal description of MIMs using process algebras and determine its computational power.
متن کاملThe Effects of Different SDE Calculus on Dynamics of Nano-Aerosols Motion in Two Phase Flow Systems
Langevin equation for a nano-particle suspended in a laminar fluid flow was analytically studied. The Brownian motion generated from molecular bombardment was taken as a Wiener stochastic process and approximated by a Gaussian white noise. Euler-Maruyama method was used to solve the Langevin equation numerically. The accuracy of Brownian simulation was checked by performing a series of simulati...
متن کاملStudy of Human Albumin Protein Interaction with Fluorouracil Anticancer Drug Using Molecular Docking Method
Introduction: Drugs are mainly delivered to the target tissues by plasma proteins, such as human serum albumin, in the human body. Practical information about the thermodynamic parameters of drugs and their stability can be obtained using simulation methods, such as molecular docking. Material & Methods: This study, investigated the molecular docking of human serum albumin with fluorouracil an...
متن کاملMolecular Detection of Enterococcal Surface Protein (esp) Gene in Enterococcus faecalis Isolated from Dental Calculus of Patients in Sari, Iran
Background: Enterococci are important gram-positive bacteria causing dental calculus in human beings; however, the role of these bacteria in oral cavity is unclear. The aim of this study was to investigate the presence of Enterococcal Surface Protein (esp) gene in Enterococcus faecalis isolated from dental calculus in the city of Sari, Iran. Materials and Methods: In the present study, 207 den...
متن کاملInteraction of Human Serum Albumin with Ethyl 2-[2-(dimethylamino)-4-(4-nitrophenyl)-1,3-thiazole-5-yl]-2-oxoacetate as a Synthesized Ligand
The interaction of human serum albumin with Ethyl 2-[2-(dimethylamino)-4-(4-nitrophenyl)- 1,3-thiazole-5-yl]-2-oxoacetate was investigated by using isothermal titration UV-visible spectrophotometry in tris-buffer, pH 7.4. According to these results, it was found that there are a set of 4 binding sites for this ligand on HSA with positive cooperativity in the binding process. This thiazole deriv...
متن کامل