DomainFinder An interactive program for the determination and characterization of dynamical domains in proteins
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analyze protein protein analysis protein characterization protein determination determination

DomainFinder Description

An interactive program for the determination and characterization of dynamical domains in proteins DomainFinder is an interactive program to analyze collective motions in large proteins, either by comparing two experimental structure, or by applying an efficient normal mode technique to a single structure. Proteins up to a few thousand residues can be treated on a desktop computer in a few minutes.Dynamical domains are an important concept in the description of protein dynamics. A dynamical domain is a region in a protein which can move essentially like a rigid body relative to other regions. Many, but not all, proteins have dynamical domains, and if they do, the relative movements of the domains are usually related to the function of the protein. The identification of dynamical domains is therefore useful in understanding the function of the protein. However, there are other situations in which the knowledge of dynamical domains is helpful. In structure determination, DomainFinder can help one to easily predict whether complexation with a crystal packing, ligand, or other external influences can lead to important conformational changes.In protein engineering, it can indicate whether a given modification is likely to change the dynamical behavior of the protein. In experimental observations of protein motion, it can suggest regions of particular interest. In numerical simulations, it can point out the slow motions whose correct sampling must be verified.DomainFinder is written in Python, a high-level object programming language that is particularly well suited to the demands of scientific computations. The speed-critical parts are implemented in C. For common operations it makes use of the Molecular Modeling Toolkit, a library of Python code for molecular modelling and simulation applications. The results of a domain analysis can be saved with all details in an MMTK data file, which permits all kinds of further analysis. Here are some key features of "DomainFinder": · computational efficiency: even large proteins can be analyzed using a desktop computer in a few minutes · ease of use: a state-of-the-art graphical user interface · export of results for visualization and further analysis (VRML, PDB, and MMTK object format)

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