Abstract
BackgroundThe ability to generate, visualize, and analyze motions of biomolecules has made a significant impact upon modern biology. Molecular Dynamics has gained substantial use, but remains computationally demanding and difficult to setup for many biologists. Elastic network models (ENMs) are an alternative and have been shown to generate the dominant equilibrium motions of biomolecules quickly and efficiently. These dominant motions have been shown to be functionally relevant and also to indicate the likely direction of conformational changes. Most structures have a small number of dominant motions. Comparing computed motions to the structure's conformational ensemble derived from a collection of static structures or frames from an MD trajectory is an important way to understand functional motions as well as evaluate the models. Modes of motion computed from ENMs can be visualized to gain functional and mechanistic understanding and to compute useful quantities such as average positional fluctuations, internal distance changes, collectiveness of motions, and directional correlations within the structure.ResultsOur new software, MAVEN, aims to bring ENMs and their analysis to a broader audience by integrating methods for their generation and analysis into a user friendly environment that automates many of the steps. Models can be constructed from raw PDB files or density maps, using all available atomic coordinates or by employing various coarse-graining procedures. Visualization can be performed either with our software or exported to molecular viewers. Mixed resolution models allow one to study atomic effects on the system while retaining much of the computational speed of the coarse-grained ENMs. Analysis options are available to further aid the user in understanding the computed motions and their importance for its function.ConclusionMAVEN has been developed to simplify ENM generation, allow for diverse models to be used, and facilitate useful analyses, all on the same platform. This represents an integrated approach that incorporates all four levels of the modeling process - generation, evaluation, analysis, visualization - and also brings to bear multiple ENM types. The intension is to provide a versatile modular suite of programs to a broader audience. MAVEN is available for download at http://maven.sourceforge.net.
Highlights
The ability to generate, visualize, and analyze motions of biomolecules has made a significant impact upon modern biology
The first publication widely recognized as a Molecular Dynamics (MD) simulation came two years later [2] and presented a simulation of the 56 residue bovine pancreatic trypsin inhibitor
Methods have been developed to determine the dominant motions within the trajectory - Principal Component Analysis (PCA) based on average covariances across the trajectory or Essential Dynamics [9]
Summary
The ability to generate, visualize, and analyze motions of biomolecules has made a significant impact upon modern biology. Elastic network models (ENMs) are an alternative and have been shown to generate the dominant equilibrium motions of biomolecules quickly and efficiently. These dominant motions have been shown to be functionally relevant and to indicate the likely direction of conformational changes. While true to the underlying atomic theories, this level of randomness may be distracting when analyzing motions of biomolecules on the longer time scale To overcome such randomness, methods have been developed to determine the dominant motions within the trajectory - Principal Component Analysis (PCA) based on average covariances across the trajectory or Essential Dynamics [9]. The rigor of molecular dynamics simulations makes them ideal for investigating specific events, but less applicable for extracting mechanisms, and overly detailed for general purposes
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