Abstract
Despite recent advances in molecular simulation technologies, analysis of high-molecular-weight structures is still challenging. Here, we propose an automated model reduction procedure aiming to enable modular analysis of these structures. It employs a component mode synthesis for the reduction of finite element protein models. Reduced models may consist of real biological subunits or artificial partitions whose dynamics is described using the degrees of freedom at the substructural interfaces and a small set of dominant vibrational modes only. Notably, the proper number of dominant modes is automatically determined using a novel estimator for eigenvalue errors without calculating the reference eigensolutions of the full model. The performance of the proposed approach is thoroughly investigated by analyzing 50 representative structures including a crystal structure of GroEL and an electron density map of a ribosome.
Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
