all atom molecular dynamics flexible fitting mdff  (Molecular Dynamics Inc)

Journal: The international journal of high performance computing applications

Article Title: Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action

doi: 10.1177/10943420221113513

Figure Lengend Snippet: The atomistic representation of a functional RTC monomer (A) with the RNA (red), extended to the active site of the other nsp14–10 unit of the opposite monomer (nsp14B - orange), and the exit site on the helicase of the same monomer (nsp13–2A). The mechanism of RNA unwinding using non-equilibrium molecular dynamics simulations starting from the initial structure as captured in 7EGQ (B-left), to the final structure (B-right). The RNA backbone is restrained with an mdff grid, represented in a grey mesh, while using colvars to pull the strands to the active sites on the protein. This is an unprecedented simulation of the mechanism of RNA unwinding which can give significant insight into the RTC function.

Article Snippet: To speed up these empirical studies, instead of the all-atom representation, the protein was represented by a molecular dynamics flexible fitting mdff grid map exerting a repulsive gridForce ( Trabuco et al., 2009 ).

Techniques: Functional Assay

Journal: The international journal of high performance computing applications

Article Title: Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action

doi: 10.1177/10943420221113513

Figure Lengend Snippet: Summary of AAMD simulations.

Article Snippet: To speed up these empirical studies, instead of the all-atom representation, the protein was represented by a molecular dynamics flexible fitting mdff grid map exerting a repulsive gridForce ( Trabuco et al., 2009 ).

Techniques: Sampling