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Structure prediction and molecular dynamics data from Human cytomegalovirus deploys molecular mimicry to recruit VPS4A to sites of virus assembly


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Description

AlphaFold2-multimer model of human cytomegalovirus pUL71 vMIM2 in complex with human VPS4A MIT domain, and of homologous complexes from other betaherpesviruses, are deposited along with relevant quality statistics (prefix: AF). Models and molecular dynamics trajectories for the Umbrella sampling analysis of pUL71 vMIM2:VPS4A MIT domain complex, with wild-type and mutant pUL71 vMIM2, are also deposited (prefix: umbrella).

Version

Software / Usage instructions

All non-text files are XZ compressed tar file and can be extracted using the command "tar -xvJf tar_file_name.tar.xz" on a Unix system or with Windows subsystem for Linux. Within the AF tar.xz files: - .pdb files can be opened with structural visualisation programmes like ChimeraX [https://www.cgl.ucsf.edu/chimerax/]. - .fasta files can be opened with a text editor. - .csv files can be opened with a text editor or spreadsheet programme like Microsoft Excel. Within the umbrella tar.xz files: - .top files are the GROMACS topology files for each simulation [can be opened in a text editor] - .mpd files are the GROMACS shared parameter files [can be opened in a text editor] - .pdb are atomic coordinates for each trajectory [can be opened using ChimeraX] - .xtc are the trajectory files for the umbrella sampling [can be opened along with the corresponding atomic coordinates in a trajectory visualisation programme like VMD (https://www.ks.uiuc.edu/Research/vmd/alpha/) or ChimeraX]

Keywords

molecular dynamics, structure prediction, virology, human cytomegalovirus, protein structure

Publisher

Sponsorship
Wellcome Trust (098406/Z/12/Z)
Wellcome Trust (098406/Z/12/B)
A Titan V graphics card used for this research was donated by the NVIDIA Corporation. BGB was a Wellcome Trust PhD student.
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