Research Data supporting "Thermodynamic signatures for hexapeptides with propensity for phase separation and amyloid formation"
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Description
These databases are analysed in the PhD thesis of the author and a subset of these databases are also analysed in various papers (DOI links included below).
These discrete path sampling databases are created using GMIN, OPTIM, and PATHSAMPLE interfaced with AMBER and LAMMPS software packages. The Mpipi potential implemented in LAMMPS software has been used to explore energy landscapes of some oligomers.
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Software / Usage instructions
GMIN, OPTIM, and PATHSAMPLE are open access softwares. The source code for these are available from their respective websites.
GMIN (https://www-wales.ch.cam.ac.uk/GMIN/)
OPTIM (https://www-wales.ch.cam.ac.uk/OPTIM/)
PATHSAMPLE (https://www-wales.ch.cam.ac.uk/PATHSAMPLE/)
The steps to create and analyse the database are explained in detail on the personal github page of the author. The links to these repositories are mentioned here.
https://github.com/nicy-nicy/peptide-energy-landscape-exploration
https://github.com/nicy-nicy/energy-landscape-cv-analysis
https://github.com/nicy-nicy/LAMMPS_Mpipi_energy_landscape
Similar datasets are also provided in the following links.
https://doi.org/10.17863/CAM.96759 and https://doi.org/10.17863/CAM.96972.
Keywords
discrete path sampling, hexapeptides, LAMMPS-GMIN/OPTIM, potential energy landscapes
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Sponsorship
This work was supported by Engineering and Physical Sciences Research Council (EPSRC) (D.J.W, grant number EP/N035003/1); the Cambridge Commonwealth, European and International Trust; the Allen, Meek and Read Fund; the Santander fund, St Edmund’s College, University of Cambridge; and the Trinity-Henry Barlow Honorary Award (Nicy).