https://github.com/jbarnoud/simulation_yellow_pages

Inventory of places that host or inventory molecular simulations.
https://github.com/jbarnoud/simulation_yellow_pages

Last synced: 16 days ago
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Inventory of places that host or inventory molecular simulations.

• Host: GitHub
• URL: https://github.com/jbarnoud/simulation_yellow_pages
• Owner: jbarnoud
• Created: 2018-11-27T01:08:36.000Z (about 6 years ago)
• Default Branch: master
• Last Pushed: 2018-11-27T01:11:06.000Z (about 6 years ago)
• Last Synced: 2024-12-24T04:41:58.647Z (18 days ago)
• Size: 1.95 KB
• Stars: 1
• Watchers: 3
• Forks: 0
• Open Issues: 1
• Metadata Files:
  • Readme: README.md

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README

        
Yellow pages of molecular simulation sources

============================================

This is an attenmpt to inventory places that makes molecular simulations available. This list started in the context of the workshop on ["Sharing Data from Molecular Simulations"](https://bioexcel.eu/events/workshop-on-sharing-data-from-molecular-simulations/).

You can contribute to this list by posting a pull request or an issue.

Collaborative hosting databases

-------------------------------

Databases that host simulations and accept external submissions.

### GPCRmd 

This database is at the prototype stage. It allows to search, vizualize and download molecular dynamic simulations of GPCRs. It provides search criteria and analyses specialized for the field.

Aggregation databases

---------------------

Databases that aggregate simulations hosted somewhere else.

### NMRLipids 

Database of simulations for the [NMRLipids project](http://nmrlipids.blogspot.fi). It aggregates and annotates simulations of lipid bilayers carried out with various force field and various conditions. The simulations are mostly hosted on Zenodo.

### MDAnalysisData 

Collection of links to dataset used to demonstrate, teach, or test MDAnalysis. The collection can be accessed *via* the website, or throught a python library.

Single-lab databases

--------------------

Databases that host simulations but do not accept external submissions.

### MemProtMD 

Collection of coarse grained molecular dynamics simulations of membrane proteins in a membrane environment carried out with an automatic pipeline. The database allows to search proteins, to vizualize snapshots of the simulations, to see and download the result of analyses relevant for membrane proteins, and to download starting files to carry out a simulation of the system.

### MoDEL 

Other places

------------

* [Datasets on Zenodo that includes a TPR](https://zenodo.org/search?page=1&size=20&q=filetype:tpr#)

* [Datasets on Zenodo that include a DCD file](https://zenodo.org/search?page=1&size=20&q=filetype:dcd)

* ["molecular dynamics" in Google Dataset Search]()