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How to Use NucleicNet with Webserver
The NucleicNet is a software that analyse on protein atomic model to predict binding preference of RNA constituents (Phosphate, Ribose and 4 bases AUCG) on any location of the given protein surface.
Three major utilities are provided on this webserver:
- Analyse custom protein surface
- Users can upload protein structure written in PDB file format to our "Protein Surface Analysis" tab and follow instructions therein. This utility corresponds with Fig. 3 of our manuscript.
- Example of file upload can be found on https://github.com/NucleicNet/NucleicNet/tree/master/GridData.
- Generating Sequence Logo
- Users can upload additional RNA-protein complex structure to our "Logo" tab to generate sequence logos. This utility corresponds with Fig. 3-4 of our manuscript.
- Example of the first file upload can be found on https://github.com/NucleicNet/NucleicNet/tree/master/GridData.
- Example of the second file upload can be found on https://github.com/NucleicNet/NucleicNet/tree/master/Control.
- Scoring miRNA loading preference
- Users can input comma-separated miRNA sequence on our "hAgo2-miRNA Scoring" tab and follow instructions therein. This utility corresponds with Fig. 5 of our manuscript.
Source code of our server is provided on our Github page https://github.com/NucleicNet/NucleicNet/ For more information on software dependencies, instructions on installation and usage, please refer to our Wiki page https://github.com/NucleicNet/NucleicNet/wiki
Further specification on the input PDB file can be found on https://github.com/NucleicNet/NucleicNet/wiki/Specification-on-PDB-input-files.
This page is copied from https://github.com/NucleicNet/NucleicNet/wiki/How-to-Use-NucleicNet-with-Webserver