| Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over popular bioinformatics tools. The latest documentation of our biobb collections can be found in our readthedocs sites:
biobb_io: Biobb collection to fetch data to be consumed by the rest of the Biobbs. biobb_model: Biobb collection to check and model 3d protein structures. biobb_md : Biobb collection to perform molecular dynamics simulations. |
hg clone https://toolshed.g2.bx.psu.edu/repos/spanish_national_institue_of_bioinformatics/biobb
| Name | Description | Version | Minimum Galaxy Version |
|---|---|---|---|
| : get PDB from rcsb.org | 0.1.3 | 16.01 | |
| : get list of mutants from mmb.irbbarcelona.org | 0.1.3 | 16.01 | |
| : creates a Gromacs file adding the information of the solvent box to the input | 0.1.5 | 16.01 | |
| :Gromacs preprocessor. Reads topology file to create TPR atomic description | 0.1.5 | 16.01 | |
| : mutate one aminoacid by another | 0.1.5 | 16.01 | |
| : creates a new zip Gromacs topology applying the indicated force restrains | 0.1.5 | 16.01 | |
| : performs molecular dynamics simulations from an input Gromacs TPR file. | 0.1.5 | 16.01 | |
| : creates a ZIP Gromacs topology from a given PDB file. | 0.1.5 | 16.01 | |
| : adding ions to Gromacs topology | 0.1.5 | 16.01 | |
| : creates a Gromacs topology file adding solvent molecules to a given input. | 0.1.5 | 16.01 | |
| : reconstructs the missing side chains and heavy atoms. | 0.1.5 | 16.01 | |
| : get zip from mmb.irbbarcelona.org | 0.1.3 | 16.01 | |
| : creates a Gromacs index file (NDX). | 0.1.5 | 16.01 | |
| : creates a Gromacs topology applying the force restrains | 0.1.5 | 16.01 | |
| : performs a RMSD analysis. | 0.1.3 | 16.01 | |
| : creates cluster structures from a given input trajectory. | 0.1.3 | 16.01 | |