All Published Workflows
12 workflows that have been reviewed and published
peptide matcher dataset workflow
This repository contains the workflow used to generate fasta datasets compatible with Peptide matcher or potentially othe...
Quantitative shotgun MS proteomics
Quantitative shotgun MS proteomics as done in Lehtio lab
The pipeline is built using Nextflow , a workflow...
Protein 3D structure prediction pipeline
nf-core/proteinfold is a bioinformatics best-practice analysis pipeline for Protein 3D structure prediction pipeline. The ...
Identify and quantify MHC eluted peptides from mass spectrometry raw data
nfcore/mhcquant is a bioinformatics analysis pipeline used for quantitative processing of data dependent (DDA) peptidomics...
Integrated Metabolome Annotation Workflow (MAW): LC-MS2 Data Processing
This repository hosts Metabolome Annotation Workflow (MAW). The workflow takes MS2 .mzML format data files as an input in R. ...
Generation of protein conformational ensembles
This tutorial aims to illustrate the process of generating protein conformational ensembles from** 3D structures **and an...
Protein Conformational Ensemble Generation and Analysis Workflow using ELIXIR 3D-Bioinfo and PDBe-KB
Protein Conformational ensembles generation This tutorial aims to illustrate the process of generating protein conformation...
Jupyter Notebook Protein conformational ensembles generation
Protein Conformational ensembles generation This tutorial aims to illustrate the process of generating protein conformation...
JSON
PDB
Clustering
biobb_structure_utils
biobb_analysis
biobb_flexdyn
biobb_flexserv
biobb_gromacs
biobb_io
concoord
nolb
Gromacs
IMOD
NGLview
NMA
Pandas
ProDy
CPPTRAJ
biobb-analysis
biobb-flexdyn
biobb-flexserv
biobb-gromacs
biobb-io
biobb-structure-utils
ipython
ipywidgets
numpy
plotly
simpletraj
Protein structure analysis
EJP-RD WP13 case-study: CAKUT proteome, peptidome and miRNome data analysis using WikiPathways
In this analysis, we created an extended pathway, using the WikiPathways repository (Version 20210110) and the three -omics...
AMBER Protein MD Setup tutorials using BioExcel Building Blocks (biobb)
Based on the official GROMACS tutorial .
This tutorial aims to illustrate the process of setting up a simulation system c...
Protein MD Setup tutorial using BioExcel Building Blocks (biobb) in Galaxy
Galaxy workflow example that illustrate the process of setting up a simulation system containing a protein, step by step, usi...
Cheminformatics - XChem combined virtual screening of the SARS-CoV-2
This workflow is used for the virtual screening of the SARS-CoV-2 main protease (de.NBI-cloud, STFC). It includes Charge enum...