Workflows

Created At
Go
31 Workflows visible to you, out of a total of 69
Work-in-progress

This tutorial aims to illustrate the process of setting up a simulation system containing a protein in complex with a ligand, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the T4 lysozyme L99A/M102Q protein (PDB code 3HTB), in complex with the 2-propylphenol small molecule (3-letter Code JZ4).

Workflow engine is a jupyter notebook. It can be run in binder, following the link given, or locally. Auxiliar libraries used are: nb_conda_kernels, ...

Type: Unrecognized workflow type

Creator: Genís Bayarri

Submitter: Douglas Lowe

Work-in-progress

This tutorial aims to illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Lysozyme protein (PDB code 1AKI).

Workflow engine is a jupyter notebook. It can be run in binder, following the link given, or locally. Auxiliar libraries used are: nb_conda_kernels, nglview, ipywidgets, plotly, and simpletraj. Environment can be setup using the included environment.yml file.

Type: Unrecognized workflow type

Creator: Genís Bayarri

Submitter: Douglas Lowe

Work-in-progress

This tutorial aims to illustrate the process of ligand parameterization for a small molecule, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Ibuprofen small compound (3-letter code IBP, Drugbank code DB01050), a non-steroidal anti-inflammatory drug (NSAID) derived from propionic acid and it is considered the first of the propionics.

OpenBabel and ACPype packages are used to add hydrogens, energetically minimize the structure, and generate ...

Type: Unrecognized workflow type

Creator: Genís Bayarri

Submitter: Douglas Lowe

Work-in-progress

This tutorial aims to illustrate how to compute a fast-growth mutation free energy calculation, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Staphylococcal nuclease protein (PDB code 1STN), a small, minimal protein, appropriate for a short tutorial.

Workflow engine is a jupyter notebook. Auxiliary libraries used are nb_conda_kernels, os, and plotly. Environment setup can be carried out using the environment.yml in the code repository. The ...

Type: Unrecognized workflow type

Creator: Genís Bayarri

Submitter: Douglas Lowe

a workflow added through the api

Type: Unrecognized workflow type

Creators: None

Submitter: Stuart Owen

Work-in-progress

Common Workflow Language example that illustrate the process of setting up a simulation system containing a protein, step by step, using the BioExcel Building Blocks library (biobb). The particular example used is the Lysozyme protein (PDB code 1AKI).

Type: Common Workflow Language

Creators: None

Submitter: Robin Long

Stable

VIRify is a recently developed pipeline for the detection, annotation, and taxonomic classification of viral contigs in metagenomic and metatranscriptomic assemblies. The pipeline is part of the repertoire of analysis services offered by MGnify. VIRify’s taxonomic classification relies on the detection of taxon-specific profile hidden Markov models (HMMs), built upon a set of 22,014 orthologous protein domains and referred to as ViPhOGs.

Type: Nextflow

Creator: Martín Beracochea

Submitter: Laura Rodriguez-Navas

Powered by
(v.1.12.2)
Copyright © 2008 - 2022 The University of Manchester and HITS gGmbH