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ask.bioexcel.eu is a forum to support the community for computational biomolecular research in academia and industry, with particular focus on biomolecular simulation and modelling and using high-performance computing (HPC) and high-throughput computing (HTC).

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Packages

Below you can find the list of all the packages and a link to their corresponding contact section in GitHub:

biobb_amber

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biobb_analysis

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biobb_chemistry

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biobb_cmip

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biobb_common

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biobb_cp2k

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biobb_dna

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biobb_flexdyn

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biobb_flexserv

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biobb_godmd

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biobb_gromacs

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biobb_haddock

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biobb_io

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biobb_md

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biobb_mem

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biobb_ml

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biobb_model

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biobb_pdb_tools

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biobb_pmx

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biobb_pytorch

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biobb_structure_utils

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biobb_vs

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Workflows

Below you can find the list of all the workflows and a link to their corresponding contact section in GitHub:

GROMACS Protein MD Setup

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Automatic Ligand parameterization

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GROMACS Protein-Ligand Complex MD Setup

Open new issue for GROMACS Protein-Ligand Complex MD Setup workflow
Mutation Free Energy Calculations

Open new issue for Mutation Free Energy Calculations workflow
Protein-ligand Docking (Cluster90)

Open new issue for Protein-ligand Docking (Cluster90) workflow
Protein-ligand Docking (PDBe REST-API)

Open new issue for Protein-ligand Docking (PDBe REST-API) workflow
Protein-ligand Docking (fpocket)

Open new issue for Protein-ligand Docking (fpocket) workflow
Molecular Interaction Potentials

Open new issue for Molecular Interaction Potentials workflow
Protein conformational ensembles generation

Open new issue for Protein conformational ensembles generation workflow
Macromolecular Coarse-Grained Flexibility

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Protein conformational transitions calculations

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AMBER Protein MD Setup

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AMBER Protein-ligand complex MD Setup

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AMBER Constant pH MD setup

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ABC MD Setup

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Structural DNA helical parameters

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Molecular Structure Checking

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{···} REST API

Click the button below and open a new BioBB REST API issue:

Open new issue in BioBB REST API GitHub

BioBB Workflows

Click the button below and open a new BioBB Workflows website issue:

Open new issue in the BioBB Workflows website

Generic contact

Only in case your request is not related to some of the previous subjects, click the button below to open a generic issue:

Open new issue in BioBB GitHub