BioExcel Building Blocks Workflows list

BioExcel Building Blocks Workflows

In this page, users can find a list of all available BioExcel Building Blocks Workflows. A list of main steps and a direct launch button are provided for each workflow.

They can also be found in a GitHub repository in all their versions with all the instructions and sample files needed for executing them at home in the users' own premises.

ABC MD Setup pipeline

This workflow provides a pipeline to setup DNA structures following the recommended guidelines by the Ascona B-DNA Consortium (ABC) members. It follows the work started with the NAFlex tool to offer a single, reproducible pipeline for structure preparation, ensuring reproducibility and coherence between all the members of the consortium.

Workflow main steps

  1. Modeling Nucleic Acids 3D Structure
  2. Generating Topology
  3. Adding Water Box (with given input parameters. Default: 15Å, truncated octahedron box, opcbox water model (SPC/E + Joung-Chetham monovalent ions + Li/Merz highly charged ions)
  4. Neutralizing the system (with K+ ions) and Adding additional Ionic Concentration (with given input parameters. Default: 100 Mol/L)
  5. Randomizing Ions
  6. Generating Topology with Hydrogen Mass Partitioning (allowing 4fs timestep MD)
  7. Equilibrating the System (10-steps protocol Daniel R. Roe and Bernard R. Brooks):
    1. Eq Step 1 -- System Energetic Minimization, 5 Kcal/mol heavy atoms restraints (1000 cycles)
    2. Eq Step 2 -- NVT Equilibration, 5 Kcal/mol heavy atoms restraints, timestep 1fs (15ps)
    3. Eq Step 3 -- System Energetic Minimization, 2 Kcal/mol heavy atoms restraints (1000 cycles)
    4. Eq Step 4 -- System Energetic Minimization, 0.1 Kcal/mol heavy atoms restraints (1000 cycles)
    5. Eq Step 5 -- System Energetic Minimization (1000 cycles)
    6. Eq Step 6 -- NPT Equilibration, 1 Kcal/mol heavy atoms restraints, timestep 1fs (5ps)
    7. Eq Step 7 -- NPT Equilibration, 0.5 Kcal/mol heavy atoms restraints, timestep 1fs (5ps)
    8. Eq Step 8 -- NPT Equilibration, 0.5 Kcal/mol backbone atoms restraints, timestep 1fs (10ps)
    9. Eq Step 9 -- NPT Equilibration, timestep 2fs, unrestrained MD simulation, writing every 1ps (20ps, 20 frames)
    10. Eq Step 10 -- NPT Equilibration, timestep 2fs, unrestrained MD simulation, writing every 1ps (20ps, 20 frames)
  8. Running Final Free (unrestrained) Short MD Simulation, timestep 4fs, unrestrained MD simulation, writing every 1ps (500ps, 500 frames)

Note: Please check steps done previously to launch this workflow in the corresponding help section. In this case, the nucleic acid 3D structure is previously computed by BioBB Workflows.

Background information

Launch ABC MD Setup workflow

amber md na
python cwl hpc
Automatic Ligand parameterization for AMBER MD

This workflow performs an automatic ligand parameterization for a small molecule using GAFF force field, generating parameters compatible with the AMBER MD package.

Workflow main steps

  1. Energetically Minimize Hydrogen Atoms (with given input parameters. Default: Steepest Descent algorithm)
  2. Generating Ligand Parameters (with given input parameters. Default: GAFF ff, pH 7.4, charge depending on the protonation state)

Note: Please check steps done previously to launch this workflow in the corresponding help section. In this case, small molecule protonation states are previously computed by BioBB Workflows, including the major (de)protonated form of the molecule at a specified pH 7.4 (major microspecies) and a list of (de)protonated forms of the molecule at a specified pH in range from 0 to 14.

Background information

Launch AMBER Ligand Parameterization workflow

amber ligand
python cwl
AMBER Protein Ligand Complex MD Setup

This workflow performs a simulation setup of a protein-ligand(s) complex system, compatible with the AMBER MD package.

Workflow main steps

  1. Extracting Protein Structure
  2. Preparing Protein PDB structure for AMBER
  3. Creating Protein-Ligand Complex Topology (with given input parameters. Default: protein.ff14SB + gaff ffs)
  4. Energetically Minimizing the Structure
    1. Step 1: Hydrogen minimization, 500 cycles, applying position restraints (50 Kcal/mol.Å2) to the protein heavy atoms.
    2. Step 2: System minimization, 500 cycles, applying position restraints (500 Kcal/mol.Å2) to the small molecule.
  5. Creating Solvent Box and Solvating the System (with given input parameters. Default: truncated octahedron, 9Å, TIP3P water model)
  6. Neutralizing the system and Adding an additional Ionic Concentration (Sodium (Na+) and Chloride (Cl-) counterions with a given input additional ionic concentration. Default: 150mM.)
  7. Energetically Minimizing the System (Steepest descent algorithm, 500 cycles, applying position restraints (15 Kcal/mol.Å2) to the solute atoms)
  8. Heating the System (From 0 to 300K. Solute atoms restrained (force constant of 10 Kcal/mol.Å2). Length 100ps.)
  9. Equilibrating the System (NVT. Heavy atoms restrained (force constant of 5 Kcal/mol.Å2). 25000 steps, 2fs timestep. Length 50ps)
  10. Equilibrating the System (NPT. Heavy atoms restrained (force constant of 2.5 Kcal/mol.Å2). 25000 steps, 2fs timestep. Length 50ps)
  11. Free (unrestrained) Molecular Dynamics Simulation (NPT. Unrestrained. 250000 steps, 2fs timestep. Length 500ps)
  12. Post-processing and Visualizing Resulting 3D Trajectory (Remove PBC, RMSd, Rgyr)

Note: Please check steps done previously to launch this workflow in the corresponding help section. In this case, an exhaustive protein structure checking is previously run by BioBB Workflows.

Background information

Launch AMBER Complex Set Up workflow

amber md protein ligand
python cwl hpc
AMBER Protein MD Setup

This workflow performs a simulation setup of a protein system, compatible with the AMBER MD package.

Workflow main steps

  1. Preparing Protein PDB structure for AMBER
  2. Creating Protein Topology (with given input parameters. Default: protein.ff14SB)
  3. Energetically Minimizing the Structure
    1. Step 1: Hydrogen minimization, 500 cycles, applying position restraints (50 Kcal/mol.Å2) to the protein heavy atoms.
    2. Step 2: System minimization, 500 cycles, applying position restraints (50 Kcal/mol.Å2) to the protein heavy atoms.
  4. Creating Solvent Box and Solvating the System (with given input parameters. Default: truncated octahedron, 9Å, TIP3P water model)
  5. Neutralizing the system and Adding an additional Ionic Concentration (Sodium (Na+) and Chloride (Cl-) counterions with a given input additional ionic concentration. Default: 150mM.)
  6. Energetically Minimizing the System (Steepest descent algorithm, 500 cycles, applying position restraints (50 Kcal/mol.Å2) to the solute atoms)
  7. Heating the System (From 0 to 300K. Solute atoms restrained (force constant of 10 Kcal/mol.Å2). Length 100ps.)
  8. Equilibrating the System (NVT. Heavy atoms restrained (force constant of 5 Kcal/mol.Å2). 25000 steps, 2fs timestep. Length 50ps)
  9. Equilibrating the System (NPT. Heavy atoms restrained (force constant of 2.5 Kcal/mol.Å2). 25000 steps, 2fs timestep. Length 50ps)
  10. Free (unrestrained) Molecular Dynamics Simulation (NPT. Unrestrained. 250000 steps, 2fs timestep. Length 500ps)
  11. Post-processing and Visualizing Resulting 3D Trajectory (Remove PBC, RMSd, Rgyr)

Note: Please check steps done previously to launch this workflow in the corresponding help section. In this case, an exhaustive protein structure checking is previously run by BioBB Workflows.

Background information

Launch AMBER Set Up workflow

amber md protein
python cwl hpc
Automatic Ligand parameterization for CNS/XPLOR MD

This workflow performs an automatic ligand parameterization for a small molecule using GAFF force field, generating parameters compatible with the CNS/XPLOR MD package.

Workflow main steps

  1. Energetically Minimize Hydrogen Atoms (with given input parameters. Default: Steepest Descent algorithm)
  2. Generating Ligand Parameters (with given input parameters. Default: GAFF ff, pH 7.4, charge depending on the protonation state)

Note: Please check steps done previously to launch this workflow in the corresponding help section. In this case, small molecule protonation states are previously computed by BioBB Workflows, including the major (de)protonated form of the molecule at a specified pH 7.4 (major microspecies) and a list of (de)protonated forms of the molecule at a specified pH in range from 0 to 14.

Background information

Launch CNS/XPLOR Ligand Parameterization workflow

ligand
python cwl
GROMACS Protein Ligand Complex MD Setup

This workflow performs a simulation setup of a protein-ligand complex system, compatible with the GROMACS MD package.

Workflow main steps

  1. Fixing Protein Structure
  2. Creating Protein Topology (with given input parameters. Default: amber99sb-ildn)
  3. Generating Protein-Ligand complex structure and topology
  4. Creating Solvent Box and Solvating the System (with given input parameters. Default: cubic, 1nm, SPC water model)
  5. Neutralizing the system and Adding an additional Ionic Concentration (Sodium (Na+) and Chloride (Cl-) counterions with a given input additional ionic concentration. Default: 50mM.)
  6. Energetically Minimizing the System (Steepest descent algorithm, 5000 steps, maximum force placed at 500 KJ/mol.nm2)
  7. Equilibrating the System (NVT. Heavy atoms restrained (force constant of 1000 KJ/mol.nm2). 50000 steps, 2fs timestep. Length 100ps)
  8. Equilibrating the System (NPT. Heavy atoms restrained (force constant of 1000 KJ/mol.nm2). 50000 steps, 2fs timestep. Length 100ps)
  9. Free (unrestrained) Molecular Dynamics Simulation (NPT. Unrestrained. 250000 steps, 2fs timestep. Length 500ps)
  10. Post-processing and Visualizing Resulting 3D Trajectory (Remove PBC, RMSd, Rgyr)

Note: Please check steps done previously to launch this workflow in the corresponding help section. In this case, an exhaustive protein structure checking is previously run by BioBB Workflows.

Background information

Launch GROMACS Complex Set Up workflow

gmx md protein ligand
python cwl hpc
Structural DNA helical parameters

This workflow extracts structural and dynamical properties from a DNA or RNA MD trajectory, including helical parameters, stiffness, bimodalities and correlations.

Workflow main steps

  1. Extracting Helical Parameters from input trajectory (with Curves+ and Canal tools)
  2. Computing Average Helical Parameters
    1. Base Pair Step (Inter Base Pair) Average Parameters
    2. Base Pair (Intra Base Pair) Average Parameters
    3. Axis Average Parameters
    4. Grooves Average Parameters
    5. Backbone Torsions Average Parameters
  3. Computing Time Series Helical Parameters
    1. Base Pair Step (Inter Base Pair) Time Series Parameters
    2. Base Pair (Intra Base Pair) Time Series Parameters
    3. Axis Time Series Parameters
    4. Grooves Time Series Parameters
    5. Backbone Torsions Time Series Parameters
  4. Computing Stiffness
    1. Base Pair Step (Inter Base Pair) Stiffness
    2. Base Pair (Intra Base Pair) Stiffness
  5. Computing Bimodality
    1. Base Pair Step (Inter Base Pair) Bimodality
  6. Computing Correlations
    1. Base Pair Step (Inter Base Pair) Sequence Correlations
    2. Base Pair (Intra Base Pair) Sequence Correlations
    3. Base Pair Step (Inter Base Pair) Helical Parameter Correlations
    4. Base Pair (Intra Base Pair) Helical Parameter Correlations
    5. Base Pair Step (Inter Base Pair) Neighboring Steps Correlations
    6. Base Pair (Intra Base Pair) Neighboring Steps Correlations

Note: Please check steps done previously to launch this workflow in the corresponding help section. In this case, the nucleic acid sequence (needed for the Helical parameter analysis) is previously extracted from the structure by BioBB Workflow. Besides, the trajectory is shown in the NGL visualizer to quickly check for inconsistencies.

Background information

Launch DNA helical parameters workflow

na md
python
Protein-ligand docking

This workflow performs a protein-ligand docking with AutoDock Vina.

Workflow main steps

  1. Generating Cavity Box from Pocket (with given input parameters. Default: 12Å offset)
  2. Preparing Small Molecule (ligand) for Docking
  3. Preparing Target Protein for Docking
  4. Running the Docking

Note: Please check steps done previously to launch this workflow in the corresponding help section. In this case, a pocket search on the protein structure is previously run by BioBB Workflows, which helps finding the proper box to use in the Docking process.

Background information

Launch Docking Autodock Vina workflow

docking ligand protein
python cwl
Automatic Ligand parameterization for GROMACS

This workflow performs an automatic ligand parameterization for a small molecule using GAFF force field, generating parameters compatible with the GROMACS MD package.

Workflow main steps

  1. Energetically Minimize Hydrogen Atoms (with given input parameters. Default: Steepest Descent algorithm)
  2. Generating Ligand Parameters (with given input parameters. Default: GAFF ff, pH 7.4, charge depending on the protonation state)

Note: Please check steps done previously to launch this workflow in the corresponding help section. In this case, small molecule protonation states are previously computed by BioBB Workflows, including the major (de)protonated form of the molecule at a specified pH 7.4 (major microspecies) and a list of (de)protonated forms of the molecule at a specified pH in range from 0 to 14.

Background information

Launch GROMACS Ligand Parameterization workflow

gmx ligand
python cwl
Automatic Ligand parameterization for OPLS/AA

This workflow performs an automatic ligand parameterization for a small molecule using GAFF force field, generating parameters compatible with the GROMACS MD package and the OPLS/AA force field.

Workflow main steps

  1. Energetically Minimize Hydrogen Atoms (with given input parameters. Default: Steepest Descent algorithm)
  2. Generating Ligand Parameters (with given input parameters. Default: GAFF ff, pH 7.4, charge depending on the protonation state)

Note: Please check steps done previously to launch this workflow in the corresponding help section. In this case, small molecule protonation states are previously computed by BioBB Workflows, including the major (de)protonated form of the molecule at a specified pH 7.4 (major microspecies) and a list of (de)protonated forms of the molecule at a specified pH in range from 0 to 14.

Background information

Launch GROMACS OPLS/AA Ligand Parameterization workflow

gmx ligand
python cwl
Protein MD Analysis

This workflow computes a set of Quality Control (QC) analyses on top of an uploaded MD trajectory. QC analyses include positional divergence (RMSd), change of shape (Radius of Gyration), identification of flexible regions (atomic/residue fluctuations), and identification of different molecular conformations (trajectory clustering).

Workflow main steps

  1. Calculating Average structure
  2. Computing Root Mean Square deviations (RMSd) against the first structure from the trajectory (equilibrated system) and against the average structure.
  3. Computing residue fluctuation (Bfactor)
  4. Computing Radius of Gyration
  5. Computing cluster families using RMSd between snapshots as metrics

Note: Please check steps done previously to launch this workflow in the corresponding help section. In this case, the molecule sequence is previously extracted from the structure by BioBB Workflow. Besides, the trajectory is shown in the NGL visualizer to quickly check for inconsistencies.

Background information

Launch Protein MD Analysis workflow

protein md
python
GROMACS Protein MD Setup with mutations

This workflow performs a simulation setup of a protein system after modeling one (or many) protein residue mutations. Results are compatible with the GROMACS MD package.

Workflow main steps

These steps are executed for each mutation.

  1. Fixing Protein Structure
  2. Creating Protein Topology (with given input parameters. Default: amber99sb-ildn)
  3. Creating Solvent Box and Solvating the System (with given input parameters. Default: cubic, 1nm, SPC water model)
  4. Neutralizing the system and Adding an additional Ionic Concentration (Sodium (Na+) and Chloride (Cl-) counterions with a given input additional ionic concentration. Default: 50mM.)
  5. Energetically Minimizing the System (Steepest descent algorithm, 5000 steps, maximum force placed at 500 KJ/mol.nm2)
  6. Equilibrating the System (NVT. Heavy atoms restrained (force constant of 1000 KJ/mol.nm2). 50000 steps, 2fs timestep. Length 100ps)
  7. Equilibrating the System (NPT. Heavy atoms restrained (force constant of 1000 KJ/mol.nm2). 50000 steps, 2fs timestep. Length 100ps)
  8. Free (unrestrained) Molecular Dynamics Simulation (NPT. Unrestrained. 250000 steps, 2fs timestep. Length 500ps)
  9. Post-processing and Visualizing Resulting 3D Trajectory (Remove PBC, RMSd, Rgyr)

Note: Please check steps done previously to launch this workflow in the corresponding help section. In this case, an exhaustive protein structure checking is previously run by BioBB Workflows.

Background information

Launch GROMACS Set Up Mutations workflow

gmx md protein
python cwl hpc
GROMACS Protein MD Setup

This workflow performs a simulation setup of a protein system, compatible with the GROMACS MD package.

Workflow main steps

  1. Fixing Protein Structure
  2. Creating Protein Topology (with given input parameters. Default: amber99sb-ildn)
  3. Creating Solvent Box and Solvating the System (with given input parameters. Default: cubic, 1nm, SPC water model)
  4. Neutralizing the system and Adding an additional Ionic Concentration (Sodium (Na+) and Chloride (Cl-) counterions with a given input additional ionic concentration. Default: 50mM.)
  5. Energetically Minimizing the System (Steepest descent algorithm, 5000 steps, maximum force placed at 500 KJ/mol.nm2)
  6. Equilibrating the System (NVT. Heavy atoms restrained (force constant of 1000 KJ/mol.nm2). 50000 steps, 2fs timestep. Length 100ps)
  7. Equilibrating the System (NPT. Heavy atoms restrained (force constant of 1000 KJ/mol.nm2). 50000 steps, 2fs timestep. Length 100ps)
  8. Free (unrestrained) Molecular Dynamics Simulation (NPT. Unrestrained. 250000 steps, 2fs timestep. Length 500ps)
  9. Post-processing and Visualizing Resulting 3D Trajectory (Remove PBC, RMSd, Rgyr)

Note: Please check steps done previously to launch this workflow in the corresponding help section. In this case, an exhaustive protein structure checking is previously run by BioBB Workflows.

Background information

Launch GROMACS Set Up workflow

gmx md protein
python cwl hpc