Help - Workflows

  • Home
  • Help
  • Workflows
Workflows

Workflows

This website has been built with the aim of running several predefined workflows in an automatic way. In the Workflows section there is a list with all the available workflows. On the top of the list there is a search box for performing searches on the list through tags.

Each of the blocks of the list shows the information of its corresponding workflow:

  1. Workflow's title
  2. Opens workflow's flowchart
  3. Link to workflow's example in BioExcel Building Blocks official website
  4. Workflow's descriptive image
  5. Workflow's description
  6. Description of workflow main steps (click to show)
  7. Link to create project starting with current workflow selected beforehand
  8. Workflow's tags list
  9. Workflow's accepted execution types:
    1. python: the current workflow can be run at home through Python (custom code is automatically generated before the Run project step)
    2. cwl: the current workflow can be run at home through Common Workflow Language (custom code is automatically generated before the Run project step)
    3. hpc: the current workflow can run a production MD in a HPC supercomputer (take into account that, to perform this, you must register to the website and configure the SSH keys of the chosen supercomputer)

Below there is a list with all the available workflows:

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.

More information about ABC MD Setup workflow

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.

More information about AMBER Ligand Parameterization workflow

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.

More information about AMBER Complex Set Up workflow

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.

More information about AMBER Set Up workflow

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.

More information about CNS/XPLOR Ligand Parameterization workflow

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.

More information about GROMACS Complex Set Up workflow

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.

More information about DNA helical parameters workflow

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.

More information about Docking Autodock Vina workflow

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.

More information about GROMACS Ligand Parameterization workflow

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.

More information about GROMACS OPLS/AA Ligand Parameterization workflow

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.

More information about Protein MD Analysis workflow

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.

More information about GROMACS Set Up Mutations workflow

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.

More information about GROMACS Set Up workflow

For more information about the workflows such as flowchart schemas and related workflows on the official website, please visit the workflows section, where users will also be able to start the process of creating a new project starting from a predefined workflow.

This website uses cookies to ensure you get the best experience on our website. Our Cookie Policy
Understand
2024 © Molecular Modeling and Bioinformatics Group