POSIT - Ligand Guided Small Molecule Posing

Category Paths

Follow one of these paths in the Orion user interface, to find the floe.

  • Role-based/Computational Chemist

  • Solution-based/Small Molecule Lead-opt

  • Task-based/Ligand Posing & Analysis

  • Product-based/OEDocking


POSIT - Ligand Guided Small Molecule Posing poses multiple ligands against multiple receptors. POSIT works best when fitting to a collection of co-crystal ligands. However, it can also be used for single ligand targets. Each pose that POSIT generates is analyzed with a simple heuristic and marked with a probability.

The minimal inputs into POSIT are protein receptor(s) and SMILES strings of ligand molecules to pose.

Output from the POSIT floe consists of pose structures of the input ligands, associated probabilities, protein-ligand clash information, and interaction energies.

Running POSIT with multiple receptors requires careful consideration of the hardware memory limits. The memory requirement increases with the number of receptors. The default setup is sufficient when the number of receptors is ~100 or less. Please contact support@eyesopen.com for help, is case when you want to run this floe with more receptors than 100.

Promoted Parameters

Title in user interface (promoted name)


Ligand Database (in): Dataset containing the ligand molecules to generate pose

  • Required

  • Type: data_source

Receptors (receptors): Dataset containing the receptors

  • Required

  • Type: data_source

Output parameters

Output Dataset (out): Output dataset of successful calculations

  • Required

  • Type: dataset_out

  • Default: Output for POSIT - Ligand Guided Small Molecule Posing

Failed Dataset (failed): Output dataset of failed calculations.

  • Required

  • Type: dataset_out

  • Default: Failed Output for POSIT - Ligand Guided Small Molecule Posing

POSIT settings

Number of poses (num_poses): Number of poses to generate per ligand.

  • Type: integer

  • Default: 1

Best Receptor Only (best_receptor_only): Only use the best receptor, instead of exploring all the receptors, while generating multiple poses.

  • Type: boolean

  • Default: True

  • Choices: [True, False]

None (min_prob): The minimum probability that a ligand crystal will be within 2A of the predicted pose. This probability assumes the ligand binds, which may not be the case.

  • Type: decimal

  • Default: 0.33

Relaxation Mode (relax_mode): Mode to determine if a post pose prediction relaxation should be performed

  • Type: string

  • Default: NONE

  • Choices: [‘ALL’, ‘CLASHED’, ‘NONE’]

Allowed clash type (allow_clash_type): Types of clashes acceptable between protein and ligand in the pose.

  • Type: string

  • Default: HYDROGEN

  • Choices: [‘ANY’, ‘HYDROGEN’, ‘NONE’]

Generate Interaction Depictions (make_depictions): Whether or not to generate interaction depictions

  • Required

  • Type: boolean

  • Default: False

  • Choices: [True, False]