Pose Analysis MD

Pose-analysis MD accepts selectable small-molecule, protein, and water force fields. Mean and medoid structures are available through the same result helpers as protein MD.

Pose-analysis MD workflow - molecular dynamics simulations for ligand-protein complexes.

TrajectoryResult dataclass

TrajectoryResult(uuid: str, ligand_rmsd: list[float], contacts: list[BindingPoseContact], sasa: list[float | None], polar_sasa: list[float | None], isotropic_radius_of_gyration: list[float], cluster_centroid_indices: list[int], cluster_indices_by_frame: list[int], protein_rmsd: list[float] = list(), rmsf: list[float] = list(), potential_energy: list[float] = list(), mmgbsa_scores: list[float | None] = list(), mean_structure_uuid: str | None = None, median_structure_frame_index: int | None = None)

Results from a single MD trajectory replicate.

Attributes:

Name	Type	Description
uuid	str	UUID of the trajectory calculation
ligand_rmsd	list[float]	ligand RMSD values over time (Angstrom)
contacts	list[BindingPoseContact]	ligand-protein contacts with occupancy over the trajectory
sasa	list[float | None]	solvent-accessible surface area per analyzed frame (populated when analysis_interval_ps is set)
polar_sasa	list[float | None]	polar solvent-accessible surface area per analyzed frame (populated when analysis_interval_ps is set)
isotropic_radius_of_gyration	list[float]	radius of gyration per analyzed frame
cluster_centroid_indices	list[int]	frame indices of the cluster centroids (populated when clustering is set)
cluster_indices_by_frame	list[int]	cluster assignment for each frame (populated when clustering is set)
protein_rmsd	list[float]	per-frame Cα RMSD from the first frame, in angstrom
rmsf	list[float]	per-Cα RMSF from the mean structure, in angstrom
potential_energy	list[float]	per-frame potential energy of the simulated system, in Hartree
mmgbsa_scores	list[float | None]	per-frame MM/GBSA interaction energy, in kcal/mol
mean_structure_uuid	str | None	UUID of the coordinate-averaged structure
median_structure_frame_index	int | None	frame index of the medoid structure

PoseAnalysisMDResult dataclass

PoseAnalysisMDResult(workflow_data: dict[str, Any], workflow_type: str, workflow_uuid: str, complete: bool = True)

Bases: _MolecularDynamicsResult

Result from a Pose-Analysis Molecular Dynamics (MD) workflow.

trajectories property

trajectories: list[TrajectoryResult]

Results from each trajectory replicate.

Each trajectory contains RMSD values, contact analysis, and cluster assignments.

hydration_sites property

hydration_sites: list[HydrationSite]

Hydration sites identified across all trajectories.

average_rmsds property

average_rmsds: list[float | None]

Average ligand RMSD per trajectory (Angstrom).

messages property

messages: list[Message]

Any messages or warnings from the workflow.

submit_pose_analysis_md_workflow

submit_pose_analysis_md_workflow(protein: Protein | ProteinUUID, initial_smiles: str, num_trajectories: int = 4, small_molecule_ff: Literal['off_sage_2_0_0', 'off_sage_2_2_1', 'off_sage_2_3_0', 'mango_1_0_0'] = 'off_sage_2_3_0', protein_ff: ProteinForceField | str = ProteinForceField.FF14SB, water_ff: WaterForceField | str = WaterForceField.TIP3P, equilibration_time_ns: float = 0.5, simulation_time_ns: float = 10, temperature: float = 300, pressure_atm: float = 1.0, langevin_timescale_ps: float = 1.0, timestep_fs: float = 4, hydrogen_mass: float = 3, constrain_hydrogens: bool = True, nonbonded_cutoff: float = 8.0, ionic_strength_M: float = 0.0, water_buffer: float = 8.0, ligand_residue_name: str = 'LIG', protein_restraint_cutoff: float | None = 7.0, protein_restraint_constant: float = 100, save_solvent: bool = False, num_solvent_to_save: int | None = None, analysis_interval_ps: float | None = None, clustering: KMeansClusteringSettings | GreedyClusteringSettings | None = None, validate_forcefield: bool = True, name: str = 'Pose-Analysis MD Workflow', folder_uuid: str | None = None, folder: Folder | None = None, max_credits: int | None = None, webhook_url: str | None = None, is_draft: bool = False) -> Workflow[PoseAnalysisMDResult]

Submits a Pose-Analysis Molecular Dynamics (MD) workflow to the API.

Parameters:

Name	Type	Description	Default
protein	Protein | ProteinUUID	Holo protein on which MD will be run. Can be input as a UUID or a Protein object	required
initial_smiles	str	SMILES for the ligand	required
num_trajectories	int	number of trajectories to run	4
small_molecule_ff	Literal['off_sage_2_0_0', 'off_sage_2_2_1', 'off_sage_2_3_0', 'mango_1_0_0']	force field for the ligand	'off_sage_2_3_0'
protein_ff	ProteinForceField | str	force field for proteins	FF14SB
water_ff	WaterForceField | str	force field for water	TIP3P
equilibration_time_ns	float	equilibration time per trajectory, in ns	0.5
simulation_time_ns	float	simulation time per trajectory, in ns	10
temperature	float	temperature, in K	300
pressure_atm	float	pressure, in atm	1.0
langevin_timescale_ps	float	timescale for the Langevin integrator, in ps⁻¹	1.0
timestep_fs	float	timestep, in femtoseconds	4
hydrogen_mass	float	hydrogen mass, in atomic mass units	3
ligand_residue_name	str	name of the residue corresponding to the ligand	'LIG'
constrain_hydrogens	bool	whether to use SHAKE to freeze bonds to hydrogen	True
nonbonded_cutoff	float	nonbonded cutoff for particle-mesh Ewald, in Å	8.0
ionic_strength_M	float	ionic strength of the solution, in M (molar)	0.0
water_buffer	float	amount of water to add around the protein, in Å	8.0
protein_restraint_cutoff	float | None	cutoff past which alpha-carbons will be constrained, in Å, measured from the ligand. None applies no restraints	7.0
protein_restraint_constant	float	force constant for backbone restraints, in kcal/mol/Ų	100
save_solvent	bool	whether to save solvent molecules	False
num_solvent_to_save	int | None	number of solvent molecules to save (the N nearest the ligand each frame). None saves all solvent when save_solvent is True	None
analysis_interval_ps	float | None	interval at which to compute per-frame SASA and polar SASA, in ps. None disables those analyses	None
clustering	KMeansClusteringSettings | GreedyClusteringSettings | None	how to cluster trajectory frames. None disables clustering; pass a KMeansClusteringSettings (num_clusters) or GreedyClusteringSettings (cutoff_angstrom)	None
validate_forcefield	bool	validate the protein forcefield compatibility before submitting. Raises an error early if the protein cannot be parameterized or has clashing residues	True
name	str	name of the workflow	'Pose-Analysis MD Workflow'
folder_uuid	str | None	UUID of the folder to place the workflow in	None
folder	Folder | None	destination folder	None
max_credits	int | None	maximum credits for the workflow	None
webhook_url	str | None	URL that Rowan will POST to when the workflow completes	None
is_draft	bool	save as a draft without starting execution	False

Returns:

Type	Description
Workflow[PoseAnalysisMDResult]	submitted workflow

Raises:

Type	Description
HTTPStatusError	request to the API fails