Protein Conformational Ensembles (FlexDyn)

Generate protein conformational ensembles with five coarse-grained methods (CONCOORD, ProDy ANM, FlexServ BD/DMD/NMA, NOLB, iMODS), cluster the meta-trajectory and analyse its principal motions.

by Temple Compute

Run Protein Conformational Ensembles (FlexDyn) on Horus

W-19 · Protein Conformational Ensembles

Generate protein conformational ensembles with five coarse-grained methods (CONCOORD, ProDy ANM, FlexServ BD/DMD/NMA, NOLB, iMODS), cluster the meta-trajectory and analyse its principal motions.

Domain: BioExcel Building Blocks

Overview

Generates protein conformational ensembles with five coarse-grained methods (CONCOORD, ProDy ANM, FlexServ BD/DMD/NMA, NOLB, iMODS), illustrated with adenylate kinase (PDB 1AKE, chain A). All ensembles are concatenated into a meta-trajectory, clustered with GROMACS, and analysed by PCA for B-factors, hinge points, stiffness and collectivity. The workflow has 43 tasks.

Pipeline

fetch_pdb -> extract_model -> extract_chain -> cpptraj_mask_backbone / cpptraj_mask_ca
concoord_dist -> concoord_disco -> cpptraj_rms_concoord -> cpptraj_convert_concoord    CONCOORD
prody_anm -> cpptraj_rms_prody -> cpptraj_convert_prody                                ProDy ANM
bd_run / dmd_run / nma_run -> cpptraj_rms_* (-> cpptraj_convert_nma)                   FlexServ BD / DMD / NMA
nolb_nma -> cpptraj_rms_nolb -> cpptraj_convert_nolb                                   NOLB
imod_imode -> imod_imc -> cpptraj_rms_imods -> cpptraj_convert_imods                   iMODS
zip_trajectories -> trjcat                         Concatenate ensembles into meta-trajectory
make_ndx -> gmx_cluster -> cpptraj_rms_meta        Cluster meta-trajectory (GROMACS)
pcz_zip_classic / pcz_zip_gaussian                 PCA compression
pcz_info, pcz_evecs                                PCA statistics and eigenvectors
pcz_animate -> cpptraj_convert_proj                Animate along PC1
pcz_bfactor                                        B-factors from PCA modes
pcz_hinges_bfactor / _dyndom / _fcte               Hinge points (3 methods)
pcz_stiffness, pcz_collectivity                    Apparent stiffness, collectivity index

Inputs / Outputs

Outputs (results/):

input.pdb and the extracted model, monomer and masks
Per-method ensemble trajectories (.trr) and RMSD .dat files
concat_traj.*, concat_cluster.pdb, meta_traj_*: meta-trajectory and GROMACS cluster output
concat_ensemble.pcz, concat_ensemble_gaussian.pcz: compressed PCA trajectories
bfactor_all.*, hinges_{bfactor,dyndom,fcte}_report.json, pcz_stiffness.json, pcz_collectivity.json: flexibility analysis

Parameters

| id | Default | Meaning | |---|---|---| | pdb_id | 1ake | PDB code to download; leave empty to use structure. | | structure | examples/1ake.pdb | PDB file used when pdb_id is empty. | | chain | A | Chain to analyse. | | n_structures | 300 | Conformations per ensemble method (10-5000). | | cluster_cutoff_nm | 0.12 | RMSD cutoff of the GROMACS linkage clustering (0.02-1.0). |