HADDOCK2.2 protein-ligand protocol


Omega TK 2.6.4, MMTSB Tool Set,ProFit 3.1,PRODRG,HADDOCK2.2 webserver,PyMOL v1.8.4

System Preparation Parameters

Assumed pH neutral
Protein charges from OPLS force field
Ligand parameters and charges from PRODRG

System Preparation Method

Receptor template structures were retrieved using the advanced search at http://www.rcsb.org/ with more than 80% sequence similarity (Blast) and presence of a ligand. Structures with missing regions were manually removed and the remaining structures clustered using RMSD values calculated by ProFit with an RMSD cutoff of 0.5 and a minimum cluster size of 2. Based on the clusters 4 template structures (1osv, 1ot7, 3dct, and 3olf) were selected for ensemble docking. During ensemble generation residues not matching the target sequence were mutated to the corresponding amino acid in PyMOL. Based on ligand positioning in templates, the binding pocket was defined as all residues within 4 to their respective ligand in the various receptors.

For the ligands, we converted the SMILES strings provided by the organisers, to 3D structures using Omega while generating conformers using Omega torsional sampling at the same time. The maximum number of conformers generated per ligand was capped to 100. The clustering of conformers is performed by MMTSB tools using the following settings: jclust hierarchical clustering with maximum number of clusters set to 10 and minimum number of elements is set to 4 per cluster. Representative structure from each cluster is selected, an ensemble is formed by representatives for each ligand.

Pose Prediction Parameters

Default HADDOCK2.2 server setting except for the following changes
it0 sampling (rigid body docking): 10000 models
it1 sampling (flexible refinement): 400 models
delenph = False
inter_rigid = 0.001
tadinit2_t = 500
tadfinal2_t = 50
tadinit3_t = 500
tadfinal3_t = 50
initiosteps = 0
cool1_steps = 0
w_vdw_0 =0.0
amb = ExtStageConstants (firstit = 0, lastit = 0,)

Pose Prediction Method

The docking was performed using the HADDOCK2.2 web server (van Zundert et al. J. Mol. Biol. 2015) using default parameters except for those specified above. Ensembles of 5 receptor structures and various ligand conformations were provided as input for ensemble docking.

Two restraints files were provided to the server to guide the docking: 1) an ambig.tbl file in which the ligand and all residues in the binding pocket were defined as active - this file was only used in it0 and 50% of the restraints were randomly deleted for each docking trial 2) an unambig.tbl file in which only the ligand is defined as active and the protein binding pocket as passive (meaning that no energy penalty is generated if a binding pocket residue does not contact the ligand). This second file was used at all stages of the docking protocol.

The top 5 poses from the HADDOCK2.2-it1 stage were selected for submission.

The scoring function used for ranking the poses is the standard HADDOCK score for the flexible refinement (It1) which is defined as: HADDOCK-score = 1.0*Evdw + 1.0*Eelec + 1.0*Edesol - 0.01*BSA, where BSA is the buried surface area in Angstrom**2, Edesol an empirical desolvation energy term (Fernandez-Recio et al. J. Mol. Biol. 2004). The intermolecular energies are calculated using the OPLS united atom force field parameters (Jorgensen, W. L. & Tirado-Rives. J. Am. Chem. Soc. 1988) for non-bonded atoms, using a 8.5 angstrom cut-off with a shifting function for the electrostatic energy and switching function between 6.5 and 8.5 angstrom for the van der Waals energy. For the electrostatics energy, a dielectric constant of 10 is used.