LightDock Protein-Protein Benchmark 5 Data

Description

• results: this folder contains for each complex from the BM5 and for each scenario (BLIND, TI, TI-SINGLE, TI-REC, TI-50, TI-25, TI-REC-50, TI-REC-25, TI-RANDOM-50 and TI-RANDOM-25) a file with extension .list where for each structure predicted by the protocol its name, interface-RMSD, ligand-RMSD, fraction of native contacts and the final score.

• data: for each complex, the initial PDB structures used ($complex_A-noh.pdb, $complex_B-noh.pdb), the reference (*.segid.pdb) and for each scenario setup.json and lightdock.info files. A script run.sh with all the necessary steps to reproduce is available.

• restraints: restraint files used for each of the scenarios above-mentioned named as $complex-[scenario]-restraints.list. In the case of the BLIND scenario, this file is not available as this scenario corresponds to the full ab initio mode.

Scenarios

• BLIND: ab initio docking, no restraints used.
• TI: true interface residues considered.
• TI-SINGLE: only a residue restraints pair is considered, this pair is assured to be interacting.
• TI-ONE: only a residue restraint is considered in the receptor side (same receptor residue than in TI-SINGLE).
• TI-REC: only residues from the receptor true interface are considered.
• TI-50: true interface is split in two parts and extended with residues which are not in the true interface, but are contiguous to the selected patch and don't belong to the other half of true interface residues.
• TI-25: true interface is split in four parts and extended with residues which are not in the true interface, but are contiguous to the selected patch and don't belong to any of the other original parts.
• TI-REC-50: same as TI-50 but only considering receptor true interface residues.
• TI-REC-25: same as TI-25 but only considering receptor true intterface residues.
• TI-RANDOM-50: 50% of the true interface is randomly selected as restraints.
• TI-RANDOM-25: 25% of the true interface is randomly selected as restraints.

Reproduction of results

For the reported results, the following parameters were used:

• initial_swarms: 400
• number_of_glowworms: 200
• number_of_steps: 100
• scoring_function: fastdfire
• number_of_cores: 48
• distance_in_Å: 5.0
• fraction_of_input_restraints: 0.4 (40%)
• ch_rec: receptor chain id
• ch_lig: ligand chain id