Dataset used to train and validate the PBEE pipeline. See publication here.
wget https://github.com/chavesejf/PBEE_dataset/releases/download/v1.1.0/PBEE_v1.1.0_dataset.tar.xz
tar -xvJf PBEE_v1.1.0_dataset.tar.xz
The following directory tree will be created:
PBEE_datasets/
├── v1.1.0/
│ ├── 0_input_structures/
│ │ ├── test/
│ │ └── train/
│ │
│ ├── 1_processed_structures/
│ │ ├── test/
│ │ └── train/
│ │
│ └── 2_data/
│ ├── test/
│ └── train/This directory contains the raw structures used in the training and testing stages of PBEE version 1.1.0 (regressor), all from specific databases (PDBbind, SKEMPI, AffinityBenchmark, and PRODIGY) previously published.
This directory contains structures that have been processed by the PBEE pipeline.
This directory contains .json files with structural information about the processed structures. Below is a description of the file contents:
{
"3G6D": { <- name of the raw structure
"structure": "_pbee_3G6D", <- name of the processed structure
"partner1": "str", <- chain ids that belongs to the receptor or ligand (p1)
"partner2": "str", <- chain ids that belongs to the receptor or ligand (p2)
"atoms": "int", <- number of atoms in the processed structure
"ions": "int", <- number of ions detected in the processed structure
"int_ss_p1": { <- secondary structure content of the interface of p1 that interacts with p2
"helix": "int", <- alpha-helix percentage
"sheet": "int", <- beta-sheet percentage
"loop": "int" <- loop percentage
},
"int_ss_p2": { <- secondary structure content of the interface of p2 that interacts with p1
"helix": "int", <- same as int_ss_p1
"sheet": "int",
"loop": "int"
},
"int_restp_p1": { <- residue type content of the interface of p1 that interacts with p2
"aromatic": "int", <- percentage of aromatic residues
"neutral": "int", <- percentage of neutral residues
"apolar": "int", <- percentage of apolar residues
"polar_pos": "int", <- percentage of polar positive residues
"polar_neg": "int" <- percentage of polar negative residues
},
"int_restp_p2": { <- residue type content of the interface of p2 that interacts with p1
"aromatic": "int", <- same as int_restp_p1
"neutral": "int",
"apolar": "int",
"polar_pos": "int",
"polar_neg": "int"
},
"int_aa_comp_p1": { <- amino acid composition (%) of the interface of p1 that interacts with p2
"A": "int", <- total ALA
"C": "int", <- " CYS
"D": "int", <- " ASP
"E": "int", <- " GLU
"F": "int", <- " PHE
"G": "int", <- " GLY
"H": "int", <- " HIS
"I": "int", <- " ILE
"K": "int", <- " LYS
"L": "int", <- " LEU
"M": "int", <- " MET
"N": "int", <- " ASN
"P": "int", <- " PRO
"Q": "int", <- " GLN
"R": "int", <- " ARG
"S": "int", <- " SER
"T": "int", <- " THR
"V": "int", <- " VAL
"W": "int", <- " TRP
"Y": "int" <- " TYR
},
"int_aa_comp_p2": { <- amino acid composition (%) of the interface of p2 that interacts with p1
"A": "int",
"C": "int",
"D": "int",
"E": "int",
"F": "int",
"G": "int",
"H": "int",
"I": "int",
"K": "int",
"L": "int",
"M": "int",
"N": "int",
"P": "int",
"Q": "int",
"R": "int",
"S": "int",
"T": "int",
"V": "int",
"W": "int",
"Y": "int"
},
"int_seq_p1": {}, <- primary structure content (per chain) of the interface of p1 that interacts with p2
"int_seq_p2": {}, <- primary structure content (per chain) of the interface of p2 that interacts with p1
"int_resid_p1": {}, <- index of interface residues of p1 that interacts with p2 (ref: raw structure)
"int_resid_p2": {}, <- index of interface residues of p2 that interacts with p1 (ref: raw structure)
"seq_p1": {}, <- primary structure content (per chain) of the p1
"seq_p2": {}, <- primary structure content (per chain) of the p2
"time": { <- time elapsed to complete the stages of the PBE pipeline
"pre_processing": "float",
"post_processing": null
},
"dG_exp": "float", <- experimental binding affinity of the complex (p1:p2)
"rosetta_int_descriptors": { <- scores and interface descriptors obtained with Rosetta
"dslf_fa13": "float",
"fa_atr": "float",
"fa_dun_dev": "float",
"fa_dun_rot": "float",
"fa_dun_semi": "float",
"fa_elec": "float",
"fa_intra_atr_xover4": "float",
"fa_intra_elec": "float",
"fa_intra_rep_xover4": "float",
"fa_intra_sol_xover4": "float",
"fa_rep": "float",
"fa_sol": "float",
"lk_ball": "float",
"lk_ball_bridge": "float",
"lk_ball_bridge_uncpl": "float",
"lk_ball_iso": "float",
"hbond_bb_sc": "float",
"hbond_lr_bb": "float",
"hbond_sc": "float",
"hbond_sr_bb": "float",
"hxl_tors": "float",
"omega": "float",
"p_aa_pp": "float",
"rama_prepro": "float",
"ref": "float",
"total_score": "float",
"cms": "float",
"ifa_complex_normalized": "float",
"ifa_dG_cross": "float",
"ifa_dG_separated": "float",
"ifa_dSASA_hphobic": "float",
"ifa_dSASA_int": "float",
"ifa_dSASA_polar": "float",
"ifa_delta_unsatHbonds": "float",
"ifa_hbond_E_fraction": "float",
"ifa_hbonds_int": "float",
"ifa_nres_all": "float",
"ifa_nres_int": "float",
"ifa_packstat": "float",
"ifa_per_residue_energy_int": "float",
"ifa_sc_value": "float",
"ifa_side1_normalized": "float",
"ifa_side1_score": "float",
"ifa_side2_normalized": "float",
"ifa_side2_score": "float"
}
}