PubChem Dock

From Chemical Informatics and Cyberinfrastructure Collaboratory

Table Summary

The database aims to store the results of large scale docking calculations. The result being stored include the PDB structure of the target, 3D structures of docked ligands and the docking scores. We currently evaluate four (arbitrarily chosen) scoring functions provided by Openeye's fred, namely

• chemgauss3
• shapegauss
• oechemscore
• plp

For each scoring function we save the total score as well as the component scores.

The database currently has docking result against one protein (1YC4) but we plan on populating it with docking results for families of proteins at a time. One possible use is then to screen ligands over families using a similarity approach.

The database can be accessed via a web form as well as with web services.

Table schema

dock_target (
pdbid text primary key,
structure text not null
);

dock (
dockid bigserial primary key,
cid varchar(256) not null references pubchem_compound (cid)
                 on update cascade
                 on delete cascade,
target text not null references dock_target (pdbid)
           on update cascade
           on delete cascade,
tool text not null,
unique (cid, target, tool)
);
create index dock_cid_index on dock (cid);

dockscore_chemgauss3 (
id bigint references dock (dockid) primary key
                 on update cascade
                 on delete cascade,
structure text default null,
total double precision default null,
steric double precision default null,
ligdesolv double precision default null,
prodesolv double precision default null,
acc double precision default null,
donor double precision default null,
aromatic double precision default null,
metal double precision default null
);

dockscore_plp (
id bigint references dock (dockid) primary key
                 on update cascade
                 on delete cascade,
structure text default null,
total double precision default null,
hb double precision default null,
np double precision default null,
metal double precision default null,
sulphur double precision default null
);

dockscore_shapegauss (
id bigint references dock (dockid) primary key
                 on update cascade
                 on delete cascade,
structure text default null,
total double precision default null,
shape double precision default null
);

dockscore_oechemscore (
id bigint references dock (dockid) primary key
                 on update cascade
                 on delete cascade,
structure text default null,
total double precision default null,
lipo double precision default null,
hb double precision default null,
clash double precision default null,
metal double precision default null
);

Table indices

plp_total_idx on dockscore_plp (total);

oechemscore_total_idx on dockscore_oechemscore (total);

shapegauss_total_idx on dockscore_shapegauss (total);

chemgauss3_total_idx on dockscore_chemgauss3 (total);