LIGIN
This page contains additional information that belongs to the article:
Sobolev, V., Wade, R.C., Vriend, G. & Edelman, M. Molecular docking
using surface complementarity, PROTEINS, 25, 120-129 (1996) and
illustrates ability of our approach in prediction of structure of
ligand-receptor complexes. This approach is based on information about
the molecular shape and chemical nature of the atoms of the interacting
molecules.
If you want to get graphics, you should put:
chemical/x-pdb; rasmol -pdb %s
in your .mailcap file. Also, make sure that rasmol is in your path.
You can also look at the results of LIGIN's
participation in CASP2.
Results of docking procedure using holo-protein coordinates
The crystallographical coordinats of holo-proteins with ligand in their
binding site (but with all other cofactors removed). In these files the
docked ligand with the best complementarity is included.
- view or get Dihydrofolate reductase (4dfr PDB file) complexed with methotrexate
- view or get Dihydrofolate reductase (3dfr PDB file) complexed with methotrexate
- view or get Aconitase (7acn PDB file) complexed with isocitrate
- view or get Thermolysin (1tlp PDB file) complexed with phosphoramidon
- view or get Thermolysin (2tmn PDB file) complexed with N-phosphoryl-*L-leucinamide
- view or get Penicillopepsin (1ppm PDB file) complexed with CBZ-Ala-Ala-Leu(P)-(O)Phe-OMe
- view or get Carbonic anhydrase II (1cim PDB file) complexed with PTS inhibitor
- view or get HIV-I protease (4hvp PDB file) complexed with MVT-101 inhibitor
- view or get Adipocyte lipid-binding protein (1lif PDB file) complexed with stearic acid
- view or get Retinol binding protein (1erb PDB file) complexed with N-ethyl retinamide
- view or get Ricin (1fmp PDB file) complexed with formycin-5'-monophosphate
- view or get Met holo-repressor (1cmc PDB file) complexed with corepressor
- view or get Streptavidin (1stp PDB file) complexed with biotin
The crystallographical coordinats of holo-proteins with ligand in their
binding site (but with all other cofactors removed). In these files the
docked ligand with the second best complementarity is included.
- view or get Dihydrofolate reductase (4dfr PDB file) complexed with methotrexate
- view or get Dihydrofolate reductase (3dfr PDB file) complexed with methotrexate
- view or get Aconitase (7acn PDB file) complexed with isocitrate
- view or get Thermolysin (1tlp PDB file) complexed with phosphoramidon
- view or get Thermolysin (2tmn PDB file) complexed with N-phosphoryl-*L-leucinamide
- view or get Penicillopepsin (1ppm PDB file) complexed with CBZ-Ala-Ala-Leu(P)-(O)Phe-OMe
- view or get Carbonic anhydrase II (1cim PDB file) complexed with PTS inhibitor
- view or get HIV-I protease (4hvp PDB file) complexed with MVT-101 inhibitor
- view or get Adipocyte lipid-binding protein (1lif PDB file) complexed with stearic acid
- view or get Retinol binding protein (1erb PDB file) complexed with N-ethyl retinamide
- view or get Ricin (1fmp PDB file) complexed with formycin-5'-monophosphate
- view or get Met holo-repressor (1cmc PDB file) complexed with corepressor
- view or get Streptavidin (1stp PDB file) complexed with biotin
Crystallographical coordinats of holo-proteins (dihydrofolate reductase)
with the ligand (methotrexate) and NADPH in the binding site (3dfr PDB
file). There are also coordinates of the ligand in the positions with the
best and second best complementarity, respectively.
- view or get Complex with best complementarity.
- view or get Complex with second best complementarity.
Results of docking procedure using apo-protein coordinates
Crystallographical coordinats of apo-, holo-proteins and ligand plus docked
ligand in position with best complementarity.
- view or get Adopocyte lipid-binding protein (1lib and 1lif PDB files) with stearic acid
- view or get Retinol binding protein (1hbq and 1erb PDB files) with N-ethyl retinamide
- view or get Ricin (2aai and 1fmp PDB files) with formycin-5'-monophosphate
Crystallographical coordinats of apo-, holo-proteins and ligand plus docked
ligand in position with second best complementarity.
- view or get Adopocyte lipid-binding protein (1lib and 1lif PDB files) with stearic acid
- view or get Retinol binding protein (1hbq and 1erb PDB files) with N-ethyl retinamide
- view or get Ricin (2aai and 1fmp PDB files) with formycin-5'-monophosphate
Crystallographical coordinats of apo-, holo-proteins and ligand plus docked
ligand in position with third best complementarity.
- view or get Ricin (2aai and 1fmp PDB files) with formycin-5'-monophosphate
Crystallographical coordinates of holo-protein (met repressor from
1cmc PDB file) with the ligand (corepressor s-adenosylmethionine)
in the binding site (without any other cofactors). Before ligand
docking into the apo-protein its coordinates (from 1cmb PDB file)
have been changed by superposition (using WHATIF software) with
coordinates of holo-form. The docked positions with best and second
best complementarity are given.
- view or get Complex with best complementarity.
- view or get Complex with second best complementarity.
Illustration of ability of the LIGIN software to make analysis of
ligand-receptor complexes
Lists of residues in contact and of putative H-bonds for complex
of HIV-1 protease with MVT-101 inhibitor (4dfr PDB file) in docked structure.
List of prediction of changes of normalized complementarity upon
ligand atom substitution in streptavidin - biotin complex (1stp PDB file) in
docked position.
Distribution
Distribution conditions
The LIGIN program is available without charge to academic users directly from
V. Sobolev. Comercial users should contact Yeda Corp. (Yeda Inc., Weizmann
Institute of Science, Rehovot, 76100, ISRAEL). The LIGIN program is also
available as part of the WHATIF software package (subject to the conditions
therein).
How to obtain the source
The LIGIN program for UNIX Workstations can be obtained via FTP. Send E-mail
to
lpsobol@weizmann.weizmann.ac.il for instructions
Program documentation
The LIGIN program writeup describes how to use the program.