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MolDyn |
NOTE!!
To perform docking of Ligand on Protein, one need
1) PDB file prot_Lig_Complex.pdb. The file define protein structure and Ligand initial structure.
Ligand can be near from protein surface, i.e. in contact in abbitrary position and orientation.
2) The Ligand molecular topology should be described in
~/dat/bs_lig_all94.dat file
according to general rule, see examples for TEST#1 - TEST#8
It includes CONNECTIVITY, ATOM NAMES =(equivalent to PDB), ATOM ForcrField CODE according to AMBER94 FF,
ATOMIC CHARGES.
PROCEDURE to automatically generate LIG_TOPO file from LIG.pdb file in PREPARATION.
The bs_lig_all94.dat file includes topology data for 12 Ligands.
!Note, that Ligands of peptide nature (i.e. short peptides) or oligonucleotides DO NOT NEED any topology data,
These LIGANDS will use the PREEXISTED topology for PRotein RESidues and NUcleic acid RESidues.
*************************************************************************************************
Directory ./tLg shows examples of Ligand Docking on peptides:
#
# DOCK TEST#1
./1bty - trypsine-benzamidine complex
1bty.ben.Native.pdb - protein-lig complex with NATIVE binding mode for Ligand
1bty.ben.notNative.pdb - protein-lig complex with notNATIVE (arbitryry) mode for Ligand
the both files can be used as inPDB file
#
#Run the mDyn program:
> $MDYN09HOME/mDynQ09 -c 1bty.P.pdb -cL ben.notNative.pdb -i MdynPar_1bty.inp -sa SAprotocol_long.inp -mn 1bty -o 1bty.out
#
UNDESTANDING DOCKING RESULTS:
1) file 1bty.bSiteAtOnSAS00.pdb shows positions of binding site candidates
on the protein surface
#LigBindGridOnSAS:
ATOM 1 LBSt 1 16.536 26.130 8.764 11
ATOM 2 LBSt 2 29.319 14.972 16.378 11
ATOM 3 LBSt 3 6.595 15.454 32.366 9
ATOM 4 LBSt 4 28.049 26.396 3.572 9
ATOM 5 LBSt 5 37.370 14.662 29.278 8
ATOM 6 LBSt 6 9.605 28.662 39.481 7
ATOM 7 LBSt 7 18.280 35.574 15.402 7
ATOM 8 LBSt 8 30.648 34.679 44.060 7
ATOM 9 LBSt 9 34.040 33.767 21.484 7
ATOM 10 LBSt 10 5.056 19.922 18.987 6
ATOM 11 LBSt 11 25.308 5.865 13.437 6
ATOM 12 LBSt 12 13.241 31.812 30.019 6
...
ATOM 40 LBSt 40 25.260 6.929 29.909 4
ATOM 41 LBSt 41 26.781 13.047 43.008 4
Docking alhorithm put ligand center into this positions with SCore >= 6
and refine ligand orientation and conformation
via semiglobal optimization by Simulated annealing coupled with protein-Ligand force field deformation.
#
The resulting ligand positions are collected in the files :
1bty.LigDockFin000.001.pdb
1bty.LigDockFin000.002.pdb
1bty.LigDockFin000.003.pdb
1bty.LigDockFin001.001.pdb
1bty.LigDockFin001.002.pdb
1bty.LigDockFin001.003.pdb
...
1bty.LigDockFin015.003.pdb
#
File 1bty.LigDockFin.ePL.res :
collects the refined total Potential energy of internal Lig-Lig + Lig-Prot
interactions for final Ligand Docking modes from
files 1bty.LigDockFin*.pdb
#
NN LigDockFinXXX.XXX.pdb ePLtot eVDW eCoul eHb eSolv eGeo tempTAv
1 ./LigDockFin001.001.pdb -24.3 -11.6 -0.6 -9.4 -6.9 4.3 50.2
2 ./LigDockFin001.002.pdb -24.2 -11.0 -1.2 -9.8 -6.8 4.6 50.2
3 ./LigDockFin001.003.pdb -24.0 -10.7 -1.3 -9.6 -6.9 4.5 50.2
4 ./LigDockFin002.001.pdb -39.3 -20.7 -6.2 -11.0 -4.5 3.1 51.8 - best RMSD mode
5 ./LigDockFin002.002.pdb -39.3 -20.6 -6.1 -12.8 -4.5 4.8 51.8
6 ./LigDockFin002.003.pdb -39.1 -20.7 -7.0 -10.3 -4.5 3.4 51.8
7 ./LigDockFin003.001.pdb -18.6 -1.2 -2.5 -9.4 -6.8 1.3 46.5
8 ./LigDockFin003.002.pdb -17.7 -2.4 -1.6 -9.6 -6.5 2.5 46.5
9 ./LigDockFin003.003.pdb -17.7 -2.1 -2.7 -9.7 -6.7 3.6 46.5
10 ./LigDockFin004.001.pdb -27.8 -4.5 -7.6 -9.9 -7.5 1.7 51.0
11 ./LigDockFin004.002.pdb -27.7 -5.6 -7.5 -9.6 -7.4 2.4 51.0
12 ./LigDockFin004.003.pdb -27.7 -5.4 -7.3 -9.9 -7.4 2.3 51.0
13 ./LigDockFin005.001.pdb -30.1 -10.8 -5.6 -9.6 -6.3 2.2 48.5
14 ./LigDockFin005.002.pdb -29.8 -11.6 -5.2 -9.5 -6.3 2.8 48.5
15 ./LigDockFin005.003.pdb -29.6 -12.4 -4.5 -9.5 -6.3 3.1 48.5
16 ./LigDockFin006.001.pdb -22.7 -9.0 -1.5 -9.5 -6.3 3.5 50.4
17 ./LigDockFin006.002.pdb -22.5 -8.6 -1.6 -9.4 -6.4 3.5 50.4
18 ./LigDockFin006.003.pdb -22.5 -7.9 -2.1 -9.3 -6.1 3.0 50.4
#
****************************************************************
#
# DOCK TEST#2
alpha-thrombin/bemzamidine complex : 1dwb
#
#Run the mDyn program:
> $MDYN09HOME/mDynQ09 -c 1dwb.P.pdb -cL ben.notNative.pdb -i MdynPar_1dwb.inp -sa SAprotocol_long.inp -mn 1dwb -o
1dwb.out
#
file 1dwb.LigDockFin.ePL.res: - total potential energy of Lig-Lig + Lig-Prot interactions:
#
NN LigDockFinXXX.XXX.pdb ePLtot eVDW eCoul eHb eSolv eGeo tempTAv
1 1dwb.LigDockFin001.001. -43.7 -16.6 -11.6 -13.9 -5.5 3.9 47.4 - best docking mode
2 1dwb.LigDockFin001.002. -43.3 -16.5 -11.0 -14.3 -5.5 4.0 47.4 -best docking mode
3 1dwb.LigDockFin001.003. -43.3 -17.1 -10.7 -14.1 -5.5 4.1 47.4 - best docking mode
4 1dwb.LigDockFin002.001. -25.2 -8.2 -2.9 -9.7 -7.7 3.4 48.4
5 1dwb.LigDockFin002.002. -24.9 -8.3 -3.4 -9.6 -7.7 4.0 48.4
6 1dwb.LigDockFin002.003. -24.6 -7.4 -3.4 -9.8 -7.6 3.6 48.4
7 1dwb.LigDockFin003.001. -31.6 -10.7 -6.1 -10.9 -7.1 3.2 50.1
8 1dwb.LigDockFin003.002. -31.2 -9.9 -6.3 -11.1 -6.9 2.9 50.1
9 1dwb.LigDockFin003.003. -31.2 -11.1 -5.8 -10.4 -7.0 3.1 50.1
10 1dwb.LigDockFin004.001. -20.2 -9.0 -2.1 -7.9 -5.6 4.4 50.4
11 1dwb.LigDockFin004.002. -19.7 -8.3 -2.2 -8.1 -5.7 4.5 50.4
12 1dwb.LigDockFin004.003. -19.4 -9.0 -2.3 -8.0 -5.7 5.5 50.4
13 1dwb.LigDockFin005.001. -29.9 -4.5 -9.4 -9.9 -8.3 2.2 52.1
14 1dwb.LigDockFin005.002. -29.9 -8.9 -10.7 -11.8 -9.0 10.5 52.1
15 1dwb.LigDockFin005.003. -29.8 -10.7 -6.4 -7.1 -9.0 3.4 52.1
16 1dwb.LigDockFin006.001. -21.9 -5.9 -2.0 -9.4 -7.3 2.7 51.3
17 1dwb.LigDockFin006.002. -21.8 -7.3 -1.7 -9.1 -7.2 3.5 51.3
18 1dwb.LigDockFin006.003. -21.7 -6.3 -2.4 -9.5 -7.2 3.6 51.3
19 1dwb.LigDockFin007.001. -23.7 -8.4 -1.2 -9.5 -7.8 3.2 49.4
20 1dwb.LigDockFin007.002. -23.6 -8.2 -1.8 -9.2 -7.8 3.3 49.4
21 1dwb.LigDockFin007.003. -23.1 -7.9 -2.1 -9.5 -7.6 4.0 49.4
..
***************************************************************************************
#DOCK TEST#3
./1dwc - alpha-Thrombin/MIT ligand complex
#
#Run the mDyn program:
> $MDYN09HOME/mDynQ09 -c 1dwc.P.pdb -cL 1dwc.Lig.pdb -i MdynPar_d21.inp -sa SAprotocol_long.inp -mn 1dwc -o
1dwc.out
#
Docking result potential energy file:
1dwc.ePL.LigDockFin.res:
#
NN LigDockFinXXX.XXX.pdb ePLtot eVDW eCoul eHb eSolv eGeo tempTAv
1 1dwc.LigDockFin001.001. -64.5 -45.0 -14.3 -20.9 -17.5 33.3 49.7 - best eP_mode
2 1dwc.LigDockFin001.002. -61.2 -42.9 -16.0 -22.3 -14.7 34.7 49.7 - best rmsd_mode
3 1dwc.LigDockFin001.003. -52.8 -33.9 -15.4 -22.3 -24.3 43.0 49.7
4 1dwc.LigDockFin002.001. -53.7 -35.1 -10.4 -24.2 -23.2 39.3 50.7
5 1dwc.LigDockFin002.002. -49.9 -30.1 -16.1 -21.7 -23.6 41.7 50.7
6 1dwc.LigDockFin002.003. -44.6 -29.8 -10.3 -22.1 -21.5 39.1 50.7
7 1dwc.LigDockFin003.001. 338.3 194.2 5.7 -4.2 -13.8 156.4 53.1
8 1dwc.LigDockFin003.002. 340.4 230.8 -12.9 -19.3 -15.6 157.4 53.1
9 1dwc.LigDockFin003.003. 368.8 224.5 -2.5 -10.8 -13.3 170.9 53.1
10 1dwc.LigDockFin004.001. -49.8 -34.1 -13.2 -24.9 -14.4 36.8 50.5
11 1dwc.LigDockFin004.002. -48.6 -26.5 -13.2 -27.2 -14.5 32.8 50.5
12 1dwc.LigDockFin004.003. -47.2 -27.0 -16.5 -27.6 -12.1 36.1 50.5
13 1dwc.LigDockFin005.001. 165.1 81.5 -2.2 -13.8 -19.8 119.4 52.8
14 1dwc.LigDockFin005.002. 290.1 183.9 -8.2 -13.1 -11.4 138.8 52.8
15 1dwc.LigDockFin005.003. 303.4 147.8 2.2 -8.3 -17.0 178.7 52.8
16 1dwc.LigDockFin006.001. -58.5 -37.5 -15.3 -18.4 -25.9 38.6 47.6
17 1dwc.LigDockFin006.002. -58.4 -37.1 -17.6 -25.7 -21.6 43.6 47.6
18 1dwc.LigDockFin006.003. -57.2 -30.6 -16.8 -18.6 -26.7 35.6 47.6
19 1dwc.LigDockFin007.001. -58.9 -26.3 -26.3 -29.3 -19.0 42.0 49.0
20 1dwc.LigDockFin007.002. -57.6 -26.6 -21.5 -24.0 -20.4 35.0 49.0
21 1dwc.LigDockFin007.003. -57.3 -28.2 -21.7 -24.5 -19.3 36.3 49.0
...
****************************************************************************************
#
DOCK TEST#4
./1stp : complex streptavidine/biotin
#
#Run the mDyn program:
> $MDYN09HOME/mDynQ09 -c 1stp.P.pdb -cL 1stp.btn.Lig.pdb -i MdynPar_d21.inp -sa SAprotocol_long.inp -mn 1stp -o
1stp.out
Docking result potential energy file:
1stp.LigDockFin.ePL.res
#
NN LigDockFinXXX.XXX.pdb ePLtot eVDW eCoul eHb eSolv eGeo tempTAv
1 1stp.LigDockFin001.001. -56.1 -35.0 -12.9 -25.5 -8.0 25.4 49.4 - best eP_mode/rmsd_mode
2 1stp.LigDockFin001.002. -55.7 -34.5 -13.4 -25.3 -7.7 25.2 49.4
3 1stp.LigDockFin001.003. -55.7 -33.8 -13.9 -25.6 -7.8 25.4 49.4
4 1stp.LigDockFin002.001. -19.5 -21.3 -5.0 -8.6 -10.3 25.7 50.8
5 1stp.LigDockFin002.002. -18.5 -26.3 -4.6 -8.6 -7.5 28.5 50.8
6 1stp.LigDockFin002.003. -17.5 -20.7 -6.5 -9.5 -11.0 30.3 50.8
7 1stp.LigDockFin003.001. -19.9 -16.5 -9.4 -14.4 -10.2 30.6 50.6
8 1stp.LigDockFin003.002. -19.7 -19.5 -10.2 -14.6 -5.8 30.3 50.6
9 1stp.LigDockFin003.003. -19.3 -19.1 -8.5 -13.8 -6.3 28.5 50.6
10 1stp.LigDockFin004.001. -11.7 -12.3 -6.4 -9.5 -9.3 25.8 51.0
11 1stp.LigDockFin004.002. -11.6 -14.5 -4.3 -9.8 -10.2 27.2 51.0
12 1stp.LigDockFin004.003. -10.3 -12.8 -5.5 -9.6 -8.9 26.5 51.0
13 1stp.LigDockFin005.001. -12.9 -14.9 -7.7 -9.8 -6.9 26.3 51.1
14 1stp.LigDockFin005.002. -12.8 -16.8 -5.1 -4.9 -11.0 25.2 51.1
15 1stp.LigDockFin005.003. -11.0 -13.1 -9.3 -8.7 -7.2 27.3 51.1
16 1stp.LigDockFin006.001. -26.2 -17.1 -15.3 -18.3 -2.5 27.1 49.4
17 1stp.LigDockFin006.002. -26.2 -17.2 -15.4 -18.4 -2.6 27.3 49.4
18 1stp.LigDockFin006.003. -23.0 -17.9 -13.3 -14.9 -3.9 26.9 49.4
19 1stp.LigDockFin007.001. -30.4 -16.2 -17.2 -27.9 0.2 30.8 47.0
20 1stp.LigDockFin007.002. -29.2 -12.6 -18.3 -28.0 1.3 28.4 47.0
21 1stp.LigDockFin007.003. -28.1 -15.0 -18.5 -22.6 -0.2 28.2 47.0
..
NOTE!: three mode 1stp.LigDockFin001.001.pdb
1stp.LigDockFin001.002.pdb
1stp.LigDockFin001.003.pdb
are found by MD SA optimization from different initial orientations of the ligand
****************************************************************************************
#
#DOCK TEST#5
./3tpi : complex Trypsinogen/ILE-VAL dipeptide
#
#Run the mDyn program:
> $MDYN09HOME/mDynQ09 -c 3tpi.IV.Prot.pdb -cL 3tpi.IV.notNative.pdb -i MdynPar_d21.inp -sa SAprotocol_long.inp -mn 3tpi -o 3tpi.out
#
Docking result potential energy file:
3tpi.LigDockFin.ePL.res:
#
NN LigDockFinXXX.XXX.pdb ePLtot eVDW eCoul eHb eSolv eGeo tempTAv
1 3tpi.LigDockFin001.001. -80.1 -36.5 -24.1 -22.3 -10.1 12.8 51.7
2 3tpi.LigDockFin001.002. -79.8 -35.0 -23.8 -21.4 -10.6 11.0 51.7
3 3tpi.LigDockFin001.003. -77.7 -34.5 -24.2 -22.5 -10.3 13.9 51.7
4 3tpi.LigDockFin002.001. -47.9 -20.2 -13.8 -17.7 -4.8 8.5 51.9
5 3tpi.LigDockFin002.002. -45.9 -20.4 -17.1 -16.9 -4.0 12.5 51.9
6 3tpi.LigDockFin002.003. -44.1 -15.2 -19.0 -17.4 -3.4 11.0 51.9
7 3tpi.LigDockFin003.001. -54.0 -16.8 -21.2 -21.0 -6.5 11.5 49.1
8 3tpi.LigDockFin003.002. -53.9 -17.3 -21.0 -20.9 -6.4 11.7 49.1
9 3tpi.LigDockFin003.003. -52.8 -17.7 -20.5 -18.7 -5.6 9.7 49.1
10 3tpi.LigDockFin004.001. -81.8 -35.4 -24.5 -22.1 -10.5 10.7 50.4 best eP_mode/rmsd_mode
11 3tpi.LigDockFin004.002. -80.9 -36.4 -24.2 -22.4 -10.5 12.7 50.4 best eP_mode/rmsd_mode
12 3tpi.LigDockFin004.003. -72.0 -39.0 -17.8 -16.9 -10.8 12.5 50.4
13 3tpi.LigDockFin005.001. -40.9 -16.3 -16.4 -19.9 -10.9 22.7 49.4
14 3tpi.LigDockFin005.002. -39.6 -13.3 -16.1 -17.3 -7.8 14.9 49.4
15 3tpi.LigDockFin005.003. -38.3 -15.3 -12.8 -19.4 -1.8 11.0 49.4
16 3tpi.LigDockFin006.001. -43.1 -19.4 -11.1 -15.8 -9.1 12.3 52.0
17 3tpi.LigDockFin006.002. -41.4 -14.3 -9.6 -19.1 -12.4 13.9 52.0
18 3tpi.LigDockFin006.003. -37.9 -13.1 -14.6 -8.6 -9.4 7.9 52.0
19 3tpi.LigDockFin007.001. -41.1 -14.6 -22.9 -18.5 -3.3 18.2 49.0
20 3tpi.LigDockFin007.002. -40.7 -11.4 -23.3 -17.9 -3.4 15.3 49.0
21 3tpi.LigDockFin007.003. -40.0 -12.5 -23.7 -17.7 -2.5 16.5 49.0
...
#
****************************************************************************************
#DOCK TEST#6
./1hvr - complex HIV-1 protease/XK263 ligand : 1hvr PdB code
#
#Run the mDyn program:
> $MDYN09HOME/mDynQ09 -c 1hvr.P.pdb -cL 1hvr.Lig.pdb -i MdynPar_d21.inp -sa SAprotocol_long.inp -mn 1hvr -o 1hvr.out
#
Docking result potential energy file:
1hvr.ePL.LigDockFin.res:
NN LigDockFinXXX.XXX.pdb ePLtot eVDW eCoul eHb eSolv eGeo tempTAv
1 1hvr.LigDockFin001.001. -54.0 -74.9 -13.1 -13.8 9.3 38.5 49.3 best eP_mode/rmsd mode
2 1hvr.LigDockFin001.002. -53.8 -76.0 -14.2 -13.9 9.2 41.1 49.3 best eP_mode/rmsd mode
3 1hvr.LigDockFin001.003. -52.9 -76.6 -12.8 -14.3 9.3 41.5 49.3
4 1hvr.LigDockFin002.001. -16.9 -56.4 -9.8 -11.7 10.0 51.0 48.2
5 1hvr.LigDockFin002.002. -10.4 -37.7 -9.2 -13.7 12.2 37.9 48.2
6 1hvr.LigDockFin002.003. -10.1 -44.5 -9.8 -13.0 12.2 45.1 48.2
7 1hvr.LigDockFin003.001. -24.1 -56.5 -11.2 -9.9 9.2 44.3 49.8
8 1hvr.LigDockFin003.002. -17.9 -57.7 -7.3 -8.7 9.1 46.8 49.8
9 1hvr.LigDockFin003.003. -12.2 -40.8 -9.5 -17.4 12.4 43.1 49.8
10 1hvr.LigDockFin004.001. -3.6 -35.4 -8.1 -9.1 14.6 34.4 49.5
11 1hvr.LigDockFin004.002. -2.7 -33.5 -4.0 -16.5 15.7 35.6 49.5
12 1hvr.LigDockFin004.003. -2.4 -36.0 -9.8 -11.2 14.6 40.0 49.5
13 1hvr.LigDockFin005.001. -2.5 -29.9 -7.8 -9.9 15.4 29.7 50.4
14 1hvr.LigDockFin005.002. -0.8 -38.8 -3.2 -9.1 14.3 35.9 50.4
15 1hvr.LigDockFin005.003. 0.4 -37.4 -4.4 -7.7 14.6 35.4 50.4
16 1hvr.LigDockFin006.001. -6.6 -42.2 -6.4 -10.0 14.0 38.0 49.1
17 1hvr.LigDockFin006.002. -5.8 -35.5 -6.9 -13.0 14.1 35.5 49.1
18 1hvr.LigDockFin006.003. -4.1 -38.7 -5.9 -9.8 14.4 35.9 49.1
19 1hvr.LigDockFin007.001. -3.5 -35.0 -6.1 -13.2 14.0 36.8 50.7
20 1hvr.LigDockFin007.002. -3.2 -35.4 -6.5 -13.2 14.5 37.4 50.7
21 1hvr.LigDockFin007.003. 0.9 -30.9 -5.0 -11.0 14.5 33.3 50.7
...
#
*************************************************************************************
#
#DOCK TEST#7
./4phv
Complex HIV-1 protease with inhibitor VAC : PDB code 4phv
#
#Run the mDyn program:
> $MDYN09HOME/mDynQ09 -c 4phv.P.pdb -cL 4phv.Lig.pdb -i MdynPar_d23.inp -sa SAprotocol_long.inp -mn 4phv -o 4phv.out
#
Docking result potential energy file:
4phv.ePL.LigDockFin.res:
#
N LigDockFinXXX.XXX.pdb ePLtot eVDW eCoul eHb eSolv eGeo tempTAv
1 4phv.LigDockFin001.001. -57.1 -79.5 -12.2 -27.1 4.6 57.0 49.1 best eP_mode/rmsd_mode
2 4phv.LigDockFin001.002. -51.8 -81.4 -16.3 -24.6 4.6 65.9 49.1
3 4phv.LigDockFin001.003. -48.3 -68.8 -17.7 -32.5 6.6 64.1 49.1
4 4phv.LigDockFin002.001. -44.4 -74.5 -10.9 -20.7 6.2 55.4 49.9
5 4phv.LigDockFin002.002. -41.2 -62.0 -15.2 -32.4 6.7 61.8 49.9
6 4phv.LigDockFin002.003. -38.0 -60.6 -16.6 -27.3 6.8 59.7 49.9
7 4phv.LigDockFin003.001. -43.5 -69.4 -15.7 -28.6 6.9 63.2 48.9
8 4phv.LigDockFin003.002. -35.5 -67.0 -15.2 -25.2 7.5 64.4 48.9
9 4phv.LigDockFin003.003. -32.3 -59.6 -15.1 -23.6 7.5 58.5 48.9
10 4phv.LigDockFin004.001. -10.4 -31.4 -16.6 -28.5 14.8 51.3 49.9
11 4phv.LigDockFin004.002. -6.8 -32.0 -14.9 -28.2 14.0 54.4 49.9
12 4phv.LigDockFin004.003. -6.8 -41.0 -15.7 -19.4 11.0 58.3 49.9
13 4phv.LigDockFin005.001. -2.6 -44.5 -4.9 -19.2 11.8 54.1 50.1
14 4phv.LigDockFin005.002. -0.4 -39.1 -10.8 -18.1 13.0 54.5 50.1
15 4phv.LigDockFin005.003. 1.0 -38.3 -9.9 -17.8 13.6 53.5 50.1
16 4phv.LigDockFin006.001. -20.0 -39.4 -20.1 -24.9 13.3 51.1 52.8
17 4phv.LigDockFin006.002. -18.5 -47.1 -12.5 -23.2 10.5 53.8 52.8
18 4phv.LigDockFin006.003. -16.0 -35.0 -19.1 -29.6 13.4 54.1 52.8
19 4phv.LigDockFin007.001. -28.8 -56.6 -13.0 -19.9 9.1 51.6 51.4
20 4phv.LigDockFin007.002. -27.6 -55.7 -15.1 -27.2 7.0 63.4 51.4
21 4phv.LigDockFin007.003. -24.2 -57.9 -10.1 -17.2 8.4 52.7 51.4
...
#
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#DOCK TEST#8
./1hiv
Complex HIV-1 protease with inhibitor NOA Ligand (119 atoms): PDB code 1hiv
#
Docking with option $doLigDock=21 provides a small number (24) initial orientations for Lig and is unsufficient.
Docking with option $doLigDock=23 provides 72 initial Lig orientations and allows to find the same pose for two
different initial orientations.
#
Docking result potential energy file:
1hiv.ePL.DockFin.res:
NN LigDockFinXXX.XXX.pdb ePLtot eVDW eCoul eHb eSolv eGeo tempTAv
1 1hiv.LigDockFin001.001. -84.9 -86.6 -28.0 -41.4 10.4 60.7 51.3 best eP_mode/rmsd
2 1hiv.LigDockFin001.002. -84.6 -91.0 -28.1 -41.3 10.4 65.5 51.3 best eP_mode/rmsd
3 1hiv.LigDockFin001.003. -70.4 -78.5 -29.8 -39.8 7.7 70.0 51.3
4 1hiv.LigDockFin002.001. -78.3 -80.3 -29.0 -40.8 10.9 61.0 50.1
5 1hiv.LigDockFin002.002. -74.1 -82.0 -28.9 -44.6 10.2 71.3 50.1
6 1hiv.LigDockFin002.003. -54.7 -67.2 -26.8 -40.8 12.0 68.1 50.1
7 1hiv.LigDockFin003.001. -15.0 -38.9 -22.9 -24.6 18.4 52.8 50.9
8 1hiv.LigDockFin003.002. -8.9 -37.8 -22.6 -22.9 19.4 55.0 50.9
9 1hiv.LigDockFin003.003. -8.3 -39.9 -19.9 -20.0 19.0 52.5 50.9
10 1hiv.LigDockFin004.001. -24.1 -48.2 -23.7 -32.6 16.3 64.1 49.9
11 1hiv.LigDockFin004.002. -23.9 -47.8 -20.0 -35.7 22.0 57.7 49.9
12 1hiv.LigDockFin004.003. -19.2 -45.8 -22.1 -30.0 17.2 61.5 49.9
13 1hiv.LigDockFin005.001. -18.8 -50.8 -21.0 -24.2 18.1 59.1 50.8
14 1hiv.LigDockFin005.002. -15.7 -42.8 -25.0 -29.7 18.7 63.2 50.8
15 1hiv.LigDockFin005.003. -14.1 -39.7 -23.7 -29.6 18.3 60.6 50.8
16 1hiv.LigDockFin006.001. -38.1 -61.4 -24.1 -28.0 17.4 58.0 50.9
17 1hiv.LigDockFin006.002. -34.9 -62.4 -25.7 -29.8 16.6 66.4 50.9
18 1hiv.LigDockFin006.003. -33.5 -60.3 -23.5 -31.2 15.1 66.3 50.9
19 1hiv.LigDockFin007.001. -40.2 -67.9 -24.6 -31.8 9.8 74.4 50.0
20 1hiv.LigDockFin007.002. -38.3 -75.4 -22.5 -20.7 6.6 73.6 50.0
21 1hiv.LigDockFin007.003. -36.2 -70.3 -20.6 -33.4 8.0 80.1 50.0
22 1hiv.LigDockFin008.001. -16.4 -45.3 -21.6 -22.2 14.7 57.9 51.6
....
34 1hiv.LigDockFin012.001. -84.4 -88.7 -29.7 -40.6 10.4 64.1 51.2 best eP_mode/rmsd
35 1hiv.LigDockFin012.002. -80.4 -84.1 -31.8 -42.1 8.5 69.0 51.2
36 1hiv.LigDockFin012.003. -69.9 -83.3 -31.2 -39.7 9.4 74.9 51.2
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RESUME :
1) all shown test example of docking module successevely find a set of docking modes, i.e. files
LigDockFinXXX.XXX.pdb
2) the mode with minimal potential energy of Protein-Lig interactions in the set of files
LigDockFinXXX.XXX.pdb are the mode close to the respective native ligand structure in the complex.
The RMSD of the best docking mode from the native are withng 1 - 2 A.
3) The current docking method does not guarantee a finding of the best docking solution in the one RUN.
The best docking solution can be obtained by docking with different set of initial Lig orientations
by oprion $doLigDock=21(set24), 22(set144) or 23(set72 orientations)
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