PLDbench allows user to calculate RMSD value between two molecules. This webserver consist of four modules. SINGLE, this module is restricted to calculate RMSD for the 57 complexes that have been used for the benchmarking study. In this module users need to upload the docked pose of a ligand corresponding to one of the 57 PDBIDs that have been provided in drop down menu. It supports three file format i.e.,PDB,MOL2,SDF. Users can select which kind of RMSD they want to calculate. Here, this module is capable in calculating Standard heavy-atom RMSD, Hungarian (symmetry-corrected) heavy-atom RMSD and Minimum-distance heavy-atom RMSD. By default it gives Hungarian (symmetry-corrected) heavy-atom RMSD value as a result.
BENCHMARK Using this module users can perform a benchmark analysis on a set of docked poses given in archived zip or tar file format. Users can uload a zip file for diffrent poses of a ligand obtained after docking in a specified format. The name of ligand in archive file should be in following format: " PDBID_CHAIN.predictedligand.mol2 " (Ex. 1XW7_C.predictedligand.mol2).
COMPARE module has been developed for the calculation of RMSD value between the original pose of a ligand and the pose obtained after docking.In order to calculate RMSD, users need to upload original and docked pose of a ligand in any of these three file format i.e.,PDB,MOL2,SDF. By submitting users will get the RMSD value between given two molecules.
We allow users to download datasets that we have used for the benchmarking study. Datasets section allows us to download zip file of Receptor, Crystal ligands, Minimized ligands and CCD ligands. In addition, for the convenience of users we have provided the steps that we have used in order to perform docking.
Molecular Docking Methods Used in Benchmarking Study
AutoDock: AutoDock is one of the most cited and commonly used docking program in the scientific community. For the prediction of preferred conformation of a ligand to a receptor when they bind to form a complex, AutoDock uses Lamarckian genetic algorithm (LGA). Its scoring function incorporates van der Waals, electrostatic, hydrogen bonding and desolvation terms. (Steps of AutoDock. )
AutoDock Vina: AutoDock Vina is developed by the same lab which developed AutoDock. In comparison to AutoDock 4, it is more accurate in prediction of binding mode of a ligand within active site of a receptor.It uses the PDBQT file format for liagand and receptor which is used by AutoDock. (Steps of AutoDock Vina.)
DOCK 6: DOCK 6 was developed by the Kuntz group in 1982 at UCSF. It tries to geometrically match the ligand atoms within the receptor binding site usig incremental construction approach. It uses the energy-based scoring function as well as a grid-based footprint scoring function which is used in rescoring the poses after docking. (Steps of DOCK 6.)
PLANTS: PLANTS (Protein-Ligand ANT System), a new docking method, is based on ant colony optimization (ACO) algorithm. It inherits the behavior of real ants finding the shortest path between their nest and a food source into finding the best docking solution for a ligand. In the case of molecular docking, an artificial ant colony is used to find minimum energy conformation of a ligand in the binding site. (Steps of PLANTS.)
rDock: rDock is originated from a program called RiboDock, developed for virtual screening of RNA targets. It uses stochastic as well as deterministic search techniques implementing genetic algorithm, Monte Carlo and simplex minimization stages for searching conformational space. The scoring function of rDock includes intermolecular terms like van der Waals forces and polar desolvation. rDock consist of two main programs rbcavity for the cavity generation and rbdock for the docking. (Steps of rDock.)
GEMDOCK: Generic Evolutionary Method for molecular DOCking (GEMDOCK) uses global as well as local search strategies to search for the conformational space of the ligand and uses empirical scoring function to score the generated poses. The scoring function of GEMDOCK uses energy parameters like steric, electrostatic and hydrogen bonding potentials. (steps of GEMDOCK.)
GOLD: Genetic Optimization for Ligand Docking (GOLD) is one of the very popular molecular docking tool. In order to predict the possible conformation of a ligand into the active site of receptor it applies genetic algorithm. GOLD works on the basis of a fundamental requirement that the ligand molecule should have the capability to displace water molecules which are loosely bound to the receptor. (Steps of GOLD.)
Steps to perform Docking:
Preparation of receptor: python bin/prepare_receptor4.py -r recep.pdb -A hydrogens -o protein.pdbqt
Preparation of ligand: python bin/prepare_ligand4.py -l lig.pdb -A hydrogens -o ligand.pdbqt
Preparation of grid parameter file: python bin/prepare_gpf4.py -l ligand.pdbqt -r protein.pdbqt -p npts="40,40,40" -p gridcenter='$x,$y,$z'* -o protein.gpf
Preparation of docking parameter file: python bin/prepare_dpf4.py -l ligand.pdbqt -r protein.pdbqt -o protein.dpf -p ga_run=30
Run Autogrid: ./autogrid4 -p protein.gpf -l protein.glg
Run Autodock: ./autodock4 -p protein.dpf -l protein.dlg
NOTE: $x,$y,$z are the coordinates for center of mass of a ligand. For the center of mass for all 57 PDBIDs click on gridcenter.Whereas, here npts="40,40,40" defines the grid size for docking area.
[ Here, you can download all of the poses generated by autodock for all 57 PDBIDs Download ] Go to Top
"bin/vina --receptor protein.pdbqt --ligand ligand.pdbqt --size_x 40 --size_y 40 --size_z 40 --center_x $x --center_y $y --center_z $z --num_modes 30 --cpu 10 > result.txt"
NOTE: $x,$y,$z are the coordinates for center of mass of a ligand. For the center of mass for all 57 PDBIDs click on gridcenter.
[ Here, you can download all of the poses generated by AutoDock Vina for all 57 PDBIDs Download ] Go to Top
Dock 6 takes mol2 file format of ligand,so its foremost step is to convert your ligand file into mol2 file format.
obabel -ipdb lig.pdb -omol2 -O lig.mol2
Path of dms/bin/dms rec.pdb -a -n -w 1.4 -o rec.ms
/dock6/bin/sphgen
/dock6/bin/sphere_selector rec.sph lig.mol2 10
/dock6/bin/showbox < box.in
/dock6/bin/grid -i grid.in
/dock6/bin/dock6 -i rigid.in
[ Here, you can download all of the poses generated by DOCK 6 for all 57 PDBIDs Download ] Go to Top
"./PLANTS1.2_64bit --mode screen config.txt"
[ Here, you can download all of the poses generated by PLANTS for all 57 PDBIDs Download ] Go to Top
rbcavity -was -d -r input.prm
rbdock -i ligand.sd -o out -r input.prm -p dock.prm -n 30 allH
[ Here, you can download all of the poses generated by rDock for all 57 PDBIDs Download ] Go to Top
[ Here, you can download all of the poses generated by GEMDOCK for all 57 PDBIDs Download ] Go to Top
[ Here, you can download all of the poses generated by GOLD for all 57 PDBIDs Download ] Go to Top