Features of Molecular Docking Server

You can

start single molecular docking calculations or high-throughput virtual screening with few clicks
carry out focused docking to a known binding site
carry out blind docking experiments to determine possible binding site(s)
calculate inhibition constants, binding geometry, secondary interactions & much more
prepare publication quality figures and a method section for your reports automatically
organize proteins and ligands into user-defined libraries
carry out molecular docking on-line

Steps of ligand docking

STEP 1 – Preparation of ligands

Draw your ligands using a Java applet, upload a single ligand file or multiple ligands.
Draw chemical structures by MarvinSketch, a Java based program with a constantly growing list of editing features and a number of templates to make molecule drawing simpler.
Upload a ligand in MDL MOL, SYBYL MOL2, PDB, HYPERCHEM HIN or SMILES format.
Upload multiple ligands in SDF format.
You can set various parameters during the simulation such as desired pH, structure optimization and partial charge calculations using molecular mechanics or semiempirical quantumchemical methods.
Set up rotatable bonds and atom types automatically or modify manually.
Download the attached files in several file formats including mol, pdb, mol2 and pdbqt.
Organize your ligands into self-defined folders. This way the ligands are saved for later docking calculations.

STEP 2 – Preparation of proteins

Upload protein structures from your files or download them from the Protein Data Bank using Docking Server by providing the entry code or by text search.
Select the protein chain, heteroatoms, ligands and waters present in the protein pdb file that you want to be included in docking calculation in the process of protein setup.
Setup the simulation box using one of the following ways:
- select known binding site through a co-crystallized ligand
- select the center of mass of the protein
- select the coordinates of the box center
- select amino acid residues that define the binding site
Molecular Docking Server calculates necessary map files for each atom type and prepares the input files for docking calculations.

STEP 3 – Setup ligand protein docking calculations

Select a protein and a ligand from your library.
Modify advanced parameters during the simulation, such as number of runs, number of evaluations etc.

STEP 4 – Evalution of results