Flexible ligand docking to poteins, in silico screening and results clustering

VcPpt is an independently developed extension for Vina, a program for flexible ligand docking under Windows OS

Carry out high-throughput screening of compound libraries with Vina and cluster resulting PDB files of ligands by binding energies and by binding positions. Results processing functions do not require Vina installed. Screening scale is unlimited.

Note that grid parameters are automatically computed at step 1 to cover the entire Protease.pdbqt. Optionally (for advanced users) - to focus fitting on a specific protein pocket - enter the x, y, z manually.

At step 3, any number of ligands (100,000 ? - sure) can be drag-dropped for automatic screening.

"Grid box" is a selection of 3D space around the protein.
Ligands are being moved and docked only within constraints of this 3D box.
Box center = "grid center", box size = "grid size".

Docking or screening with VcPpt can be set up in four mouse moves:

Kinase inhibitor docked into a kinase active site

How good can docking predictions be? See this calculation vs a real Xray structure:

"not bad at all" result thanks to the algorithm in vina.exe

For more information on VINA, pdbqt and on how to convert PDB, mol, SMILES
or other files to pdbqt, please visit MGL tools web site and read our formats page.

Search keywords
drug discovery, drug targeting, medicine, biomedicine, pharmacology software,
drug development, small molecule inhibitors