Molecular docking is a method that predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex. It has been used a computational tool in the area of Structure-Based Drug Design (SBDD).
Molecular docking or docking has been widely used to predict the binding orientation of small molecule drug candidates to their protein targets in order to in turn predict the affinity and activity of the small molecule. It therefore plays an important role in SBDD. Full definition can be found in wikipedia:
http://en.wikipedia.org/wiki/Docking_(molecular)
there is a lot of molecular docking software around, free and commercial. basically, there are a few types of docking; ligand-protein docking, ligand-DNA/RNA docking and protein-protein docking. the purpose for all the three types are to predict bound orientation of the complex which will give insights into the affinity and activity of the each molecule at the molecular level; something which is sometime difficult to get from experimental techniques.
1. Autodock.
Autodock was originally developed by Prof. Arthur Olson from Scripp Ins. Later taken over by Dr. Garrett Morris. It has been used in many areas. Many publications can be found using this software. It’s one of the most widely accepted program for docking. The latest version Autodock 4.0 further enhanced it’s capabilities with some features for side chains flexibility of the protein/target making the docking results more accurate/reliable. It uses genetic algorithm and simulated annealing methods with emphasize on free energy calculations.
2. Arguslab.
if you are not comfortable with Linux based softwares such as Autodock but you still would like to do some docking with your set of small molecule/ligand with protein etc., you might want to try Arguslab. It can run on any Windows O/S. It was developed by Dr. Mark Thompson of Planaria Software. I have tried the program. It’s quite heavy on the memory. Well, if you would still like to try (to avoid unnecessary hassle to learn linux/unix). Another good thing about it is that it’s free! here is the link:
3. DOCK.
DOCK is another docking program from UCSF. Originally, DOCK algorithm addressed rigid body docking using geometric matching to superimpose the ligand onto the negative image of the target’s binding pocket. Newer version of the program however, have added new algorithm for flexible ligand docking. There are many publication that can be found using this program. I have no experience using DOCK before, but I believe it can only be use on SGI machines. On the other hand, I have tried Autodock and Arguslab on a PC and it works fine. (It’s free for academic use). Anyway, you can give it a try:
4. DockVision
DockVision is a docking program which runs on Linux/Unix SGI machines. It includes Monte Carlo, Genetic Algorithm, and database screening algorithm in one complete package. The program has a 3D viewer called DockCam 3D that allows you to view your immediate active site in wireframe. It was developed by Steven Ness, Trevor Hart, and Randy Read. The ligand can be set flexible. The target on the other hand is rigid I believe. Its a commercial program. Do check out the program:
5. FlexiDock
FlexiDock is a docking program incorporated in Tripos Biopolymer program. It allows conformational flexibility in both ligand and the receptor. It runs on IRIX/SGI machines and Linux (x86) machines. It uses genetic algorithm for conformational search together with grid-based energy evaluation to score resulting interactions. The scoring function is based on Tripos Force Field. (It’s a commercial software). You can find more information on the link below:
6. FRED
FRED is another commercial docking software from OpenEye Scientific Software. It uses shape complementarity and pharmacophoric features before selecting a single pose based upon a consensus of scoring functions. It uses ChemScore, PBSA (ZAP), ChemGauss, PLP, and ScreenScore scoring functions. It can handle multiple file format such as SMILES, SLN, SDF, MOL, MOL2, PDB, FASTA, MOPAC, MacroModel, XYZ, CCP4, XPLOR, and OEBinary. Another good thing about this program is that it can run on multiple platforms such as Linux, Windows, Mac OS X and many flavors of Unix in both 32 and 64 bit. Do check out the link:
7. FlexX
FlexX is a commercial program develop by BioSolveIT. It claims to be one of the most cited commercial docking software. It has the best enrichment tool in Structure Based Drug Design. It can generate precise poses of lead structures in a protein binding site using it’s SIS-algorithm. It also has the ability to dock gigantic libraries of ~1 000 000 compounds by using ultra high-speed docking (less than 1s for a ligand) in about 8 hours on a 30-node cluster.
The latest version is FlexX 3.1.0 which was released on 15.10.2008. FlexX Release 3 is available for Linux (32bit and 64bit) and Windows platforms. In the latest version, you can do all the set ups and visualize your docking results in a user friendly graphical environment. You can request for a trial copy by registering yourself:
http://www.biosolveit.de/FlexX/
8. GLIDE
GLIDE is a commercial docking program from Schrödinger GmbH. It offers the full spectrum of speed and accuracy from high-throughput virtual screening of millions of compounds to extremely accurate binding mode predictions. The developer of the program claimed that GLIDE performs better compared to GOLD and FlexX when tested with PDB structures:
http://www.imb-jena.de/jcb/ppi/PPI_PDF_free/GlideDataSheet.pdf
They have also tested their program against another well known program (DOCK).
