Directory of in silico Drug Design tools - FAQ

More information can be found on Click2Drug, which provides a comprehensive list of computer-aided drug design
software and web services, both for structure-based and ligand-based calculations.

This article has been translated into Serbo-Croatian language by Jovana Milutinovich and into French by Kate Bonderava.

I need to draw rapidly the chemical structure of a compound.

Several web services are available for that, like ChemWriter, jsMolEditor, the Marvin molecule editor and viewer and the Molinspiration WebME Molecule Editor.

I have the SMILES of a molecule and would like to know to which molecule it corresponds, or get a drawing of it.

You can use the Smi2Depict web service to do draw the chemical structure of your molecule from a SMILES. You can also see it in 3D using the Corina online demo.

I have a molecule file in one format, but would like to convert it into another format.

You can use the E-Babel web servive.

I would like to generate several possible conformers of my molecule.

You can use Frog2 or e-LEA3D for this.

I have a small molecule, and would like to know to which protein it might bind.

The TarFisDock web service tries to answer this question using reverse docking. The PharmMapper service does it using a pharmacophore mapping approach.

I have a small molecule, and would like to find similar ones.

This can be done using the Superimposé web service.

Is it possible to predict the binding sites on my protein?

This can be done online using the 3DLigandSite and PASS web services.

I would like to dock a molecule into a protein binding site.

Several web services are available for that like SwissDock, Pardock and MetaDock, which are free for academic users, and DockingServer, which is free for academic users for a limited number of dockings per day.

I have a protein, and would like to perform an extensive virtual screening of small molecules on it.

This can be done using the Blaster web service.

I need to perform some structure-based calculations, but there is no experimental structure for my protein. How can I obtain a structural model of my protein?

The homology model of your protein might have been already calculated and may be available in the SWISS-MODEL Repository or at ModBase. Otherwise, you can calculate the homology model using the SWISS-MODEL web service.

I need to perform Molecular Mechanics calculations on a protein-ligand complex, but I don't have parameters for the small molecule.

You can use the SwissParam web service to get parameters and topologies for small organic molecules, for use with CHARMM and GROMACS. Dundee PRODRG2 Server also provides topology and parameters for GROMACS.

I need to perform Molecular Mechanics calculations on a protein, but don't know how to setup the system.

You can use the web service to setup a protein for use with CHARMM.

How can I estimate the affinity of a small molecule for a protein?

Several web services are available, like DrugScoreONLINE, and the BAPPL server or BAPPL-Z server. The latter can be used for Zinc-based proteins.

How can I design a ligand of a protein, based on the 3D structure of the binding site?

Scaffold-hopping can be performed online using the e-LEA3D web service.

I would like to calculate physico-chemical parameters and descriptors of several small molecules to perform QSAR calculations.

This can be performed using the MolInfo and E-Dragon web services.

How can I estimate the logP value of my molecule?

the web service ALOGPS estimates logP values using several different approaches. Other web services are alos available, like XScore-LogP.

Can I estimate the toxicity of a small molecule?

You can do this using VirtualToxLab, the OSIRIS Property Explorer, ADME-Tox and Lazar

Can I estimate ADME parameters of a small molecule?

You can do this using ALOGPS, the OSIRIS Property Explorer, the MODEL - Molecular Descriptor Lab and the Free ADME Tools web services.