A blog about free research software, alternative to commercial paid software.

One way to help people is to share your knowledge with those who could benefit from it. As a researcher , constant effort to solve scientific problems have exposed me to various scientific resources that can be accessed free of charge. Especially these knowledge is useful to labs and institution unable to access expensive software or novice users due to lack of expertise. In this blog, I have provided a comprehensive list of freely available softwares, alternative to commercial software. I shall share with you all that I have learned, as I make the changes or learn something new, I shall document them. Hope this blog will help those finding the way………….

Research software and books

Jan 5, 2011

Drug discovery

This is a list of free online servers that can be used in the drug discovery research. Together, with the research software listed in the free software section, these free resources can be be used as an alternative to commercial software. I have included softwares that can be used for specific purposes for eg: docking, as well as many online servers that can do the job. I have also listed a package which can almost do all aspect drug designing Eg:Open Eye. Hope this helps....

Drug designing steps were usually divided into steps as follows:





Ligand preparation:

Ligand preparation can be subdivided into ligand retrieval or collection, liand conversion and ligand analysis.

Ligand retrievel:

This involves retrieving information from various chemical databases .

Drug Bank

The DrugBank database is a unique bioinformatics and cheminformatics research resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information.



ChemBank is intended to guide chemists synthesizing novel compounds or libraries, to assist biologists searching for small molecules that perturb specific biological pathways, and to catalyze the process by which drug hunters discover new and effective medicines.



PubChem provides information on the biological activities of small molecules. It is a component of NIH's Molecular Libraries Roadmap Initiative.


Ligand Expo

Ligand Expo (formerly Ligand Depot) provides chemical and structural information about small molecules within the structure entries of the Protein Data Bank. Tools are provided to search the PDB dictionary for chemical components, to identify structure entries containing particular small molecules, and to download the 3D structures of the small molecule components in the PDB entry.


Ligand conversion tools:


This online server can be used to convert smiles into PDB, SDF, Mol formats and both in 2D and 3D formats.



This tool was used to generate 3D structures in SDF format.



This WWW PRODRG server will convert coordinates for small molecules in PDB format to the following topology formats: GROMOS, GROMACS, WHAT IF, REFMAC5, CNS, O, SHELX, HEX and MOL2. In addition, coordinates for hydrogen atoms are generated. You can now also sketch your small molecule in a simple text editor, and paste this into the window below


Ligand analysis tools:


Molinspiration offers a molecular processing and property calculation toolkit written in Java. Calculated molecular descriptors may be used for property based virtual screening of large collections of molecules to discard structures with not drug-like properties and to pick potential drug candidates.



E-DRAGON is the electronic remote version of the well known software DRAGON, which is an application for the calculation of molecular descriptors developed by the Milano Chemometrics and QSAR Research Group of Prof. R. Todeschini. These descriptors can be used to evaluate molecular structure-activity or structure-property relationships, as well as for similarity analysis and highthroughput screening of molecule databases. DRAGON provides more than 1,600 molecular descriptors that are divided into 20 logical blocks. The user can calculate not only the simplest atom type, functional group and fragment counts, but also several topological and geometrical descriptors.


Model (Molecular Descriptor Lab)

A server Computing structural and physichemical properties of molecules from their 3D structures.



Molecular Descriptors Data Base is a free on-line database comprised of 1124 molecular descriptors calculated for 234773 molecules. At the present moment, 7159 queries have been made on the database. This data base is intended as a research and teaching tool.


Receptor preparation and target determination:

Many of the drug act by binding to a target such as hormone or receptor. Before target determination the TARGET should be prepared by structure modeling method or it might be download from the structure databases. After modeling or downloading from corresponding sources, it should be prepared properly for docking which might be achieved by using binding site analysis tools and target determination tools.

Binding site analysis:


The MEDock (Maximum-Entropy based Docking) web server is aimed at providing an efficient utility for prediction of ligand binding site for researchers.



A server for calculating Protein Pocket Negtive Image.



Binding sites and active sites of proteins and DNAs are often associated with structural pockets and cavities. castP server uses the weighted Delaunay triangulation and the alpha complex for shape measurements. It provides identification and measurements of surface accessible pockets as well as interior inaccessible cavities, for proteins and other molecules. It measures analytically the area and volume of each pocket and cavity, both in solvent accessible surface (SA, Richards' surface) and molecular surface (MS, Connolly's surface). It also measures the number of mouth openings, area of the openings, circumference of mouth lips, in both SA and MS surfaces for each pocket.



ODA (Optimal Docking Areas) is a new method to predict protein-protein interaction sites on protein surfaces. It identifies optimal surface patches with the lowest docking desolvation energy values as calculated by atomic solvation parameters (ASP) derived from octanol/water transfer experiments and adjusted for protein-protein docking.


Target identification:

TarFisDock :

Given a small molecule which can be drug, drug candidate, natural product, or new synthetic compound, TarFisDock docks it into the protein targets in PDTD (Potential Drug Target Database), and outputs the top 2%, 5% or 10% candidates ranked by the energy score, including their binding conformations and a table of the related target information.


Therapeutic Target Database

A database to provide information about the known and explored therapeutic protein and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs directed at each of these targets. Also included in this database are links to relevant databases containing information about target function, sequence, 3D structure, ligand binding properties, enzyme nomenclature and drug structure, therapeutic class, clinical development status. All information provided are fully referenced.


Binding DB:

BindingDB provides virtual screening tools to help identify the compounds in your own compound catalog that are most likely to be active against a desired target.



Protein-ligand docking


ParDOCK is an all-atom energy based Monte Carlo,rigid protein ligand docking, implemented in a fully automated, parallel processing mode which predicts the binding mode of the ligand in receptor target site.


Patch dock:


Protein- protein docking:



Fire Dock

FireDock is an efficient method for refinement and re-scoring of rigid-body protein-protein docking solutions.



GRAMM is a program for protein docking. To predict the structure of a complex, it requires only the atomic coordinates of the two molecules (no information about the binding sites is needed). The program performs an exhaustive 6-dimensional search through the relative translations and rotations of the molecules.





This is an online server for protein docking and molecular superposition program HEX.


Binding Affinity Analysis:


Program of Energetic Analysis of Receptor Ligand System (PEARL) is a server for computing small molecule ligand-protein, ligand-nucleic acid, protein-nucleic acid and ligand-protein-nucleic acid interaction energies.



AffinDB is a database of affinity data for structurally resolved protein–ligand complexes from the Protein Data Bank (PDB).



DrugScoreONLINE is a web-based user interface for the knowledge-based scoring functions DrugScoreCSD and DrugScorePDB. DrugScoreONLINE enables researcher to score protein-ligand complexes of your interest and to visualize the per-atom score contributions.