Computational resources for QSAR
Ligand-similarity based lead identification is a technique which follows the principle of similarity. It does not require information about 3D structure of the target protein. It is assumed that molecules having similar structure will have similar chemical properties. Hence, the information provided by a compound, or set of compounds known to bind to the desired target is used to identify new compounds from the external databases of chemical compounds using virtual screening approaches. The most commonly used methodology for ligand-similarity based lead identification is as follows:
Quantitative Structural Activity Relationship (QSAR) process quantitatively correlates structural molecular properties (descriptors) with functions (i.e. physicochemical properties, biological activities, toxicity, etc) for a set of similar compounds. It uses linear statistical methods such as Multiple Linear Regression, Partial Least Square, or non-linear methods like Support Vector Machines (SVM), Artificial Neural Network (ANN), Decision Trees, Bayesian Classifier, etc., to generate a mathematical model that connects experimental measures with a set of chemical descriptors. The main objective of QSAR models is to allow the prediction of biological activities of untested or novel compounds to provide insight into relevant and consistent chemical properties or descriptors (2D/3D) which defines the biological activity. Once, a series of predicted models are collected, these can be used for database mining for the identification of novel chemical compounds, particularly, for those having drug-like properties (following Lipinski’s Rule of Five) along with suitable pharmacokinetic properties.
Web Servers/Databases/Mirror Sites:
Chemical Libraries
| Chemical Libraries | Description |
|---|---|
| ZINC | A free database of commercially available compounds for virtual screening. |
| NCI | 250251 open structures ready for searching. |
Web interface on Libraries:
| Name | Description |
|---|---|
| RCDK | Allows the user to load molecules, evaluate fingerprints, calculate molecular descriptors and view structures in 2D. |
| JoeLib | A Cheminformatics algorithm library, which was designed for prototyping, data mining, graph mining, and of course algorithm development. |
| Molecular Modeliing | Open Source program library for molecular simulation applications. |
Standalone softwares
Structure Drawing
| Name | Description |
|---|---|
| ACD/ChemSketch 11.0 Freeware | It allows you to draw chemical structures including organics, organometallics, polymers, and Markush structures. |
| ACD/3D Viewer | 3D viewing tool for implementation with both ISIS Draw and ISIS Base. |
| Biomer | Java based online biomolecular modelling package. |
| MOLEKEL | An open source(GPL) multiplatform molecular visualization program. |
Descriptor Calculation
| Name | Description |
|---|---|
| ACD/LogP Freeware | Fragment-based algorithm for Logp prediction. |
| Steric | A program to calculate molecular steric effects. |
| DALTON | Program for ab-initio calculation of molecular prop. |
Chemoinformatics Kits and Optimizations
| Name | Description |
|---|---|
| Ghemical | Computational chemistry software package released under the GNU GPL. |
| gOpenMol | Tool for the visualization and analysis of molecular structures and their chemical properties. |
| LIGPLOT | Automatically plotting protein-ligand interactions. |
| VIEWMOL | Graphical front end for some quantum chemical and molecular modeling programmers. |
| VEGA | Molecular Software package. |
| TINKER | Software tools for Molecular Design. |
| MolPOV | A graphics file converter. |
| MOLMOL | A molecular graphics program. |
| MOPAC | Is a semiempirical quantum chemistry program based on Dewar and Thiel's NDDO approximation. |
| MEQI | Molecular Scaffold Analysis. |
| ASC | Analytic Surface Calculation Package for PDBs. |
| Babel | File format converter. |
| POWERMV | A software environment for statistical analysis, molecular viewing, descriptor generation, and similarity search. |
Links
Chemical Database With Information
Drug Database
QSAR
| QSAR studies WEB based | HADDOCK | Molinspiration | PreADMET | ProDRG | Corina | Molecular Network | Almond Generation of molecular descriptors for QSAR | ACES II Advanced Concepts in Electronic Structure | ADF Amsterdam Density Functional program | Biomer Java-based, on-line bimolecular modeling package | CACTVS A Chemistry Algorithm Development Environment | CADCOM Molecular modellg for the bench chemist | ChemViz Chemistry Visualization program at NCSA | GAMESS General ab-initio program | GRASP Graphical Representation and Analysis of Structural Properties | HASL Hypothetical Active Site Lattice method for 3D-QSAR | MDL Products Including Chime, ISIS/Draw and ISIS/Base | The Molecular Modelling Toolkit | MOLEKEL An interactive molecular graphics program in OpenGl | MolPro An ab-initio package | MoluCAD Molecular modelling and visualization tool | SPROUT de-novo ligand design | VMD Visual molecular dynamics | WebMO World Wide Web-based interface to computational chemistry packages | ChemInnovation Software | ChemAxon | Diveristy assesment | Cheminformatics information | Softwares and MATLAB routines | CAIMAN Classification And Influence Matrix ANalysis | Molecular Descriptor Correlations | QSAR WORLD | DRAGON molecular descriptors | MODEL For Computing structural and physichemical properties of molecules from their 3D structures | QSAR Builder Generate and evaluate QSAR and QSPR models | Tsar | MOLGEN Descriptor calculator |
Similarity Search
| Similarity measure based on Hasse matrices | MOLPRINT 2D |
Statistical
Datasets
| Diferent Datasets | Chemoinformatics information |