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
ZINCA free database of commercially available compounds for virtual screening.
NCI250251 open structures ready for searching.

Web interface on Libraries:

Name Description
RCDKAllows the user to load molecules, evaluate fingerprints, calculate molecular descriptors and view structures in 2D.
JoeLibA Cheminformatics algorithm library, which was designed for prototyping, data mining, graph mining, and of course algorithm development.
Molecular ModeliingOpen 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 Viewer3D viewing tool for implementation with both ISIS Draw and ISIS Base.
BiomerJava based online biomolecular modelling package.
MOLEKELAn open source(GPL) multiplatform molecular visualization program.

Descriptor Calculation

Name Description
ACD/LogP FreewareFragment-based algorithm for Logp prediction.
StericA program to calculate molecular steric effects.
DALTONProgram for ab-initio calculation of molecular prop.

Chemoinformatics Kits and Optimizations

Name Description
GhemicalComputational chemistry software package released under the GNU GPL.
gOpenMolTool for the visualization and analysis of molecular structures and their chemical properties.
LIGPLOTAutomatically plotting protein-ligand interactions.
VIEWMOLGraphical front end for some quantum chemical and molecular modeling programmers.
VEGAMolecular Software package.
TINKERSoftware tools for Molecular Design.
MolPOVA graphics file converter.
MOLMOLA molecular graphics program.
MOPACIs a semiempirical quantum chemistry program based on Dewar and Thiel's NDDO approximation.
MEQIMolecular Scaffold Analysis.
ASCAnalytic Surface Calculation Package for PDBs.
BabelFile format converter.
POWERMVA software environment for statistical analysis, molecular viewing, descriptor generation, and similarity search.


Chemical Database With Information

ChemIDPlus ACD (Available Chemicals Directory) ASINEX Bionet Database CAP (Chemicals Available for Purchase) CHEBi ChemBank ChemDB ChemStar
CSD (Cambridge Structural Database) HIC-Up (Hetero-compound Information Centre - Uppsala) Maybridge Database IBS (Inter Biosceen) Database MDPI (Molecular Diversity Preservation International) MSDchem NCI Database PDBsum PubChem

Drug Database

BIOSTER CMC (Comprehensive Medicinal Chemistry)/">CMC (Comprehensive Medicinal Chemistry) Dictionary of Drug DrugBank MDDR (MDL Drug Data Report) MedChem
PharmGKB Rx-list SDD ( Super Drug Database) WDI (The Drug Index) WOMBAT AID/DRUGS


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




Diferent Datasets Chemoinformatics information