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OSDD presents OSDDlinux (Operating System for Drug Discovery)

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 Lipinskiís Rule of Five) along with suitable pharmacokinetic properties.

Web Servers/Databases/Mirror Sites:

Chemical Libraries:
Chemical LibrariesDescription
ZINC a free database of commercially-available compounds for virtual screening
NCI250251 open structures ready for searching

Web Interface on Libraries:

NameDescription
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 Modeling ToolkitOpen Source program library for molecular simulation applications

Standalone Software:

STRUCTURE DRAWING:
NameDescription
ACD/ChemSketch 11.0 Freeware
ACD/3D Viewer 3D Viewing tool for implementation with both ISIS Draw and ISIS Base
Biomer Java-based, on-line biomolecular modeling package
MOLEKEL an opensource (GPL) multiplatform molecular visualization program

DESCRIPTOR CALCULATION:
NameDescription
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

CHEMINFORMATICS KITS AND OPTIMIZATIONS:
NameDescription
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
TINKERSoftware 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 Cheminformatics ToolkitA software environment for statistical analysis, molecular viewing, descriptor generation, and similarity search)

Links:

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
Relibase SPRESI Zinc GLIDA ChemBioGRID Ched ECOTOX QueryCHEM

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

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
Biomera Java-based, on-line bimolecular modeling package CACTVS A Chemistry Algorithm Development Environment CADCOM molecular modeling 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 modeling 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 oftwares 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 calculation

SIMILARITY SEARCH:
Similarity measure based on Hasse matrices MOLPRINT 2D

STATISTICAL:
RWeb

DATASETS:
Different Datasets Cheminformatics information

MISC:
http://ourworld.compuserve.com/homepages/RayLec/atoms.htm#download
http://www.chemistry.mcmaster.ca/faculty/bader/aim/
http://www.psi-k.org/codes.shtml#crystal
http://cheminformatics.org/
http://chemxseer.ist.psu.edu/