I am preparing a detailed LIST of CADD Tools. Has any one compiled a list of software processes both open source and priced, used in the CADD? or know A any resource to get it.
none that I know. reason is that tools are different in different domains. pharmaceutical favor QSAR and QSPR based tools like CODESSA or DRAGON Talete, chemical engineers favor Computer Aided Molecular Design tools (CAMD), which I develop myself or some colleagues (Pr Gani with his suite ICAS at DTU Capec)
Hi friends i have some softwares, but i dont have the complete list . If possible i will try to make it in the near future.
Some of the softwares i used are argus lab, hex, chemsketch, marvin sketch, cache workspace, cache project leader, amber 11, discovery accelerys, etc........... I hope this will be useful...
GOOD MORNING SIR..Below I paste some information about your CADD what are i collected.
Chemical structure representations:
ChemDraw, MarvinSketch, ACD/ChemSketch, ChemWriter, jsMolEditor, Marvin molecule editor and viewer, UCSF Chimera, Pymol, Swiss-PDB Viewer / DeepView, Daylight SMILES, InChI, Tripos Mol2,OpenBabel, LigPrep, Corina, PoseView, DS Visualizer, E-Babel, Corina online demo, Chemical Identifier Resolver, ChemMobi, ...
2D drawing:
• ChemDraw. Molecule editor developed by the cheminformatics company CambridgeSoft. For Windows and Mac.
• MarvinSketch. Advanced chemical editor for drawing chemical structures, queries and reactions developed by ChemAxon. Exists as an applet.
• ACD/ChemSketch. Molecule editor developed by ACD/Labs. Also available as freeware, with tools for 2D structure cleaning, 3D optimization and viewing, InChI generation and conversion, drawing of polymers, organometallics, and Markush structures. For Windows only.
• JChem for Excel. Integrates structure handling and visualizing capabilities within a Microsoft Excel environment. Structures are fully supported within spreadsheets and be can viewed, edited, searched, resized, ordered, managed. Provided by ChemAxon.
• JKluster. Tool of JChem for clustering, diversity calculations, and library comparisons based on molecular fingerprints and other descriptors. Useful in combinatorial chemistry, drug design, or other areas where a large number of compounds need to be analyzed. Provided by ChemAxon.
• ISIS/Draw. Chemical structure drawing program for Windows, published by MDL Information Systems. Free of charge for academic and personal use.
• ChemDoodle. Chemical structure environment with a main focus on 2D graphics and publishing to create media for structures, reactions and spectra. For Windows, Mac and Linux.
• Accelrys Draw. Allows drawing and editing complex molecules, chemical reactions and biological sequences. provided by Accelrys.
• 2Ddraw. Automated drawing of structural molecular formulas under user-defined constraints. Draw all compounds such that their 2D layout is most similar. Distibuted by BioSolveIT.
• PLT. Program for producing chemical drawings and outputting them in a variety of formats. For Windows.
• JChemPaint. Free and open source editor and viewer for chemical structures in 2D. Exists as a Java stand alone application and two varieties of Java applet that can be integrated into web pages. Platform-independent.
• BKchem. BKChem is a free open source chemical drawing program written in Python. Platform-independent.
• MolSketch. Free open source molecular drawing tool for 2D molecular structures. Available for Windows, Mac and Linux.
• JME Molecular Editor. Java applet which allows to draw / edit molecules and reactions (including generation of substructure queries) and to depict molecules directly within an HTML page. Editor can generate Daylight SMILES or MDL Molfile of created structures.
• Chem4D. Molecular drawing tool. Includes assignment of systematic names to organic structures according to IUPAC nomenclature rules, and drawing of molecules from IUPAC names. For Windows and Mac. Distributed by ChemInnovation Software.
• XDrawChem. Free open source software program for drawing chemical structural formulas, available for Windows, Unix, and Mac OS.
• iMolecular Draw. Application that can view, edit and build molecules in 2D. For iPhone.
• SketchEl. Free and open source interactive chemical molecule sketching tool, and molecular spreadsheet data entry application. Written in Java. Exists as an applet.
• Chemtool. Free open source program for drawing chemical structures on Linux and Unix systems using the GTK toolkit under X11.
• Bioclipse. Java-based, open source, visual platform for chemo- and bioinformatics based on the Eclipse Rich Client Platform (RCP).
• CLiDE. Chemical Literature Data Extraction. Chemistry intelligent equivalent of Optical Character Recognition (OCR) software. Recognizes structures, reactions and text from scanned images of printed chemistry literature and transforms the 'images' into a 'real structures' that can then be input into databases.
• Chrawler. Can scan all data sources, including local files, remote files on network, emails, web pages, SharePoint contents, etc., and find contained chemical structures, and make them structure-searchable (substructure, full-structure, similarity). Distributed by Scilligence.
• OLN Chem4SharePoint. Makes it possible to draw, display and search chemical structures in SharePoint. Distributed by Scilligence.
• ChemJuice. Molecular drawing software for iPhone.
2D drawing online:
• ChemWriter. Chemical structure editor designed for use with Web applications. Distributed by Metamolecular.
• jsMolEditor. Molecule Editor of JavaScript. Open source.
• Marvin molecule editor and viewer. Java based chemical editor for drawing chemical structures. Includes unlimited structure based predictions for a range of properties (pKa, logD, namestructure, etc.). Provided by ChemAxon.
• Molinspiration WebME Molecule Editor. Allows creation and editing of molecules in browsers without Java support and without any plugins. The editor is based on a Web2.0 Ajax technology. WebME allows therefore web-based structure input also in institutions where Java applets are not allowed and offers complete platform compatibility. The actual molecule processing in WebME is based on the JMEPro editing engine running on a server. provided by Molinspiration.
• OLN JSDraw. Javascript libary you can display and draw chemical structures in web pages, which works cross browser, including IE, Firefox, Safari, Opera and Chrome, crose platform, including Window, Mac, Linux, and even iPhone, Android and other mobile devices. Free for education. Provided by Scilligence.
3D viewers:
• UCSF Chimera. Open source, highly extensible program for interactive visualization and analysis of molecular structures and related data. Free of charge for academic, government, non-profit, and personal use. For Windows, Mac and Linux. Developed by the Resource for Biocomputing, Visualization, and Informatics, UCSF.
• Pymol. Open source, user-sponsored, molecular visualization system written in Python. Distributed by DeLano Scientific LLC. For Windows, Mac and Linux.
• Swiss-PDB Viewer / DeepView. program for 3D visualization of macromolecules, allowing to analyze several proteins at the same time. Swiss-PdbViewer is tightly linked to SWISS-MODEL, an automated homology modeling server developed within the Swiss Institute of Bioinformatics (SIB).
• Computer-Aided Drug-Design Platform using PyMOL. PyMOL plugins providing a graphical user interface incorporating individual academic packages designed for protein preparation (AMBER package and Reduce), molecular mechanics applications (AMBER package), and docking and scoring (AutoDock Vina and SLIDE).
• Autodock Vina plugin for PyMOL. Allows defining binding sites and export to Autodock and VINA input files, doing receptor and ligand preparation automatically, starting docking runs with Autodock or VINA from within the plugin, viewing grid maps generated by autogrid in PyMOL, handling multiple ligands and set up virtual screenings, and set up docking runs with flexible sidechains.
• pymacs. Python module for dealing with structure files and trajectory data from the GROMACS molecular dynamics package. It has interfaces to some gromacs functions and uses gromacs routines for command line parsing, reading and writing of structure files (pdb,gro,...) and for reading trajectory data (only xtc at the moment).
• PyRosetta. Interactive Python-based interface to the Rosetta molecular modeling suite. It enables users to design their own custom molecular modeling algorithms using Rosetta sampling methods and energy functions.
• Visual Molecular Dynamics (VMD). Free open source molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. For MacOS X, Unix, or Windows. Developed by the NIH resource for macromolecular modeling and bioinformatics, University of illinois.
• Jmol. Open source Java viewer for chemical structures in 3D.
• DS Visualizer. Free 3D visualizer of Discovery Studio. Allows sequence handling and, 2D or 3D charting. Creates 2D ligand-receptor interaction diagrams. Distributed by Accelrys. DS Visualizer ActiveX Control allows visualizing and interacting with molecules in Microsoft Office documents and Internet Explorer. For Windows and Linux.
• OpenAstexViewer. Free open source java molecular graphics program that assists in structure based drug design. It can be used as an Applet in a web page or as a desktop application. Provided by Astex Therapeutics. For Windows, linux and Mac.
• Jamberoo. Free open source program for displaying, analyzing, editing, converting, and animating molecular systems (former JMolEditor). For Windows, Mac and Linux.
• TexMol. Molecular visualization and computation package. Free and open source software.
• Chil2 Viewer. Visualization tool and graphical user interface of the Chil2 suite, with analysis tools, database integration and ruby interface. Open for general research.
• BALLView. Standalone molecular modeling and visualization application. Provides a framework for developing molecular visualization functionality. Can be used as the visualizaion component of BALL. Free and opensource. For Windows, Mac and Linux.
• Avogadro. Free, open source, molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.
• RasMol. Program for molecular graphics visualisation.
• RasTop. Free open source molecular visualization software adapted from the program RasMol. RasTop wraps a user-friendly graphical interface around the "RasMol molecular engine". Developed for educational purposes and for the analysis of macromolecules at the bench. For Windows and Linux.
• Qmol. Program for viewing molecular structures and animating molecular trajectories. Distributed by DNASTAR.
• CheVi. Program for viewing molecular structures providing an interface to eHiTS. For linux. Distributed freely by SimBioSys.
• Cn3D. Visualization tool for biomolecular structures, sequences, and sequence alignments. Maintained and distributed by the NCBI. For Windows, Mac and Linux.
• Bodil. Free, modular, multi-platform software package for biomolecular visualization and modeling. Bodil aims to provide easy three-dimensional molecular graphics closely integrated with sequence viewing and sequence alignment editing.
• COSMOS Viewer. Free software for presentation of molecules.
• BARISTA. BARISTA visualization functions create, display, and manipulate 3D depictions of molecular structures based on results computed by molecular computation programs such as Conflex, and are designed specifically to facilitate the analysis of these results. For Windows and Linux.
• BioAdviser. Visualization tool for biomolecular structures and small molecules.
• iMolecular Builder. The IMoleBuilder is an application that can view, edit and build molecules in 3D. For iPhone.
Definitions and syntax of file formats:
• Daylight SMILES. SMILES (Simplified Molecular Input Line Entry System) is a line notation (a typographical method using printable characters) for entering and representing molecules and reactions.
• InChI. (IUPAC International Chemical Identifier) is a string of characters capable of uniquely representing a chemical substance. It is derived from a structural representation of that substance in a way designed to be independent of the way that the structure was drawn (thus a single compound will always produce the same identifier). It provides a precise, robust, IUPAC approved tag for representing a chemical substance.
• Tripos Mol2. Complete description of the Mol2 file format (.mol2).
• PDB format. Complete description of the PDB file format (.pdb).
• SDF format. Complete description of the SDF file format (.sdf).
File format Converters
• OpenBabel. Free open source chemical expert system mainly used for converting chemical file formats. For Windows, Unix, and Mac OS.
• LigPrep. 2D to 3D structure conversions, including tautomeric, stereochemical, and ionization variations, as well as energy minimization and flexible filters to generate ligand libraries that are optimized for further computational analyses. Distributed by Schrodinger.
• Corina. Generates 3D structures for small and medium sized, drug-like molecules. Distributed by Molecular Networks.
• CACTVS. Universal scriptable toolkit for chemical information processing. Used by PubChem. Maintained and distributed by Xemistry. Free for academic.
• SMART. (Small Molecule Atomtyping and Rotatable Torsion assignment) automatically identifies and labels the rotatable bonds of the ligands and assigns AMBER atom types. SMART is the module used to prepare ligand structures in a modified MOL2 format for use by FITTED. Part of the Molecular FORECASTER package and FITTED Suite. Free for an academic site license (excluding cluster).
• ProCESS. (Protein Conformational Ensemble System Setup). Prepares protein files to be used with FITTED, by assigning the advanced residue names, advanced hydrogen names, atom types, and charges for the protein. Part of the Molecular FORECASTER package and FITTED Suite. Free for an academic site license (excluding cluster).
• PREPARE. (Protein Rotamers Evaluation and Protonation based on Accurate Residue Energy). Tool for protein preparation and optimization. Part of the Molecular FORECASTER package and FITTED Suite. Free for an academic site license (excluding cluster).
• DG-AMMOS. Program to generate 3D conformation of small molecules using Distance Geometry and Automated Molecular Mechanics Optimization for in silico Screening. Freely distributed by the University of Paris Diderot.
• Key3D. Molecular modeling tool to convert 2D structures (chemical structural formula) of compounds drawn by ISIS-Draw or ChemDraw to 3D structures with additional information on atomic charge etc. Distributed by IMMD.
• CONFLEX. Software for searching and analyzing the conformational space of small and large molecules.
• JOElib. Cheminformatics library mainly used for conversion of file formats. Written in Java. For Windows, Unix, and Mac OS.
• CDK (Chemistry Development Kit). LGPL-ed library for bio- and cheminformatics and computational chemistry written in Java. Opensource.
• MolEngine. .NET Cheminformatics Toolkit completely built on Microsoft .NET platform. By using Mono, MolEngine can run on other platform, such as Mac, Linux, iPad. Distributed by Scilligence.
• Indigo. Universal organic chemistry toolkit.Free and opensource. Provided by GGA.
• ChemDiff. Indigo-based utility for finding duplications and visual comparison of two files containing multiple structures. SDF, SMILES, CML, MOLFILE input formats are supported. Provided by GGA.
• RDKit. Collection of cheminformatics and machine-learning software written in C++ and Python.
• Mol2Mol. Molecule file manipulation and conversion program.
• Fconv. Molecule file manipulation and conversion program.
• smi23d. Consists of two programs that can be used to convert one or more SMILES strings to 3D. For Mac and Linux. Also exists as a web service.
• Scaffold Hunter. JAVA-based software tool for exploring the chemical space by enabling generation of and navigation in a scaffold tree hierarchy annotated with various data. The graphical visualization of structural relationships allows to analyze large data sets, e.g., to correlate chemical structure and biochemical activity. Free open source software developed and supported by the Chair of algorithm Engineering at Technical University Dortmund and the Department of Chemical Biology at Max-Planck Institute for Molecular Physiology Dortmund.
• ScaffoldTreeGenerator. Java-based program which generates the scaffold tree database independently of Scaffold Hunter. Free open source software developed and supported by the Chair of algorithm Engineering at Technical University Dortmund and the Department of Chemical Biology at Max-Planck Institute for Molecular Physiology Dortmund.
• Stripper. Program to extract scaffolds from organic drug-like molecules by 'stripping' away sidechains and representing the remaining structure in a condensed form. Open source software distributed by Silicos.
• Epik. Enumerates ligand protonation states and tautomers in biological conditions. Distributed by Schrodinger.
• iBabel. iBabel is an alternative graphical interface to Open Babel for Macintosh OS X.
• PerlMol. Collection of perl modules providing objects and methods for representing molecules, atoms, and bonds in Perl; doing substructure matching; and reading and writing files in various formats.
• The SDF Toolkit in Perl 5. The purpose of this SDF toolkit is to provide functions to read and parse SDFs, filter, and add/remove properties.
Web services:
• ALOGPS. On-line prediction of logP, water solubility and pKa(s) of compounds for drug design (ADME/T and HTS) and environmental chemistry studies. ALOGPS also displays values calculated with Pharma Algorithms LogP, LogS and pKa, Actelion LogP & LogS (many thanks to Dr Thomas Sander), Molinspiration logP, KOWWIN logP, ALOGP (Viswanadhan et al, 1989), MLOGP (Moriguchi et al, 1992) implemented in the DragonX software, XLOGP2 and XLOGP3 programs and ChemAxon logP calculator
• OSIRIS Property Explorer. Integral part of Actelion's inhouse substance registration system. Calculates on-the-fly various drug-relevant properties for drawn chemical structures, including some toxicity and druglikeness properties. Maintained by the Virtual Computational Chemistry Laboratory.
• ToxPredict. Web service to estimate toxicological hazard of a chemical structure. Molecules can be drawn, or input by any identifier (CAS, Name, EINECS) or SMILES or InChI or URL of OpenTox compound or dataset. Provided by OpenTox.
• ToxCreate. Web service to create computational models to predict toxicity. Provided by OpenTox.
• ADME-Tox. ADME-Tox (poor absorption, distribution, metabolism, elimination (ADME) or toxicity) filtering for small compounds, based on a set of elementary rules.
• STITCH. Resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature. STITCH contains interactions for over 74,000 small molecules and over 2.5 million proteins in 630 organisms.
• XScore-LogP. Calculates the octanol/water partition coefficient for a drug, based on a feature of the X-Score program.
• VirtualToxLab. ''In silico'' tool for predicting the toxic (endocrine-disrupting) potential of existing and hypothetical compounds (drugs, chemicals, natural products) by simulating and quantifying their interactions towards a series of proteins known to trigger adverse effects using automated, flexible docking combined with multi-dimensional QSAR (mQSAR).
• PharmMapper. Freely accessed web-server designed to identify potential target candidates for the given probe small molecules (drugs, natural products, or other newly discovered compounds with binding targets unidentified) using pharmacophore mapping approach.
• MODEL - Molecular Descriptor Lab. Computes structural and physichemical properties of molecules from their 3D structures.
• PreADMET. Web-based application for predicting ADME data and building drug-like library using in silico method.
• Free ADME Tools. ADME Prediction Toolbox of the SimCYP application provided free of charge by SimCYP.
• UM-BBD Pathway Prediction System. The PPS predicts plausible pathways for microbial degradation of chemical compounds. Predictions use biotransformation rules, based on reactions found in the UM-BBD database or in the scientific literature. Provided by the University of Minnesota.
• MetaPrint2D. Metabolic site predictor. MetaPrint2D is a tool that predicts xenobiotic metabolism through data-mining and statistical analysis of known metabolic transformations reported in scientific literature. MetaPrint2D-React can make predictions concerning a wider range of reactions than MetaPrint2D, and is able to predict the types of transformation that can take place at each site of metabolism, and the likely metabolite formed. Provided by the University of Cambridge.
• MetaPrint2D-React.. Metabolic site predictor. MetaPrint2D is a tool that predicts xenobiotic metabolism through data-mining and statistical analysis of known metabolic transformations reported in scientific literature. MetaPrint2D, which predicts sites of phase I metabolism, defined as the addition of oxygen (e.g. hydroxylation, oxidation, epoxidation) or elimination reactions. Provided by the University of Cambridge.
• SMARTCyp Web Service. SMARTCyp predicts the sites in molecules that are most liable to cytochrome P450 mediated metabolism. Provided by the the Department of Medicinal Chemistry at the University of Copenhagen.
Sorry sir i not seen the reply from mis.sara nichols, university of california at san diego. I taken these cadd software & tool information from http://www.click2drug.org only. I collect this some few month before but i forget the url for this site. I need to say thanks mis.mis.sara nichols mam for provide me the url.
Excellent List by Sakthi Vel;
Just add:
MOE (Molecule Operating Envorinment), GOLD, & HyperChem in LIst.
MOE is an excellent commercial application for all process, starting from structure drawing, minimization, QSAR, QSPR, HTS, Virtual Screening, LigPLot, Simulation and lots of other features as well as.
Welcome Mr.Sakthi....We are all here to share best of our knowledge! Keep updating us with the same pace. :-)
Dear Ravi Sharma,
Adding to all other suggestions, here are some other collections that might also help you having a nice list of Drug Discovery tools eventually.
http://www.osdd.net/
http://www.scfbio-iitd.res.in/bioinformatics/drugdesign.htm
http://www.cheminformatics.org/
http://ppi.fli-leibniz.de/jcb_ppi_software.html#softwarePPD
Enjoy discovering new drugs.
Jubilant
ARChem:
Automating Retrosynthetic Chemistry - Route Designer
ARChem is a retrosynthetic analysis package, which assist chemists to find routes from target molecules to readily available starting materials.
http://www.simbiosys.ca/products/leaflets/RouteDesigner.pdf
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CAESA:
Computer Aided Estimation of Synthetic Accessibility
Computer program to automatically analyse and rank sets of molecules according to their ease of synthesis. It provides structural complexity analysis and rapid retrosynthetic analysis with reaction path information including intermediates.
http://www.simbiosys.ca/products/leaflets/CAESA_folder.pdf
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CLiDE: Chemical Literature Data Extraction
CLiDE is the OCR system for chemists, it can recognize and extract structures, reactions and text from scanned images of printed chemistry literature.
What is CLiDE :
CLiDEis a utility that converts 2D molecular images into editable connection tables that can be stored in standard electronic formats. This quintessential tool allows chemists to extract chemical structures from scientific literature, patents, corporate documents and image files.
CLiDEStandard
For the chemist’s everyday use, CLiDEStandard is designed as a contemporary document viewer.
In its latest release, CLiDE 5is offered in three different flavors designed to address different scenarios, from a desktop accessory extracting individual images, to a server utility generating databases of molecules.CLiDE’sinterface offers all the basic features of a PDF/Word viewer, including text search, zooming and printing. But in addition, it allows:
•Automatic extraction of individual molecules –the images embedded in the document, or otherwise opened images in JPG, TIFF, PNG and GIF formats are converted into connection tables.
•Indicates valence violations and potential recognition errors.
•Allows editing the molecules by transferring them directly to ChemDraw, Marvin, SymyxDrawor IsisDraw.
•Allows saving the structure in ChemDraw, MOL, SD or RG format.
CLiDEProfessional
Multiple images and full documents can be processed in CLiDEProfessional in a click of a button.
In addition to all the features of CLiDEStandard , the Professional version offers the following.
•Split view for easy comparison of source and extracted structures.
•Contextual interpretation of generic structures.
•Saving work in XML format for reloading in following sessions.
•Deleting structures not to be included in the output.
•Grouping of molecules or fragments into a single structure.
CLiDEBatch
Intended for database creation and mass data production, CLiDE Batch is a Windows, Mac or Linux command-line software application that extracts molecular structures from PDF, Word and image files into MOL, SD, RG, CDX and XML files.
CHECK THIS PDF : http://www.simbiosys.ca/products/leaflets/CLiDE_folder.pdf
Sir,While we performed CADD following steps involved and the collection of tools used for these steps are--
1. Target protein identifacation and protein optimization.
At first we have to identified our target protein, referring the KEGG pathway database we can find that probably inhibition or activation of protein may effectively reduce the disease and retrived the required protein from RCSB, if the structure of required protein is not available in RCSB in that case at first we have to performed homology modelling of our target protein, for this task we can use some online tools.....
.a) SWISS-MODEL (http://swissmodel.expasy.org/)
b) Geno3d (http://geno3d-pbil.ibcp.fr)
c)LOMETS ( http://zhanglab.ccmb.med.umich.edu/LOMETS/)
d)I-TASSER ( http://zhanglab.ccmb.med.umich.edu/ITASSER/)
and we can use some stand alone software for performing homology modelling such as---
a) Modeller.
after the identification of protein our next step is to find out how many active sites are present in that protein.For identification of active site the available online tools are---
a)Q-Site Finder:Ligand Binding Site Prediction.
(http://bmbpcu36.leeds.ac.uk/qsitefinder/help.html)
b)Sanjeevini (http://www.scfbio-iitd.res.in/sanjeevini/sanjeevini.jsp) and some stand alone software for prediction of active sites are--
a)Molegro Virtual Docker.
b)Exome Horizon.
2.Ligand preparation and ligand optimization.
The 3d structure of ligand and its physiochemical properties can be downloded from several database such as
a)Chem Spider (www.chemspider.com/)
b)chEBI (http://www.ebi.ac.uk/chebi/)
c)Zinc databse.
if we are unable to retrived our required chemical component from any database in that case we can design it by own,for this purpose we can use some software----
a)Marvin Sketch (http://www.chemaxon.com/products/.)
b)Chem Sketch
(http://www.acdlabs.com/products/draw_nom/draw/chemsketch/)
c)Chem writer.(http://metamolecular.com/chemwriter/)
d)CORINA.(http://www.molecular-networks.com/products/corina)
after the preparation of ligand our next step is to find out the molecular properties based on the Lipnski's rule and toxicity of the ligand,for this purpose we can use some online tools--
a)Molinspiration( http://www.molinspiration.com/)
to predict molecular properties and bioactivity.
b) OSIRIS Property Explorer
( http://www.organic-chemistry.org/prog/peo/)
to predict mutagenic,tumorigenic,irritant,reproductive effect,Drug likeness and Drug Score.
c)ALOGPS (http://www.vcclab.org/lab/alogps/)
d)Open-Tox (http://apps.ideaconsult.net:8080/ToxPredict)
3.Docking Studies
After the preperation of target protein and ligand the next step is to performed docking.Software used for docking studies are---
a)Auto dock
b)Dock
c)Gold
d)Swiss Dock
e)Auto dock vina.
f)Exom-Horizon
g)Molegro virtual docker.
4) Visualization of docked Complex
The docked complex can visualize in ---------------------------
a)Pymol.
b)Rasmol.
c)Swiss PDB viewer.
to showing how the ligand interact with protein.
Dear Dr. Gupta, Did you try Surflex-dock for docking and Orchestrar for homology modeling
Nice list by Sakthi Vel
Khusboo thanks for explaining the steps...it was really helfull
Thanks Sakthi and Khushboo for your detailed information. Despite all freely available softwares, both Maestro and Sybyl are excellent choice for molecular modelling work. You can get all MM/MD tools in these packages. I am working on both of these packages since last couple of years, these are really good choice.
@Girdhar Deora : Do you have selected modules or complete package? out of these two which is better? What do you mean by Good choice? Have you worked with GOLD/Shrodingers GLIDE.....?
I have worked with Sybyl during my PhD in Germany and i am using it till now, i have a complete package, in cluding homolgy modeling with Orchestrar and Docking with Surflex-Dock and also 3-DQSAR (CoMFA&CoMSIA)
Good morning ravi sharma sir,
glide is one of the best for docking & lingands screening study. I using glide & discovery studio. In this two, discovery studio is user friendly & we predict the conformation of the binding site & residues close to binding site effectively . In the case of glide several steps need to fallowed & its good for study activity of 100 of ligand molecule interaction. For result conclusion i used different tools such as yasara, genious, ligand scout. Discovery studio package can identified active site region of the receptor in single steps, but i conform these prediction using some other tools to get more possible result, example i recommend metapocket 2.0 online server.
Each docking software will provide different parameter of ligand & receptor interaction result. The main challenge is to get proper conclusion from these different result. All the best for your research work sir.
I any one like to give me an idea related to these studies, i feel happy. Because i am not expert in the computational biology field.
Dear Dr. Sharma, Followings are little-bit explanation regarding your post:
1. We have Complete package for both of the software right now.
2. according to job requirement we can choose the module from the software. In my opinion (experience), for the vHTS- sybyl is very fast then Maestro, for MD simulations Maestro is more user friendly, For docking purpose we can go for either of them.
3. as I Stated earlier, I have couple of years work experience on both of the softwares.
Its really nice to see senior and experienced people like you among us. Thanks for joining us.
Regards,
Girdhar
Some more suggestions:
- YASARA does automated homology modelling and can also do docking and visualisation (not free)
- A frequently overlooked bottleneck in CADD is the quality of the input structure model. If you use structures from the PDB, have a look at PDBREPORT to see if the model is of suffient quality (free)
- A plug of my own work: the PDB_REDO databank contains the same proteins as the PDB, but the structures are re-refined and rebuilt to ensure the model optimally fits the experimental data. Most models are of improved quality and have fewer errors compared to their PDB counterpart. For drug docking studies it is worthwhile to use both the PDB and the PDB_REDO model as target (free)
Dear ravi sir,
There are many softwares & tools available for CADD. I worked on GLIDE, GOLD, SILVER, SYBYL, DISCOVERY STUDIO & vlife MDs. Out of theses softwares, i can prefer only Schrodinger GLIDE is good for molecular docking. WE can get free energy values also. As sakthivel said, every docking software will give different results based on their own parameters.
sakthi really u r good and dynamic researcher. ur reply is very informative to all researcher. Very good collection.
Very useful link for computational biology tools & software Mr.Girinath g Pillai sir. thanks
Dear Giri, Really a nice link for researcher......Thanks for sharing and your active participation :-)
Please have a look on http://crdd.osdd.net/ and on http://crdd.osdd.net/oscadd/ or http://www.imtech.res.in/raghava/ . You may get a big list. Dr Sharma can you share list of CADD software you are compiling. This list will be useful for all the persons working in this field.
Thanks Giri for providing excellent link. You are maintaining excellent collection of CADD related information, good work.
The list which i am half way through, is containing categorised tools, description, limitations, + points and availability/link, Step wise, so that a researcher (biologist/chemist) new to this in-silico world can also try and use these tools and do comparative studies also.
@Dr Girinath: Thank you for a compilation link.
@Dr Raghava: This list will be dedicated to you only.,
Hi, this is a complete list of web-server and online free tools for homology modeling and structural analysis on protein structure.....enjoy!!!!
http://www.bronaldo.it/homology.html
@AD; @GGP, Thank you very much for your links. I almost finished compiling my version of the links & tools used in CADD from my collections as well as as suggested by the contributors to this thread, but I feel that "no reinventing the wheel" once again. Instead I must give my inputs/suggestions (design-features) to make the existing resources a Final resource.
Will you welcome any suggestions?
Regards
-rks
@sakthi vel. YOUR LIST IS NOTHING ELSE THAN A COPY/PASTE OF click2drug.org. This web site was setup, is actively maintained and given to the community for free. This represents a substantial amount of work for academic researchers. Plagiarism is not only unethical but punishable as well.
Dear all,
As mentioned above, the list provided by Sakthi Vel is a unauthorized copy of http://www.click2drug.org.
Click2Drug is developed by the Swiss Institute of Bioinformatics and is its property. It contains nearly 700 links which are regularly checked and updated. It thus answers to Dr. Ravi Sharma's question.
This site has been launched several years ago, is now well established and renowned, and is visited by numerous users. It has already been cited by several scientific papers, as listed here: http://www.click2drug.org/citations.html
We apreciate that you like the Click2Drug list of CADD tools, which results from several years of dedicated work.
We would also apreciate all suggestions to improve it.
@sakthi vel. If you want to point out the existence of this list, you are encouraged to just refer to it using its web address, rather than copying its whole content and suggesting you did the collection yourself.
@Bhakat Thanks for sharing link, It is really impressive resource that provide comprehensive information on CADD. Here, I am writing few links, hope these will be useful for CADD users
http://crdd.osdd.net/
http://crdd.osdd.net/oscadd/
http://info.csir.res.in/
http://www.imtech.res.in/raghava/
I recommend to take a look at http://www.redbrick.dcu.ie/~noel/linux4chemistry/ where a lot of software e-links are accessible
Now OSDDlinux include large number of software packages for CADD
http://osddlinux.osdd.net/
Directory of in silico Drug Design tools
www.click2drug.org/
may be useful
@IG: Thank you very much for really very exhaustive resource.
With regards
-Dr Sharma
@GGP
Thank very much for giving " free Android app links", and enriching the list/directory of CADD tools
With Regards
Dr Sharma
@GR,
Thanks for a very valuable and only link from India.
With Regards
Dr Sharma
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