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Open source software and web services for designing therapeutic molecules

Open source software and web services for designing therapeutic molecules. G. P. S. Raghava, Head Bioinformatics Centre, Institute of Microbial Technology, Chandigarh. Important Web Sites Open Source Drug Discovery(OSDD) http://www.osdd.net/ CRDD Site: http://crdd.osdd.net/

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Open source software and web services for designing therapeutic molecules

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  1. Open source software and web services for designing therapeutic molecules G. P. S. Raghava, Head Bioinformatics Centre, Institute of Microbial Technology, Chandigarh Important Web Sites Open Source Drug Discovery(OSDD) http://www.osdd.net/ CRDD Site: http://crdd.osdd.net/ Raghava’s Group: http://www.imtech.res.in/raghava/

  2. Software Development for Drug Discovery Importance of Open Source for Drug Discovery • Discovery of Drug by Public for Public • Drugs for Disease Specific to Developing Countries (like India) • Development of Drugs for diseases of poor persons • Process of Discovery will be fast (few to many contributors) • Academic institutes/universities and small industry may afford

  3. Examples of open source software • Operating Systems • Linux • FreeBSD, OpenBSD, and NetBSD • Internet • Apache (> 50% of the world's web servers) • BIND: DNS for the entire Internet. • Sendmail (Most email servers) • OpenSSL (standard for secure communication) • Programming Tools • Languages (Perl, Python, PHP) • GNU compilers and tools (GCC, Make)

  4. The amount of fund required depends on the success rate at the clinical trial stage

  5. An overview of the workflow of in silico drug designing process

  6. Important Points Source of Molecules (databases or repositories) Molecular Editors (editing & viewing existing molecules) Analog Generators (software used to generate analogs) Structure Optimization (Energy/geometry of molecules) Calculation of Molecular Descriptors Chemical Similarity Search Development of QSAR/QSPR Models Classification and Clustering of Small Molecules Docking Small Molecules in Macromolecules Pharmacophore Tools/Search Software for ADMET Techniques Designing of Inhibitors Major Initiatives towards affordable drugs

  7. Databases and resources managing and hosting chemical compounds

  8. List of major molecular editors, frequently used for drawing and editing molecules

  9. Analogs generation softwares

  10. List of software and web servers used for structure optimization of molecules

  11. Important software and webserver for computing molecular descriptors

  12. Similarity search algorithms and their web links

  13. Machine learning and feature selection techniques in cheminformatics

  14. List of chemical clustering tools and their web addresses

  15. Different types of pharmocophore searching softwares

  16. Some open source initiatives for drug discovery with their research area

  17. Platform for Discovering and Designing of Drug Molecules • Load Data • Calculate descriptors • CDK • Padel • ADMET Properties • MetaPred • ToxiPred • DrugMint • Screening Databases • FDA molecules • PUBChem • Zinc datbase • Format coversion • SMILE • MOL • SDF • Babel • Pharmacophore

  18. Thankyou

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