PhD CourseWork

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Introductory course in Bioinformatics for PhD students enrolled in variety of disciplines under Life-Science domain.

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PhD CourseWork

  1. 1. AIB PhD Coursework in Life Sciences Computational Biology 28 September 2013 Dr. Puneet Kacker www.puneetsclassroom.in
  2. 2. AIBOutline  Introduction  Literature Databases  Sequence Databases  Structure Databases  Chemical Databases  Tools for Analysis  Things to Remember  Some Useful Tips 2
  3. 3. AIBOutline  Introduction  Literature Databases  Sequence Databases  Structure Databases  Chemical Databases  Tools for Analysis  Things to Remember  Some Useful Tips 3
  4. 4. AIBIntroduction 4 Computers in Life Sciences Immunoinformatics Computational Chemistry Bioinformatics Computational Biology Chemoinformatics Computational Drug Design Systems Biology Computational Neuroscience
  5. 5. AIBOutline  Introduction  Literature Databases  Sequence Databases  Structure Databases  Chemical Databases  Tools for Analysis  Things to Remember  Some Useful Tips 5
  6. 6. AIB NCBI: PubMed 6 1 2 43 http://www.ncbi.nlm.nih.gov/pubmed/
  7. 7. AIB Google Scholar 7 1 2 43 Settings http://scholar.google.co.in/ Import to RefMan
  8. 8. AIBOutline  Introduction  Literature Databases  Sequence Databases  Structure Databases  Chemical Databases  Tools for Analysis  Things to Remember  Some Useful Tips 8
  9. 9. AIB NCBI Protein 9 FASTA FASTA Formatted Sequence http://www.ncbi.nlm.nih.gov/protein/
  10. 10. AIB UniProt Database 10 Names and origin Protein attributes General annotation (Comments) Ontologies Alternative products Sequence annotation (Features) Sequences References Cross-references Entry information Relevant documents UniProt Home Page UniProt Searched for P56817 http://www.uniprot.org/
  11. 11. AIB NCBI Nucleotide 11http://www.ncbi.nlm.nih.gov/nuccore
  12. 12. AIBOutline  Introduction  Literature Databases  Sequence Databases  Structure Databases  Chemical Databases  Tools for Analysis  Things to Remember  Some Useful Tips 12
  13. 13. AIB Protein Data Bank 13www.rcsb.org/pdb
  14. 14. AIB Nucleic Acid Data Bank 14http://ndbserver.rutgers.edu/
  15. 15. AIB PDB File Format 15 1 2 3 4 Title Section Primary Structure Section HeterogenSection Secondary Structure Section Cont...
  16. 16. AIB 16 5 6 7 8 Connectivity Annotation Section Crystallographic and Coordinate Transformation Section Coordinate Section Connectivity Section Bookkeeping Section9
  17. 17. AIB Visualization 17www.rcsb.org/pdb
  18. 18. AIB Visualization 18 Aspartic Protease: 1FKN
  19. 19. AIBOutline  Introduction  Literature Databases  Sequence Databases  Structure Databases  Chemical Databases  Tools for Analysis  Things to Remember  Some Useful Tips 19
  20. 20. AIB NCBI: PubChem 20pubchem.ncbi.nlm.nih.gov/
  21. 21. AIB PubChem Results 21 Search for Similar Compounds Scores >=95%
  22. 22. AIB ZINC Database 22http://zinc.docking.org/
  23. 23. AIBOutline  Introduction  Literature Databases  Sequence Databases  Structure Databases  Chemical Databases  Tools for Analysis  Things to Remember  Some Useful Tips 23
  24. 24. AIB BLAST 24 Take a Sequence Search the similar sequences available in the database http://blast.ncbi.nlm.nih.gov/Blast.cgi
  25. 25. AIB Running Protein-BLAST http://blast.ncbi.nlm.nih.gov/Blast.cgi
  26. 26. AIB Protein-BLAST Results
  27. 27. AIB Protein-BLAST Results
  28. 28. AIB Swiss Modeler 28http://swissmodel.expasy.org/ Paste your Sequence
  29. 29. AIB DALI Server 29 Take a Structure Search the similar structure available in the PDB http://ekhidna.biocenter.helsinki.fi/dali_server/
  30. 30. AIBOutline  Introduction  Literature Databases  Sequence Databases  Structure Databases  Chemical Databases  Tools for Analysis  Things to Remember  Some Useful Tips 30
  31. 31. AIB 10 Things You Should Remember 1. Data Security on the Web 2. Remember the Server, the Database, and the Program Version 3. Write Down the Sequence Unique ID 4. Write Down the Program Parameters 5. Alternative Ways to Save Internet Results 6. Use E-Values 7. Make Sure You Can Trust Your Alignment Results 8. Use Different Programs to Verify Borderline Results 9. Avoid the Use of Unpublished Methods! 10. Use Updated Databases 31
  32. 32. AIB Food for Thought 32
  33. 33. AIB Happening Now 33
  34. 34. AIBOutline  Introduction  Literature Databases  Sequence Databases  Structure Databases  Chemical Databases  Tools for Analysis  Things to Remember  Some Useful Tips 34
  35. 35. AIB Smart Apps for Your Smartphone 35 iMolview By Molsoft iCut DNA By EpIPhone Coders' Guild EndNote for iPad By Thomson Reuters LabTimer By 0x0c PubSearch By deathraypizza ChemDraw By PerkinElmer RCSB PDB Mobile By Philip Bourne Molarity By Sigma-Aldrich
  36. 36. AIB All The Best! -:Contact:- Room Number 407, J3 Block Amity Institute of Biotechnology Amity University Uttar Pradesh Noida-201303 pkacker@amity.edu www.puneetsclassroom.in www.facebook.com/AIBBIC

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