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

1. AIB
PhD Coursework in Life Sciences
Computational Biology
28 September 2013
Dr. Puneet Kacker
www.puneetsclassroom.in

2. AIBOutline
 Introduction
 Literature Databases
 Sequence Databases
 Structure Databases
 Chemical Databases
 Tools for Analysis
 Things to Remember
 Some Useful Tips
2

3. AIBOutline
 Introduction
 Literature Databases
 Sequence Databases
 Structure Databases
 Chemical Databases
 Tools for Analysis
 Things to Remember
 Some Useful Tips
3

4. AIBIntroduction
4
Computers in
Life Sciences
Immunoinformatics
Computational Chemistry
Bioinformatics
Computational Biology
Chemoinformatics
Computational
Drug Design
Systems Biology
Computational
Neuroscience

5. AIBOutline
 Introduction
 Literature Databases
 Sequence Databases
 Structure Databases
 Chemical Databases
 Tools for Analysis
 Things to Remember
 Some Useful Tips
5

6. AIB
NCBI: PubMed
6
1 2
43
http://www.ncbi.nlm.nih.gov/pubmed/

7. AIB
Google Scholar
7
1 2
43
Settings
http://scholar.google.co.in/
Import to RefMan

8. AIBOutline
 Introduction
 Literature Databases
 Sequence Databases
 Structure Databases
 Chemical Databases
 Tools for Analysis
 Things to Remember
 Some Useful Tips
8

9. AIB
NCBI Protein
9
FASTA
FASTA Formatted Sequence
http://www.ncbi.nlm.nih.gov/protein/

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. AIB
NCBI Nucleotide
11http://www.ncbi.nlm.nih.gov/nuccore

12. AIBOutline
 Introduction
 Literature Databases
 Sequence Databases
 Structure Databases
 Chemical Databases
 Tools for Analysis
 Things to Remember
 Some Useful Tips
12

13. AIB
Protein Data Bank
13www.rcsb.org/pdb

14. AIB
Nucleic Acid Data Bank
14http://ndbserver.rutgers.edu/

15. AIB
PDB File Format
15
1
2
3
4
Title Section
Primary Structure Section
HeterogenSection
Secondary Structure Section
Cont...

16. AIB
16
5
6
7
8
Connectivity
Annotation Section
Crystallographic and
Coordinate Transformation
Section
Coordinate Section
Connectivity Section
Bookkeeping Section9

17. AIB
Visualization
17www.rcsb.org/pdb

18. AIB
Visualization
18
Aspartic Protease: 1FKN

19. AIBOutline
 Introduction
 Literature Databases
 Sequence Databases
 Structure Databases
 Chemical Databases
 Tools for Analysis
 Things to Remember
 Some Useful Tips
19

20. AIB
NCBI: PubChem
20pubchem.ncbi.nlm.nih.gov/

21. AIB
PubChem Results
21
Search for
Similar Compounds Scores >=95%

22. AIB
ZINC Database
22http://zinc.docking.org/

23. AIBOutline
 Introduction
 Literature Databases
 Sequence Databases
 Structure Databases
 Chemical Databases
 Tools for Analysis
 Things to Remember
 Some Useful Tips
23

24. AIB
BLAST
24
Take a Sequence
Search the similar sequences
available in the database
http://blast.ncbi.nlm.nih.gov/Blast.cgi

25. AIB
Running Protein-BLAST
http://blast.ncbi.nlm.nih.gov/Blast.cgi

26. AIB
Protein-BLAST Results

27. AIB
Protein-BLAST Results

28. AIB
Swiss Modeler
28http://swissmodel.expasy.org/
Paste your Sequence

29. AIB
DALI Server
29
Take a Structure
Search the similar structure
available in the PDB
http://ekhidna.biocenter.helsinki.fi/dali_server/

30. AIBOutline
 Introduction
 Literature Databases
 Sequence Databases
 Structure Databases
 Chemical Databases
 Tools for Analysis
 Things to Remember
 Some Useful Tips
30

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. AIB
Food for Thought
32

33. AIB
Happening Now
33

34. AIBOutline
 Introduction
 Literature Databases
 Sequence Databases
 Structure Databases
 Chemical Databases
 Tools for Analysis
 Things to Remember
 Some Useful Tips
34

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. 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