phd coursework

AIB

PhD Coursework in Life Sciences

Computational Biology

28 September 2013

Dr. Puneet Kackerwww.puneetsclassroom.in

AIBOutline

Introduction Literature Databases Sequence Databases Structure Databases Chemical Databases Tools for Analysis Things to Remember Some Useful Tips

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AIBOutline

Introduction Literature Databases Sequence Databases Structure Databases Chemical Databases Tools for Analysis Things to Remember Some Useful Tips

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AIBIntroduction

4

Computers in Life Sciences

Immunoinformatics

Computational Chemistry

Bioinformatics

Computational Biology

Chemoinformatics

Computational Drug Design

Systems Biology

Computational Neuroscience

AIBOutline

Introduction Literature Databases Sequence Databases Structure Databases Chemical Databases Tools for Analysis Things to Remember Some Useful Tips

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AIBNCBI: PubMed

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1 2

43

http://www.ncbi.nlm.nih.gov/pubmed/

AIBGoogle Scholar

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1 2

43

Settings

http://scholar.google.co.in/

Import to RefMan

AIBOutline

Introduction Literature Databases Sequence Databases Structure Databases Chemical Databases Tools for Analysis Things to Remember Some Useful Tips

8

AIBNCBI Protein

9

FASTA

FASTA Formatted Sequence

http://www.ncbi.nlm.nih.gov/protein/

AIBUniProt Database

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Names and originProtein attributesGeneral annotation (Comments)OntologiesAlternative productsSequence annotation (Features)SequencesReferencesCross-referencesEntry informationRelevant documents

UniProt Home Page

UniProt Searched for P56817

http://www.uniprot.org/

AIBNCBI Nucleotide

11http://www.ncbi.nlm.nih.gov/nuccore

AIBOutline

Introduction Literature Databases Sequence Databases Structure Databases Chemical Databases Tools for Analysis Things to Remember Some Useful Tips

12

AIBProtein Data Bank

13www.rcsb.org/pdb

AIBNucleic Acid Data Bank

14http://ndbserver.rutgers.edu/

AIBPDB File Format

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1

2

3

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Title Section

Primary Structure Section

HeterogenSection

Secondary Structure Section

Cont...

AIB

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5

6

7

8

Connectivity Annotation Section

Crystallographic and Coordinate Transformation

Section

Coordinate Section

Connectivity Section

Bookkeeping Section9

AIBVisualization

17www.rcsb.org/pdb

AIBVisualization

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Aspartic Protease: 1FKN

AIBOutline

Introduction Literature Databases Sequence Databases Structure Databases Chemical Databases Tools for Analysis Things to Remember Some Useful Tips

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AIBNCBI: PubChem

20pubchem.ncbi.nlm.nih.gov/

AIBPubChem Results

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Search forSimilar Compounds Scores >=95%

AIBZINC Database

22http://zinc.docking.org/

AIBOutline

Introduction Literature Databases Sequence Databases Structure Databases Chemical Databases Tools for Analysis Things to Remember Some Useful Tips

23

AIBBLAST

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Take a Sequence Search the similar sequences available in the database

http://blast.ncbi.nlm.nih.gov/Blast.cgi

AIBRunning Protein-BLAST

http://blast.ncbi.nlm.nih.gov/Blast.cgi

AIBProtein-BLAST Results

AIBProtein-BLAST Results

AIBSwiss Modeler

28http://swissmodel.expasy.org/

Paste your Sequence

AIBDALI Server

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Take a Structure Search the similar structure available in the PDB

http://ekhidna.biocenter.helsinki.fi/dali_server/

AIBOutline

Introduction Literature Databases Sequence Databases Structure Databases Chemical Databases Tools for Analysis Things to Remember Some Useful Tips

30

AIB10 Things You Should Remember

1. Data Security on the Web2. Remember the Server, the Database, and the Program

Version3. Write Down the Sequence Unique ID4. Write Down the Program Parameters5. Alternative Ways to Save Internet Results6. Use E-Values7. Make Sure You Can Trust Your Alignment Results8. Use Different Programs to Verify Borderline Results9. Avoid the Use of Unpublished Methods!10. Use Updated Databases

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AIBFood for Thought

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AIBHappening Now

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AIBOutline

Introduction Literature Databases Sequence Databases Structure Databases Chemical Databases Tools for Analysis Things to Remember Some Useful Tips

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AIBSmart Apps for Your Smartphone

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iMolviewBy Molsoft

iCut DNABy EpIPhone Coders'

Guild

EndNote for iPadBy Thomson Reuters

LabTimerBy 0x0c

PubSearchBy deathraypizza

ChemDrawBy PerkinElmer

RCSB PDB MobileBy Philip Bourne

MolarityBy Sigma-Aldrich

AIB

All The Best!

-:Contact:-Room Number 407, J3 Block

Amity Institute of BiotechnologyAmity University Uttar Pradesh

Noida-201303pkacker@amity.edu

www.puneetsclassroom.inwww.facebook.com/AIBBIC