Download - 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
3
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
5
AIBNCBI: PubMed
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1 2
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http://www.ncbi.nlm.nih.gov/pubmed/
AIBGoogle Scholar
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1 2
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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
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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
21
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
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