Bioinformatics
Lecturer: Nam Vo
Email: vtnam@[Link]
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Contents
Biological databases
Sequence comparisons and Sequence-
Based database searches
Protein structures and structure-based
rational drug design
3 Research fields in
bioinformatics???
Create databases for storing and
managing biological data sources
Introduce / Develop algorithms and
statistical methods to determine the
biological relationship between data
Use bioinformatics tools to analyze
and interpret biological data sources
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What is database???
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Database
A database is an organized collection of data, generally
stored and accessed electronically from a computer
system.
Biological databases are libraries of life sciences
information, collected from scientific experiments,
published literature, high-throughput experiment
technology, and computational analysis. They contain
information from research areas including genomics,
proteomics, metabolomics, microarray gene expression,
and phylogenetics.
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Biological Data
Sequences Structures Genomes Transcriptomes Networks
Genetics and and systems
populations
Databases Data-mining Physic and Phylogenetic
Algorithms Statistics
chemistry trees
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[Link]
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[Link]
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[Link]
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Biological database
operators
NCBI (National Center for Biotechnology Information)
EMBL-EBI (European Molecular Biology Laboratory)
DDBJ (DNA Data Bank of Japan)
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Categories
Based on kind of data they retrieve:
Primary databases
Secondary databases
Based on category of data they include:
Literature databases
Taxonomy database
Nucleotide sequence database
Genome database
Genotype-Phenotype database
Protein sequence dataset
Structure database
…
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Primary and secondary database
Primary sequence • Summarize the results from analyses
information of primary sequence databases
Sequence annotation • Other databases (literature)
information
stream
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Primary databases
Nucleotide sequence databases
Protein sequence databases
Protein structure databases
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Nucleotide sequence databases
Entrez
NIH
NCBI
•Upload
•Synchronize
GenBank
EMBL
•Upload
ENA •Synchronize
DDBJ
DDBJ EBI
NIG •Upload
•Synchronize
ENA online
getentry retrieval
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Genbank
format
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Accession number
Unique
Permanent
The only way to absolutely verify the identity of a
sequence or database entry
Used in all 3 databases (Genbank, ENA and DDBJ)
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ENA
format
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Entrez
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ENA online
retrieval
ARSA
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Protein sequence databases
Huge data:
Sequence information
Expression profiles
Secondary structures
Biological functions
Biochemical functions
UniProt (Universal Protein Resource)
NCBI protein database
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UniProt
United information from 3 databases:
Swissprot
TrEMBL
Protein Information Resource (PIR)
Consists of 3 parts:
UniProt Knowledgebase (UniProtKB)
UniProt Reference Clusters Database (UniRef)
UniProt Archive (UniPArc)
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UniProtKB
Data: Protein sequences and annotations
2 Realms:
UniProtKB/TrEMBL realm: automatically annotated
sequences (65 mil entries)
UniProtKB/SwissProt realm: manually curated and
annotated sequences (0.55 mil entries)
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UniRef
Nonredundant sequence database
Used for fast similarity searches
3 versions:
UniRef100
UniRef90
UniRef50
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Protein data bank (PDB)
Was founded at Brookhaven National
Laboratory in 1971
Database of experimentally determined crystal
structures of biological macromolecules
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PDB website
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Protein structure by NMR
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Cryo-electron microscopy
34 PDB format - ATOM
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Secondary databases
Literature databases
Motif
Protein family
Protein classification
Genotype-Phenotype database*
…
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Pubmed
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Prosite
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Sequence Motif
Short sequence regions (10-20 amino acids) that are conserved in
related proteins
Usually have a key role in the protein’s function
Provide a first hint of an affiliation to a protein family or function
Derived from multiple alignments
Example:
[GSTNE] – [GSTQCR] – [FYW] – {ANW} – x (2) – P
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Sequence Motif
Motif:
M – [ATN] – T – K – {WMC} – x (2) – P
Which of the following sequences satisfy the
motif?
A. MTTKARP
B. MNTKCARP
C. MTTKRWMP
D. AMNTKNWMP
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Pfam
Classify protein families based on profiles
Profile: pattern that evaluates the probability of the
appearance of a given amino acid, an insertion, or a
deletion at every position in a protein sequence
Search results should be reviewed
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Pfam
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PRINTS
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Interpro
Integrated Resource of Protein Families, Domains and
Sites
Merges Swissprot, TrEMBL, Prosite, Pfam, PRINTS,
ProDom, Smart, TIGRFAMS
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SCOP
SCOP – Structural Classification Of Protein
Compare retrieved protein structural
organization with that of known proteins to
predict functions
Classifications:
Families: clear evolutionary relationship (>30%
identities)
Superfamilies: low identities
Folds: The same arrangement of secondary structural
elements in the same topology
Class: based on Secondary structural elements (SSE)
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1hbg: 7 helix 1who: 8 strand
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1auz: / 1c54: +
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CATH
Compare retrieved protein structural organization with
that of known proteins to predict functions
4 caregories:
Class: proportion of secondary structural elements (SSE)
Mainly Alpha
Mainly Beta
Alpha-beta
Few SSE
Architecture: arrangement of SSE
Topology: protein form and interconnections of SSE
Homologous: homologous on protein domains
Sequence Families: >-35% identities over 60% length
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PubChem
PubChem
Compound
PubChem
Substance
PubChem
BioAssay
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1. Role of database in biological research?
2. Is it necessary to create more databases?
3. How to chose a database for collecting
certain data?
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Take home lessons
What is database and its necessary?
Distinguish between primary and secondary
databases
Know some famous databases
Read sequence motifs
Distinguish between motifs and domains
