BIO-TRAC 25 (Proteomics: Principles and Methods)

1
Tutorial Bioinformatics Resources

• BIO-TRAC 25 (Proteomics Principles and Methods)
• October 10, 2003
• NIH, Bethesda, MD
• Zhang-Zhi Hu, M.D.
• Senior Bioinformatics Scientist,
• Protein Information Resource
• National Biomedical Research Foundation, GUMC

2
What is Bioinformatics?

• Bioinformatics is the application of information
  technology to the analysis, organization and
  distribution of biological data in order to
  answer complex biological questions.

• NIH Biomedical Information Science and Technology
  Initiative (BISTI) Working Definition (2002) -
  Research, development, or application of
  computational tools and approaches for expanding
  the use of biological, medical, behavioral or
  health data, including those to acquire, store,
  organize, archive, analyze, or visualize such
  data.

3
Bioinformatics Resources

• The Molecular Biology Database Collection An
  Online Compilation of Relevant Database Resources
• 2003 update http//www3.oup.co.uk/nar/database/
  
• Nucleic Acids Research Database Issues (January
  Annually) (2003 - http//nar.oupjournals.org/conte
  nt/vol31/issue1/)
• DBcat A Catalog of gt 500 Biological Databases
• http//www.infobiogen.fr/services/dbcat/

4
Molecular Biology Database Collection
(http//nar.oupjournals.org/cgi/content/full/31/1/
1GKG120TB1)
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The Molecular Biology Database Collection 2003
update (Baxevanis, A.D.)-- An online resource of
386 key databases of 18 categories

• Major sequence repositories
• Comparative Genomics
• Gene Expression
• Gene Identification and Structure
• Genetic and Physical Maps
• Genomic Databases
• Intermolecular Interactions
• Metabolic Pathways and Cellular Regulation

• Mutation Databases
• Pathology
• Protein Sequence Motifs
• Proteome Resources
• Retrieval Systems and Database Structure
• RNA Sequences
• Structure
• Transgenics
• Varied Biomedical Content

6
Overview

• Protein Sequence Analysis
• I. Sequence Similarity Search and Alignment
• II. Family Classification Methods
• III. Structure Prediction Methods
• Molecular Biology Databases
• IV. Protein Family Databases
• V. Database of Protein Functions
• VI. Databases of Protein Structures
• Proteomic Resources
• VII. 2D-gel databases
• VIII. Proteomic analyses

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I. Sequence Similarity Search

• Find a protein sequence text search
• Based on Pair-Wise Comparisons
• BLOSUM scoring matrix
• PAM scoring matrix
• Dynamic Programming Algorithms
• Global Similarity Needleman-Wunsch (GAP/BestFit)
• Local Similarity Smith-Waterman (SSEARCH)
• Heuristic Algorithms (Sequence Database
  Searching)
• FASTA Based on K-Tuples (2-Amino Acid)
• BLAST Triples of Conserved Amino Acids
• Gapped-BLAST Allow Gaps in Segment Pairs (NREF)
• PHI-BLAST Pattern-Hit Initiated Search (NCBI)
• PSI-BLAST Iterative Search (NCBI)

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Sequence Search by Text or Unique ID
Entrez (http//www.ncbi.nlm.nih.gov/Entrez/)
(http//pir.georgetown.edu/pirwww/search/textsearc
h.html)
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Pair-Wise Comparisons

• Scoring matrix
• Global and local
• Similarity Dynamic Programming
• (Needleman-Wunsch,
• Smith-Waterman)

(http//www.ebi.ac.uk/emboss/align/)
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FASTA Search
(http//pir.georgetown.edu/pirwww/search/fasta.htm
l)
(http//www.ebi.ac.uk/fasta33/)
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Gapped-BLAST Search
(http//pir.georgetown.edu/pirwww/search/pirnref.s
html)
(http//www.ncbi.nlm.nih.gov/BLAST/)
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A BLAST Result
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PSI-BLAST Iterative Search
(http//www.ncbi.nlm.nih.gov/BLAST/)
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PSI-BLAST
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II. Family Classification Methods

• Multiple Sequence Alignment and Phylogenetic
  Analysis
• ClustalW Multiple Sequence Alignment
• Alignment Editor Phylogenetic Trees
• Searches Based on Family Information
• PROSITE Pattern Search
• Motif and Profile Search
• Hidden Markov Model (HMMs)

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Multiple Sequence Alignment

• ClustalW (http//pir.georgetown.edu/pirwww/search
  /multaln.html)

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Alignment Editor (Jalview)
(http//www.ebi.ac.uk/clustalw/)
18
Alignment Editor (GeneDoc)
(http//www.psc.edu/biomed/genedoc/)
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Phylogenetic Analysis
Tree Programs (http//evolution.
genetics.washington.edu/phylip.html)
Tree Searches (http//pauling.
mbu.iisc.ernet.in/pali/index.html)
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Phylogenetic Trees (IGFBP Superfamily)
(Radial Tree)
(Phylogram)
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PROSITE Pattern Search
(http//pir.georgetown.edu/pirwww/search/patmatch.
html)
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Profile Search
(http//bmerc-www.bu.edu/bioinformatics/profile_re
quest.html)
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Hidden Markov Model Search
(http//www.sanger.ac.uk/Software/Pfam/search.shtm
l)
(http//smart.embl-heidelberg.de)
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III. Structural Prediction Methods

• Signal Peptide SIGFIND, SignalP
• Transmembrane Helix TMHMM, TMAP
• 2D Prediction (a-helix, b-sheet, Coiled-coils)
  PHD, JPred
• 3D Modeling Homology Modeling (Modeller,
  SWISS-MODEL), Threading, Ab-initio Prediction

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StructurePredictionA Guide
(http//speedy.embl-heidelberg.de/gtsp/flowchart2.
html)
26
Protein Prediction Server
(http//www.cbs.dtu.dk/services/)
27
Signal Peptide Prediction
(http//www.stepc.gr/synaptic/sigfind.html)
(http//www.cbs.dtu.dk/services/SignalP-2.0)
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Transmembrane Helix
(http//www.cbs.dtu.dk/services/TMHMM/)
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Protein Structure Prediction
(http//cmgm.stanford.edu/WWW/www_predict.html)
(http//restools.sdsc.edu/biotools/biotools9.html)
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Structure Prediction Server
(http//cubic.bioc.columbia.edu/predictprotein/)
(http//www.compbio.dundee.ac.uk/WWW_Servers/JPred
/jpred.html)
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3D-Modelling
(http//www.salilab.org/modeller/modeller.html)
(http//www.expasy.ch/swissmod/SWISS-MODEL.html)
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IV. Protein Family Databases

• Whole Proteins
• PIR Superfamilies and Families
• COG (Clusters of Orthologous Groups) of Complete
  Genomes
• ProtoNet Automated Hierarchical Classification
  of Proteins
• Protein Domains
• Pfam Alignments and HMM Models of Protein
  Domains
• SMART Protein Domain Families
• Protein Motifs
• PROSITE Protein Patterns and Profiles
• BLOCKS Protein Sequence Motifs and Alignments
• PRINTS Protein Sequence Motifs and Signatures
• Integrated Family Databases
• iProClass Superfamilies/Families, Domains,
  Motifs, Rich Links
• InterPro Integrate Pfam, PRINTS, PROSITES,
  ProDom, SMART

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Protein Clustering
(http//www.ncbi.nlm.nih.gov/COG/)
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Protein Domains

• Pfam (http//www.sanger.ac.uk/Software/Pfam/)

• SMART (http// smart.embl-heid elberg.de/smart/
  show_motifs.pl)

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Protein Motifs

• PROSITE is a database of protein families and
  domains. It consists of biologically significant
  sites, patterns and profiles. (http//www.expasy.c
  h/prosite/)

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Integrated Family Classification

• InterPro An integrated resource unifying
  PROSITE, PRINTS, ProDom, Pfam, SMART, and
  TIGRFAMs, PIRSF. (http//www.ebi.ac.uk/interpro/se
  arch.html)

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V. Databases of Protein Functions

• Metabolic Pathways, Enzymes, and Compounds
• Enzyme Classification Classification and
  Nomenclature of Enzyme-Catalysed Reactions
  (EC-IUBMB)
• KEGG (Kyoto Encyclopedia of Genes and Genomes)
  Metabolic Pathways
• LIGAND (at KEGG) Chemical Compounds, Reactions
  and Enzymes
• EcoCyc Encyclopedia of E. coli Genes and
  Metabolism
• MetaCyc Metabolic Encyclopedia (Metabolic
  Pathways)
• WIT Functional Curation and Metabolic Models
• BRENDA Enzyme Database
• UM-BBD Microbial Biocatalytic Reactions and
  Biodegradation Pathways
• Klotho Collection and Categorization of
  Biological Compounds
• Cellular Regulation and Gene Networks
• EpoDB Genes Expressed during Human
  Erythropoiesis
• BIND Descriptions of interactions, molecular
  complexes and pathways
• DIP Catalogs experimentally determined
  interactions between proteins
• RegulonDB Escherichia coli Pathways and
  Regulation

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KEGG Metabolic Regulatory Pathways

• KEGG is a suite of databases and associated
  software, integrating our current knowledge
• on molecular interaction networks, the
  information of genes and proteins, and of
  chemical
• compounds and reactions. (http//www.genome.ad.
  jp/kegg/kegg2.html)

(http//www.genome.ad.jp/dbget-bin/show_pathway?hs
a00590874)
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BioCyc (EcoCyc/MetaCyc Metabolic Pathways)

• The BioCyc Knowledge Library is a collection of
  Pathway/Genome
• Databases (http//biocyc.org/)

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Protein-Protein Interactions DIP
(http//dip.doe-mbi.ucla.edu/)
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Protein-Protein Interaction BIND
(http//www.bind.ca/)
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BioCarta Cellular Pathways
(http//www.biocarta.com/index.asp)
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VI. Databases of Protein Structures

• Protein Structure and Classification
• PDB Structure Determined by X-ray
  Crystallography and NMR
• CATH Hierarchical Classification of Protein
  Domain Structures
• SCOP Familial and Structural Protein
  Relationships
• FSSP Protein Fold Family Database
• Protein Sequence-Structure Relationship
• PIR-NRL3D Protein Sequence-Structure Database
• PIR-RESID Protein Structure/Post-Translational
  Modifications
• HSSP Families and Alignments of
  Structurally-Conserved Regions

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PDB Structure Data
(http//www.rcsb.org/pdb/)
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PDBsum
Summary and Analysis (http//www.biochem.ucl.ac.uk
/bsm/pdbsum)
46
Protein Structural Classification
CATH Hierarchical domain classification of
protein structures (http//www.biochem. ucl.ac.uk/
bsm/cath_new/)
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Protein Structural Classification
The SCOP database aims to provide a detailed and
comprehensive description of the structural and
evolutionary relationships between all proteins
whose structure is known, including all entries
in the PDB.
(http//scop.mrc-lmb. cam.ac.uk/scop/)
48
VII. Proteomic Resources

• GELBANK (http//gelbank.anl.gov) 2D-gel patterns
  from completed genomes SWISS-2DPAGE
  (http//www.expasy.org/ch2d/)
• PEP Predictions for Entire Proteomes
  (http//cubic.bioc.columbia.edu/ pep/)
  Summarized analyses of protein sequences
• Proteome BioKnowledge Library (http//www.proteom
  e.com) Detailed information on human, mouse and
  rat proteomes
• Proteome Analysis Database (http//www.ebi.ac.uk/p
  roteome/) Online application of InterPro and
  CluSTr for the functional classification of
  proteins in whole genomes
• Expression Profiling databases GNF
  (http//expression.gnf.org/cgi-bin/index.cgi,
  human and mouse transcriptome), SMD
  (http//genome-www5.stanford.edu/MicroArray/SMD/,
  Stanford microarray data analysis), EBI
  Microarray Informatics (http//www.ebi.ac.uk/micro
  array/ index.html , managing, storing and
  analyzing microarray data)

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2D-Gel Image Databases (1)
(http//gelbank.anl.gov/2dgels/index.asp)
50
2D-Gel Image Databases (2)
(http//us.expasy.org/ch2d/2d-index.html)
(http//us.expasy.org/cgi-bin/nice2dpage.pl?P06493
)
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VIII. Proteome Analysis
(http//www.ebi.ac.uk/proteome)
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Expression Profiling

• Human and Mouse Transcriptome

(http//expression.gnf.org/cgi-bin/index.cgi)
(http//genome-www. stanford.edu/serum/)
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Lab

• Visit selected websites and analyze some protein
  sequences of
• your own choices.
• - List of Bioinformatics Resources of this
  tutorial available
• http//pir.georgetown.edu/huz/bioinfo_resourc
  e.html
• Try some of the following sequences for
  analysis
• 1) well characterized proteins
  PIRA26366(CYP17), JS0747(Sp1)
• 2) less characterized proteins
  PIRA59000(MATER)
• TrEMBLQ9QY16(GRTH)
• 3) hypothetical protein PIRT12515, T00338
  , T47130
• SWISS-PROTQ9BWT7