Protein Database

1
Protein Database

• Bioinformatics Lab

2
Sequence Databases

• GenBank--DNA sequences and derived protein
  sequences
• EMBL --DNA sequences and derived protein
  sequences
• DDBJ --DNA sequences and derived protein
  sequences
• SWISS-PROT--Protein sequences
• PDB--three-dimensional structures of protein

3
GenBank,EMBL DDBJ

• GenBank is the NIH genetic sequence database, an
  annotated collection of all publicly available
  DNA sequences .
• A new release is made every two months. GenBank
  is part of the International Nucleotide Sequence
  Database Collaboration, which is comprised of the
  DNA DataBank of Japan (DDBJ), the European
  Molecular Biology Laboratory (EMBL), and GenBank
  at NCBI.
• These three organizations exchange data on a
  daily basis.

4
GenBank,EMBL DDBJ

• GenBank Release 122.0,Feb.15,2001.
• 10,897,000 sequence records
• 11,720,000,000 bases
• EMBL Release 66,Mar.2,2000
• 11,169,673
• 11,916,112,872
• DDBJ,the Center for operating DDBJ, National
  Institute of Genetics (NIG),Japan,established in
  April 1995.

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Protein Databases

• There are many styles in protein databases,such
  as protein sequences,motif,classification,structur
  e, structure alignment, curation
• GenBANK,EMBL and DDBJ(derived sequences,
  http//www.ncbi.nlm.nih.gov/gorf/gorf.html)
• SWISS-PROT,PIR (sequences)
• PROSITE,PRINTS(sequence motifs)
• HSSP,FSSP(classification,alignment)
• PDB(3-D structure)

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SWISS-PROT/TrEMBL

• Annotated protein sequences,
• Established in 1986
• Developed by the SWISS-PROT groups at SIB and at
  EBI.
• Maintained collaboratively, since 1987, by the
  Department of Medical Biochemistry of the
  University of Geneva(???) and the EMBL Data
  Library (now the EMBL Outstation - The European
  Bioinformatics Institute (EBI)).
• Website http//www.expasy.ch/

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Different Features of SWISS-PROT

• Format follows as closely as possible that of
  EMBLs
• Curated protein sequence database
• Three differences
• Strives to provide a high level of
  annotations(??)
• Minimal level of redundancy(????)
• High level of integration with other databases
  (????)

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Three Distinct Criteria

• 1. Annotation
• The sequence data the citation information
  (bibliographical references) and the taxonomic
  data (description of the biological source of the
  protein) such as protein functions,post-translatio
  nal modifications ,domains and sites,secondary
  structure,quaternary structure,similarities to
  other proteins,diseases associated with
  deficiencies in the protein,sequence conflicts,
  variants, etc.

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• 2. Minimal Redundancy
• Many sequence databases contain, for a given
  protein sequence, separate entries which
  correspond to different literature reports.
  SWISS-PROT is as much as possible to merge all
  these data so as to minimize the redundancy. If
  conflicts exist between various sequencing
  reports, they are indicated in the feature table
  of the corresponding entry.

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• 3. Integration With Other Databases
• SWISS-PROT and TrEMBL - Protein sequences
• PROSITE - Protein families and domains
• SWISS-2DPAGE - Two-dimensional polyacrylamide gel
  electrophoresis???????
• SWISS-3DIMAGE - 3D images of proteins and other
  biological macromolecules
• SWISS-MODEL Repository - Automatically generated
  protein models
• CD40Lbase - CD40 ligand defects (?????)
• ENZYME - Enzyme nomenclature (???)
• SeqAnalRef - Sequence analysis bibliographic
  references (????????)

11
SWISS-PROT/TrEMBL

• TrEMBL is a computer-annotated supplement of
  SWISS-PROT that contains all the translations of
  EMBL nucleotide sequence entries not yet
  integrated in SWISS-PROT
• SWISS-PROT Release 39.15 of 19-Mar-2001 94,152
  entriesTrEMBL Release 16.2 of 23-Mar-2001
  436,924 entries

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SWISS-PROT FORMAT
 
 
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Access to SWISS-PROT and TrEMBL

• SRS - Access to SWISS-PROT, TrEMBL and other
  databases using the Sequence Retrieval System
• Full text search in SWISS-PROT and TrEMBL
• by accession number or ID (AC or ID line
  SWISS-PROT and TrEMBL)
• by description or identification (any word in the
  DE, OS, OG, GN and ID lines SWISS-PROT and
  TrEMBL)
• by author (RA line SWISS-PROT and TrEMBL)
• by citation (RL line SWISS-PROT only)
• Retrieve a list of SWISS-PROT/TrEMBL entries
• Randomly retrieve a SWISS-PROT/TrEMBL entry

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Protein Data Bank

• PDB is three-dimensional structure of
  proteins,some nuclei acids involved
• PDB is operated by RCSB(Research Collaboratory
  for Structural Bioinformatics),funded by NSF,
  DOE, and two units of NIHNIGMS National
  Institute Of General Medical Sciences and NLM
  National Library Of Medicine.
• Established at BNL Brookhaven National
  Laboratories in 1971,as an archive for biological
  macromolecular crystal structures
• In 1980s, the number of deposited structures
  began to increase dramatically.
• October 1998, the management of the PDB became
  the responsibility of RCSB.
• Website http//www.rcsb.org

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PDB Holdings List 27-Mar-2001
Molecule Type Molecule Type Molecule Type Molecule Type Molecule Type
Proteins, Peptides, and Viruses Protein/ Nucleic Acid Complexes Nucleic Acids Carbohydrates total
Exp. Tech. X-ray Diffraction and other 11045 526 552 14 12137
Exp. Tech. NMR 1832 71 366 4 2273
Exp. Tech. Theoretical Modeling 281 19 21 0 321
total total 13158 616 939 18 14731

• Structure Factor Files
• 968 NMR Restraint Files

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PDB Content Growth
17
PDB Growth in New Folds
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PDB Data File Format

• There are mainly two formatsPDB and CIF
• PDB is fixed format in its columns
• CIF is free format

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PDB Format

• HEADER First line of the entry, contains PDB ID
  code, classification, and date of deposition.
• OBSLTE Statement that the entry has been
  removed from distribution and list of the ID
  code(s) which replaced it.
• TITLE Description of the experiment represented
  in the entry.
• CAVEAT Severe error indicator. Entries with
  this record must be used with care.
• COMPND Description of macromolecular contents
  of the entry.
• SOURCE Biological source of macromolecules in
  the entry.
• KEYWDS List of keywords describing the
  macromolecule.
• EXPDTA Experimental technique used for the
  structure determination.
• AUTHOR List of contributors.
• REVDAT Revision date and related information.
• SPRSDE List of entries withdrawn from release
  and replaced by current entry.
• JRNL Literature citation that defines the
  coordinate set.
• REMARK General remarks, some are structured and
  some are free form.
• DBREF Reference to the entry in the sequence
  database(s).
• SEQADV Identification of conflicts between PDB
  and the named sequence database.
• SEQRES Primary sequence of backbone residues.
• MODRES Identification of modifications to
  standard residues.
• HET Identification of non-standard groups or
  residues (heterogens)
• HETNAM Compound name of the heterogens.

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• SHEET Identification of sheet substructures.
• TURN Identification of turns.
• SSBOND Identification of disulfide bonds.
• LINK Identification of inter-residue bonds.
• HYDBND Identification of hydrogen bonds.
• SLTBRG Identification of salt bridges
• CISPEP Identification of peptide residues in
  cis conformation.
• SITE Identification of groups comprising
  important sites.
• CRYST1 Unit cell parameters, space group, and
  Z.
• ORIGXn Transformation from orthogonal
  coordinates to the submitted coordinates (n 1,
  2, or 3).
• SCALEn Transformation from orthogonal
  coordinates to fractional crystallographic
  coordinates (n 1, 2, or 3).
• MTRIXn Transformations expressing
  non-crystallographic symmetry (n 1, 2, or 3).
  There may be multiple sets of these records.
• TVECT Translation vector for infinite
  covalently connected structures.
• MODEL Specification of model number for
  multiple structures in a single coordinate entry.
  
• ATOM Atomic coordinate records for standard
  groups.
• SIGATM Standard deviations of atomic
  parameters.
• ANISOU Anisotropic temperature factors.
• SIGUIJ Standard deviations of anisotropic
  temperature factors.
• TER Chain terminator.

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An Example of PDB

• HEADER IMMUNOGLOBULIN
  09-MAY-89 2MCG 2MCG 2
• COMPND IMMUNOGLOBULIN LAMBDA LIGHT CHAIN DIMER
  (/MCG) 2MCG 3
• COMPND 2 (TRIGONAL FORM)
  2MCG 4
• SOURCE HUMAN (HOMO SAPIENS)
  2MCG 5
• AUTHOR K.R.ELY,J.N.HERRON,A.B.EDMUNDSON
  2MCG 6
• REVDAT 2 15-JUL-92 2MCGA 1 SPRSDE
  2MCGA 1
• SPRSDE 15-OCT-90 2MCG 1MCG
  2MCGA 2
• JRNL AUTH K.R.ELY,J.N.HERRON,M.HARKER,A.B
  .EDMUNDSON 2MCG 9
• JRNL TITL THREE-DIMENSIONAL STRUCTURE OF
  A LIGHT CHAIN 2MCG 10
• REMARK 1 REFERENCE 1
  2MCG 16
• REMARK 1 AUTH A.B.EDMUNDSON,K.R.ELY,J.N.HERRO
  N,B.D.CHESON 2MCG 17
• SEQRES 1 1 216 PCA SER ALA LEU THR GLN PRO
  PRO SER ALA SER GLY SER 2MCG 183
• FORMUL 3 HOH 318(H2 O1)
  2MCG 217
• SSBOND 1 CYS 1 22 CYS 1 90
  2MCG 218
• CRYST1 72.300 72.300 185.900 90.00 90.00
  120.00 P 31 2 1 6 2MCG 223
• ORIGX1 0.013831 0.007985 0.000000
  0.00000 2MCG 224
• ORIGX2 0.000000 0.015971 0.000000
  0.00000 2MCG 225
• ORIGX3 0.000000 0.000000 0.005379
  0.00000 2MCG 226

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Fragment of CIF example

• ATOM_SITE
• loop_
• _atom_site.label_seq_id
• _atom_site.group_PDB
• _atom_site.type_symbol
• _atom_site.label_atom_id
• _atom_site.label_comp_id
• _atom_site.label_asym_id
• _atom_site.auth_seq_id
• _atom_site.label_alt_id
• _atom_site.cartn_x
• _atom_site.cartn_y
• _atom_site.cartn_z
• _atom_site.occupancy
• _atom_site.B_iso_or_equiv
• _atom_site.footnote_id
• _atom_site.label_entity_id

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3-D Structure from PDB

• 20 Amino acids
• http//www.clunet.edu/BioDev/omm/aa/aa.htm
• http//www.nyu.edu/pages/mathmol/library/life/
• http//inquiry.uiuc.edu/bioweb/tutorial/amino_acid
  s.htm

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How to Construct 3-D Molecule

• Read coordinates from PDB(?????)
• Set up data structure of molecules
• Form bonds among atoms and groups
• Calculate secondary structure
• Implement 3-D graphical algorithms
• Render 3-D graph in various style, wires, sticks,
  balls, ribbons, and the like.

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Bonds among atoms

• ATOM 20 N LEU 1 4 30.279 -25.716
  105.041 1.00 10.60 2MCG 249
• ATOM 21 CA LEU 1 4 31.406 -26.518
  104.496 1.00 9.39 2MCG 250
• ATOM 22 C LEU 1 4 32.658 -25.786
  105.165 1.00 8.90 2MCG 251
• ATOM 23 O LEU 1 4 32.890 -24.586
  104.967 1.00 8.74 2MCG 252
• ATOM 24 CB LEU 1 4 31.615 -26.794
  103.141 1.00 8.79 2MCG 253
• ATOM 25 CG LEU 1 4 31.552 -27.440
  101.860 1.00 8.37 2MCG 254
• ATOM 26 CD1 LEU 1 4 32.732 -26.945
  100.970 1.00 7.99 2MCG 255
• ATOM 27 CD2 LEU 1 4 31.706 -28.963
  102.016 1.00 8.09 2MCG 256

Leucine LEU L(???)
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Bonds between groups

• ATOM 9 N SER 1 2 25.548 -22.930
  103.333 1.00 16.05 2MCG 238
• ATOM 10 CA SER 1 2 26.608 -22.758
  104.327 1.00 15.38 2MCG 239
• ATOM 11 C SER 1 2 27.351 -24.076
  104.604 1.00 14.81 2MCG 240
• ATOM 12 O SER 1 2 27.530 -24.949
  103.740 1.00 15.00 2MCG 241
• ATOM 13 CB SER 1 2 25.887 -22.406
  105.682 1.00 15.73 2MCG 242
• ATOM 14 OG SER 1 2 25.193 -23.586
  106.117 1.00 15.14 2MCG 243
• ATOM 15 N ALA 1 3 27.758 -24.228
  105.876 1.00 13.72 2MCG 244
• ATOM 16 CA ALA 1 3 28.328 -25.397
  106.456 1.00 12.33 2MCG 245
• ATOM 17 C ALA 1 3 29.255 -26.303
  105.686 1.00 11.58 2MCG 246
• ATOM 18 O ALA 1 3 29.033 -27.552
  105.641 1.00 11.28 2MCG 247
• ATOM 19 CB ALA 1 3 27.101 -26.228
  106.998 1.00 12.39 2MCG 248
• ATOM 20 N LEU 1 4 30.279 -25.716
  105.041 1.00 10.60 2MCG 249
• ATOM 21 CA LEU 1 4 31.406 -26.518
  104.496 1.00 9.39 2MCG 250
• ATOM 22 C LEU 1 4 32.658 -25.786
  105.165 1.00 8.90 2MCG 251
• ATOM 23 O LEU 1 4 32.890 -24.586
  104.967 1.00 8.74 2MCG 252
• ATOM 24 CB LEU 1 4 31.615 -26.794
  103.141 1.00 8.79 2MCG 253
• ATOM 25 CG LEU 1 4 31.552 -27.440
  101.860 1.00 8.37 2MCG 254
• ATOM 26 CD1 LEU 1 4 32.732 -26.945
  100.970 1.00 7.99 2MCG 255
• ATOM 27 CD2 LEU 1 4 31.706 -28.963
  102.016 1.00 8.09 2MCG 256

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Nucleic Acid Database(NDB)

• The NDB Project is funded by the National Science
  Foundation and the Department of Energy
• The goal of NDBP is to assemble and distribute
  structural information about nucleic acids
• The format of NDB is the same as PDB.

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Molvie1.0

• A visual and interactive environment to
  display,analyze,fold and compare molecular
  structure.
• Developed in Java AWT by us.
• Java application/applet,really embedded in
  webpage.(http//www.cs.ucsb.edu/mli/Bioinf/softwa
  re/index.html)

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Some features

• Molvie 1.0 is programmed in Java, hence it is
  platform-independent.
• There is no limit on the number of molecules,
  atoms, residues or the number of animation frames
  displayed, as long as there is enough in computer
  memory.
• Molvie has many rendering(??) styles.
• Molvie can display two molecules simultaneously
  and allows the user to align secondary structure
  by dragging the mouse.
• Molvie also allows the users to click at some
  part of the 3-D structure of a protein and
  displays the corresponding primary amino acid
  sequences.

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Molvie Application Screen
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Molvie Applet Screen
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• Show Molvie