Bioinformatics

Biological Basics

1. Amino acids I 2. Peptide bond I 3. Proteins I 4. DNA I 5. Miscellaneous

3. Proteins

• macromolecules / polymers
• 'workhorses of the cell'
• made up of various L-amino acids connected by peptide bonds
• linear chains (unbranched)
  • protein molecule that consists of a single polypeptide chain is said to be monomeric
  • proteins made up of more than one polypeptide chain are called oligomeric
• interact with other proteins, nucleic acids, small molecules, ions, etc.

Protein Structure

Helpful tools

CATH Protein Structure Classification (University College, London)

• hierarchical classification of protein domain structures, which clusters proteins at four major levels:
• Class (C), Architecture (A), Topology (T) and Homologous superfamily (H)

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• Orengo, C.A.; Michie, A.D.; Jones, S.; Jones, D.T.; Swindells, M.B.; Thornton, J.M.; Structure 1997, 5(8), 1093-1108. CATH - a hierarchic classification of protein domain structures. [PDF I PubMed]
• Orengo, C.A.; Pearl, F.M.; Thornton, J.M.; Methods Biochem. Anal. 2003, 44, 249-271. The CATH domain structure database. [PubMed]
• Pearl,F.M.; Bennett, C.F.; Bray, J.E.; Harrison, A.P.; Martin, N.; Shepherd, A.; Sillitoe, I.; Thornton, J.; Orengo, C.A.; Nucleic Acids Res. 2003, 31(1), 452-455. The CATH database: an extended protein family resource for structural and functional genomics. [PDF I PubMed]

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DALI server (EMBL/EBI)

• 3D comparison of protein structure
• network service

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• Dietmann, S.; Park, J.; Notredame, C.; Heger, A.; Lappe, M.; Holm, L.; Nucleic Acids Res. 2001, 29(1), 55-57. A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3. [PDF I PubMed]
• Holm, L.; Sander, C.; Nucleic Acids Res. 1998, 26(1), 316-319. Touring protein fold space with Dali/FSSP. [PDF I PubMed]
• Holm, L.; Sander, C.; Nucleic Acids Res. 1999, 27(1), 244-247. Protein folds and families: sequence and structure alignments. [PDF I PubMed]

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FSSP - families of structurally similiar proteins (EMBL/EBI)

• database of structural alignments of proteins in the PDB (Protein Data Bank)
• fold classification based on structure-structure alignment of proteins

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• Getz, G.; Starovolsky, A.; Domany, E.; Bioinformatics 2004, 20(13), 2150-2152. FSSP to SCOP and CATH (F2CS) prediction server. [PubMed]
• Holm, L.; Sander, C.; Nucleic Acids Res. 1996, 24(1), 206-209. The FSSP database: fold classification based on structure-structure alignment of proteins. [PDF I PubMed]
• Holm, L.; Sander, C.; Nucleic Acids Res. 1994, 22(17), 3600-3609. The FSSP database of structurally aligned protein fold families. [PDF I PubMed]

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Protein Composition (Colorado State University)

• estimate the amino acid composition for a given protein sequence

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Protein Hydrophobicity Plots (Colorado State University)

• obtain plots, that characterize the hydrophobic character for a given protein sequence
• plots may be useful in predicting membrane-spanning domains, potential antigenic sites and regions that are likely exposed on the protein's surface

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SCOP - Structural Classifications of Proteins (MRC Cambridge)

• database provides a comprehensive and detailed description of the evolutionary and structural relationships of the proteins of known structure [PDB]
• fundamental classification unit in the SCOP database: protein domain
• domain is defined as an evolutionary unit observed in nature either in isolation or in more than one context in multidomain proteins
• protein domains are classified hierarchically into families, superfamilies, folds and classes

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  • Andreeva, A.; Howorth, D.; Brenner, S.E.; Hubbard, T.J.; Chothia, C.; Murzin, A.G.; Nucleic Acids Res. 2004, 32, D226-D229. SCOP database in 2004: refinements integrate structure and sequence family data. [PDF I PubMed]
• Hubbard, T.J.; Murzin, A.G.; Brenner, S.E.; Chothia, C.; Nucleic Acids Res. 1997, 25(1), 236-239. SCOP: a structural classification of proteins database. [PDF I PubMed]
• Murzin, A.G.; Brenner, S.E.; Hubbard, T.; Chothia, C.; J. Mol. Biol. 1995, 247(4), 536-540. SCOP: a structural classification of proteins database for the investigation of sequences and structures. [PDF I PubMed]

• LIFE - The Science of Biology (7th edition) (by W.K. Purves, D. Sadava, G.H. Orians, H. Craig Heller)
• Protein Structure by Molecular Graphics (University of Cambridge)
• Protein Structure Classification (by O. Lund, Technical University of Denmark)
• Protein Structure: Understanding Protein Conformation (by H. Jakubowski, St. John's University)
• Cozzone, A.J.; Encyclopedia of Life Sciences 2002, 1-10. Proteins: fundamental chemical properties. [PDF]
• Hadley, C.; Jones, D.T.; Structure Fold. Des. 1999, 7(9), 1099-1112. A systematic comparison of protein structure classifications: SCOP, CATH and FSSP. [PubMed]
• Ouzounis, C.A.; Coulson, R.M.; Enright, A.J.; Kunin, V.; Pereira-Leal, J.B.; Nat. Rev. Genet. 2003, 4(7), 508-519. Classification schemes for protein structure and function. [PDF I PubMed]
• Saito, N.; Adv. Biophys. 1989, 25, 95-132. Principles of protein architecture. [PubMed]
• Shakhnovich, B.E.; Max Harvey, J.; J. Mol. Biol. 2004, 337(4), 933-949. Quantifying structure-function uncertainty: a graph theoretical exploration into the origins and limitations of protein annotation. [PubMed]

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