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Bioinformatics for protein sequence, structure and function

To read during Protein Structure (W44-48).

Here is a list of people who passed the assignments.

• W 44 Signals in proteins and alignments of proteins.
  
  • T.D. Schneider and R.M. Stephens "Sequence logos: a new way to display consensus sequences" Nucleic Acids Research 1990 80:6097-6100
  • S.R. Presnell and F.E. Cohen "Artifical neural networks for pattern recoginition in biochemical sequences" Annu. Rev. Biophys. Biomol. Struct. 1993 22:283-99
  1. Excercises: Predictions of signal sequences..
  2. Excercises: How do I detect a pattern in a protein
  3. Excercises: Logo creations.
  4. Excercises: How do I align two proteins.
  
  
• W 45 Secondary structure predictions and membrane predictions.
  
  • B. Rost and C. Sander, Prediction of protein secondary structure at better than 70% accuracy, J. Mol. Biol., 232, 584-599 (1993).
    
  • J Mol Biol 1995 Mar 17;247(1):11-5 Prediction of protein secondary structure by combining nearest-neighbor algorithms and multiple sequence alignments. Salamov AA, Solovyev VV
  • von Heijne, G. (1992) Membrane Protein Structure Prediction: Hydrophobicity Analysis and the "Positive Inside" Rule. J.Mol.Biol. 225,
  487-494.
  1. Excercises: Can I predict the secondary structure of a protein?
     
  2. Excercises: Can I predict what part of a protein is in a membrane?
     
• W 46 Threading and protein families.
  
  • Bowie, J. U.; Lüthy, R; Eisenberg, D. "A method to identify protein sequences that fold into a known three-dimensional structure", Science 253 164-170 (1991).
  • Jones, D.T. and Taylor, W.R. and Thornton, J.M. A new appoach to protein fold recognition Nature 1992 358 86 -- 89
  • Protein Sci 1996 May;5(5):947-55 Protein fold recognition using sequence-derived predictions. Fischer D, Eisenberg D
  • Proteins 1997 Jul;28(3):405-20 Pfam: a comprehensive database of protein domain families based on seed alignments. Sonnhammer EL, Eddy SR, Durbin R
  1. Excercises: Does my protein belong to a known protein family?
  2. Excercises: Is my protein related to a protein of known structure?
  3. Excercises: Structural databases.
• W 47 Homology modelling and verification of structures.
  
  • Timothy Cardozo, Maxim Totrov and Ruben Abagyan "Homology Modeling by the ICM method"Proteins, structure function and genetics199523:3 403-414
  • A, Sali, Blundell, T.L. "Comparative protein modelling by satisfaction of spatial restraints " J. Mol. Biol, 1993 234:779-815
  • C. Colovos and T.O. Yeates "Verification of protein structures:" Protein Science 19931511-1519
  • Lüthy, R. Bowie, J.U., Eisenberg, D "Assesment of protein models with three-dimensional profiles" Nature, 1992 Mar 5;356(6364):83-85
  • Laskowski R A, MacArthur M W, Moss D S & Thornton J M (1993). PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst., 26, 283-291.
  1. Excercises: How do I build a 3D-model of my protein?
  2. Excercises: How do I know if my 3D-model is correct ?