Problems and Perspectives in Computational Molecular Biology

Cornell University
Spring 2002

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(1) Correlated mutations contain information about protein-protein interaction. abstract, paper (2) Coevolving Protein Residues: Maximum Likelihood Identification and Relationship to Structure. abstract, paper (3) Co-evolution of Proteins with their Interaction Partners. abstract, paper

Previous presentations and presentation files (Fall 2001)

Time and Place

1 credit, S/U only.
Prerequisites:  Permission of instructor.
The seminar is required from students of the Computational Molecular Biology Program.

Instructors

Links

• Introduction
• Books on Bioinformatics and Computational Biology
• Journal webpages
• Recommended background reading
• Suggested papers
  • Structure Analysis
  • Co-evolution, Protein-protein interactions
  • Gene networks, Whole-cell simulations

session 1

Prof. Ron Elber

session 2 (two papers out of five)

• Rost, B., Schneider, R. & Sander, C. (1997). Protein fold recognition by prediction-based threading. J. Mol. Biol. 270, 471-480. abstract
• Jaroszewski, L., Rychlewski, L., Zhang, B. & Godzik, A. (1998). Fold prediction by a hierarchy of sequence, threading, and modeling methods. (1998). Protein Sci 7, 1431-1440. abstract
• Olmea, O., Rost, B. & Valencia, A. (1999). Effective use of sequence correlation and conservation in fold recognition. J Mol Biol. 293, 1221-1239. abstract
• Karplus, K., Barrett, C., Cline, M., Diekhans, M., Grate, L. & Hughey, R. (1999). Predicting protein structure using only sequence information. Proteins 37, 121-125. abstract
• Jones, D. T. (1999). GenTHREADER: an efficient and reliable protein fold recognition method for genomic sequences. J. Mol. Biol. 287, 797-815. abstract

  session 3 (two papers out of four)

• Lemer, C. M., Rooman, M. J. & Wodak, S. J. (1995). Protein structure prediction by threading methods: evaluation of current techniques. Proteins 23, 337-355. abstract
• Bryant, S. H. (1996). Evaluation of threading specificity and accuracy. Proteins 26, 172-185. abstract
• Mirny, L. A. & Shakhnovich, E. I. (1998). Protein structure prediction by threading. Why it works and why it does not. J. Mol. Biol. 283, 507-526. abstract
• Bienkowska JR, Yu L, Zarakhovich S, Rogers RG Jr, Smith TF. (2000). Protein fold recognition by total alignment probability. Proteins 40, 451-62. abstract

session 4 (two papers our of three)

• Nussinov R, Wolfson HJ. (1991). Efficient detection of three-dimensional structural motifs in biological macromolecules by computer vision techniques. Proc Natl Acad Sci USA. 88, 10495-10499. abstract
• Holm, L. & Sander, C. (1997). Dali/FSSP classification of three-dimensional protein folds. Nucl. Acids Res. 25, 231-234. abstract
• Shindyalov, I. N. \& Bourne, P. E. (1998). Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng. 11, 739-747. abstract

  session 5 (two papers out of three)

• Levitt, M & Gerstein, M. (1998). A Unified Statistical Framework for Sequence Comparison and Structure Comparison. Proc. Natl. Acad. Sci. USA 95, 5913-5920. abstract
• Jongsun Jung and Byungkook Lee. (2000). Protein structure alignment using environmental profiles. Protein Eng. 13, 535-543. abstract
• Hadley, C. & Jones, D. T. (1999). A systematic comparison of protein structure classifications: SCOP, CATH and FSSP. Structure Fold Des. 7, 1099-1112. abstract

session 6 (two papers out of three)

• Holm, L. & Sander, C. (1994). Parser for protein folding units. Proteins 19, 256-268. abstract
• Sowdhamini R, Blundell TL. (1995). An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins. Protein Sci 4, 506-520. abstract
• Jones, S., Stewart, M., Michie, A., Swindells, M. B., Orengo, C. & Thornton, J. M. (1998). Domain assignment for protein structures using a consensus approach: characterization and analysis. Protein Sci. 7, 233-242. abstract

  session 7 (two papers out of three)

• Taylor, W. R. (1999). Protein structural domain identification. Protein Eng. 12, 203-216. abstract
• Xu, Y., Xu, D. & Gabow, H. N. (2000). Protein domain decomposition using a graph-theoretic approach. Bioinformatics 16, 1091-1104. abstract
• Kael F. Fischer, Susan Marqusee. (2000). A Rapid Test for Identification of Autonomous Folding Units in Proteins. J Mol Biol. 302, 701-12. abstract

session 8 (two papers out of four)

• Pellegrini M, Marcotte EM, Thompson MJ, Eisenberg D, Yeates TO. (1999). Assigning protein functions by comparative genome analysis: protein phylogenetic profiles. Proc Natl Acad Sci USA. 96, 4285-8. abstract
• Marcotte EM, Xenarios I, van Der Bliek AM, Eisenberg D. (2000). Localizing proteins in the cell from their phylogenetic profiles. Proc Natl Acad Sci USA 97, 12115-20. abstract
• Kelley, L. A., MacCallum, R. M. & Sternberg, M. J. (2000). Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol. 299, 499-520. abstract
• Marcotte EM, Pellegrini M, Thompson MJ, Yeates TO, Eisenberg D. (1999).A combined algorithm for genome-wide prediction of protein function. Nature 402, 83-6. abstract

session 9

• Marcotte EM, Pellegrini M, Ng HL, Rice DW, Yeates TO, Eisenberg D. (1999). Detecting protein function and protein-protein interactions from genome sequences. Science 285, 751-3. abstract
• Enright AJ, Iliopoulos I, Kyrpides NC, Ouzounis CA. (1999). Protein interaction maps for complete genomes based on gene fusion events. Nature 402, 86-90. abstract

  session 10 (two papers out of three)

• Schwikowski B, Uetz P, Fields S. (2000). A network of protein-protein interactions in yeast. Nat Biotechnol. 18, 1257-61. abstract
• Gallet X, Charloteaux B, Thomas A, Brasseur R. (2000). A fast method to predict protein interaction sites from sequences. J Mol Biol. 302, 917-26. abstract
• Park J, Lappe M, Teichmann SA. (2001). Mapping protein family interactions: intramolecular and intermolecular protein family interaction repertoires in the PDB and yeast. J Mol Biol. 307, 929-38. abstract

  session 11 (two papers out of three)

• Pazos, F., Helmer-Citterich, M., Ausiello, G. \& Valencia, A. (1997). Correlated mutations contain information about protein-protein interaction. J. Mol. Biol. 271, 511-523. abstract
• David D. Pollock, William R. Taylor, Nick Goldman. (1999). Coevolving Protein Residues: Maximum Likelihood Identification and Relationship to Structure. Journal of Molecular Biology 287, 187-198. abstract
• Goh CS, Bogan AA, Joachimiak M, Walther D, Cohen FE. (2000). Co-evolution of Proteins with their Interaction Partners. J Mol Biol. 299, 283-93. abstract

session 12

• Wessels LF, van Someren EP, Reinders MJ. (2001). A comparison of genetic network models. Pac Symp Biocomput. 508-19. abstract
• Maki Y, Tominaga D, Okamoto M, Watanabe S, Eguchi Y. (2001). Development of a system for the inference of large scale genetic networks. Pac Symp Biocomput. 446-58. abstract
• Saqi MA, Sternberg MJ. (2001). A structural census of metabolic networks for E. coli. J Mol Biol. 313, 1195-206. abstract

  session 13

• Friedman N, Linial M, Nachman I, Pe'er D. (2000). Using Bayesian networks to analyze expression data. J Comput Biol. 7, 601-20. abstract
• Pe'er D, Regev A, Elidan G, Friedman N. (2001). Inferring subnetworks from perturbed expression profiles. Bioinformatics 17 abstract

  session 14

• Karp PD. (2001). Pathway databases: a case study in computational symbolic theories. Science. 293, 2040-4. abstract
• Ideker T, Galitski T, Hood L. (2001). A new approach to decoding life: systems biology. Annu Rev Genomics Hum Genet. 2, 343-72. abstract