CAP5515: Computational Molecular Biology
Term: Spring 2010
Time: Tuesday 9:35am-10:30am, Thursday 9:35am-11:30am
Location: CSE 107
Office hours: Tuesday 1:00pm-3:00pm
Professor: Alper Üngör

syllabus announcements schedule projects references

Announcements

Schedule

Date Lecture Topic Speaker
Jan 7 Th Introduction
syllabus, course structure, course work, resources, academic rules. 		A
Jan 12 Tu Algorithms and Molecular Biology
Partial Digest Problem, Slides 		A
Jan 14 Th Molecular Biology Primer A
Jan 19 Tu A
Jan 21 Th A
Jan 26 Tu A
Jan 28 Th NO CLASS -- TRAVEL
Feb 2 Tu A
Feb 4 Th A
Feb 9 Tu
Feb 11 Th
Feb 16 Tu
Feb 18 Th
Feb 23 Tu
Feb 25 Th
Mar 2 Tu
Mar 4 Th
Mar 9 Tu SPRING BREAK
Mar 11 Th SPRING BREAK
Mar 16 Tu
Mar 18 Th
Mar 23 Tu
Mar 25 Th
Mar 30 Tu
Apr 1 Th
Apr 6 Tu
Apr 8 Th EXAM
Apr 13 Tu Project Presentations
Apr 15 Th Project Presentations
Apr 20 Tu Project Presentations

References

Books
[HSRF03] Molecular Modeling: Basic Principles and Applications, 2nd Edition,
Hans-Dieter Höltje, Wolfgang Sippl, Didier Rognan, Gerd Folkers, September 2003, Wiley-VCH.
[BW02] Structural Bioinformatics, Philip E. Bourne, Helge Weissig, 2002. Wiley-Liss.
[BT99] Introduction to Protein Structure, Carl Branden, John Tooze, Garland Publishing, 2nd Edition, January 1999.
[L01] Molecular Modelling: Principles and Applications, 2nd edition, Andrew R. Leach, Published by Pearson Education EMA, January 2001.

Links
  • Pacific Symposium on Biocomputing (PSB) Online Proceedings
  • RECOMB Online Proceedings
  • Algorithms in Bioinformatics (WABI) Online Proceedings
  • Intelligent Systems in Molecular Biology (ISMB) Online Proceedings
  • BioInformatics Online journal papers
  • Proteins: Structure, Function, and Bioinformatics
  • Protein Data Bank (PDB)
  • Mage and King Softwares
  • Alpha Shapes Software
  • Molden Software
  • Molekel Software

    Papers

  • De Novo Protein Design: Fully Automated Sequence Selection. Science (1997) October 3; 278 (5335):82 B. I. Dahiyat and S. L. Mayo.
  • C. Bailey-Kellogg, A. Widge, J. J. Kelley III, M. J. Berardi, J. H. Bushweller, and B. R. Donald. The NOESY Jigsaw: Automated protein secondary structure and main-chain assignment from sparse, unassigned NMR data. Jour. Comp. Biol., 3-4(7):537-558, 2000.
  • A Polynomial-Time Algorithm for De Novo Protein Backbone Structure Determination from NMR Data. Journal of Computational Biology 2006; 13(7): 1276-1288.
  • K. Noonan, D. O'Brien, and J. Snoeyink. Probik: Protein Backbone Motion by Inverse Kinematics. The International Journal of Robotics Research 2005; 24(11): 971 - 982.
  • R. Singh, B. Berger. ChainTweak: Sampling from the Neighbourhood of a Protein Conformation. Pacific Symposium on Biocomputing 2005: 54-65.
  • Desjarlais JR, Handel TM. Side-chain and backbone flexibility in protein core design. J Mol Biol. 1999 Jul 2;290(1):305-18.
  • Huang YJ, Tejero R, Powers R, Montelione GT. A topology-constrained distance network algorithm for protein structure determination from NOESY data. Proteins. 2006 Mar 15;62(3):587-603.
  • Jung YS, Zweckstetter M. Mars -- robust automatic backbone assignment of proteins. J Biomol NMR. 2004 Sep; 30(1): 11-23.
  • Nabuurs SB, Spronk CA, Vuister GW, Vriend G. Traditional biomolecular structure determination by NMR spectroscopy allows for major errors. PLoS Comput Biol. 2006 Feb;2(2):e9.
  • Kamisetty H, Bailey-Kellogg C, Pandurangan G. An efficient randomized algorithm for contact-based NMR backbone resonance assignment. Bioinformatics. 2006 Jan 15;22(2):172-80.
  • Lopez-Mendez B, Guntert P. Automated protein structure determination from NMR spectra. J Am Chem Soc. 2006 Oct 11;128(40):13112-22.
  • Foster MP, McElroy CA, Amero CD. Solution NMR of large molecules and assemblies. Biochemistry. 2007 Jan 16;46(2):331-40.
  • Rohl CA, Baker D. De novo determination of protein backbone structure from residual dipolar couplings using Rosetta. J Am Chem Soc. 2002 Mar 20;124(11):2723-9.
  • Xu Y, Zheng Y, Fan JS, Yang D. A new strategy for structure determination of large proteins in solution without deuteration. Nat Methods. 2006 Nov;3(11):931-7.
  • Lindorff-Larsen K, Best RB, Depristo MA, Dobson CM, Vendruscolo M. Simultaneous determination of protein structure and dynamics. Nature. 2005 Jan 13;433(7022):128-32.
  • Ashworth J, Havranek JJ, Duarte CM, Sussman D, Monnat RJ Jr, Stoddard BL, Baker D. Computational redesign of endonuclease DNA binding and cleavage specificity. Nature. 2006 Jun 1;441(7093):656-9.
  • Bernard Chazelle, Carl Kingsford, Mona Singh: A Semidefinite Programming Approach to Side Chain Positioning with New Rounding Strategies. INFORMS Journal on Computing 16(4): 380-392 (2004).
  • S. Wells, S. Menor, B. Hespenheide, and M.F. Thorpe. Constrained Geometric Simulation of Diffusive Motion in Proteins. Phys. Biol. 2 (2005) S127-S136.
  • Halperin I, Ma B, Wolfson H, Nussinov R. Principles of docking: An overview of search algorithms and a guide to scoring functions. Proteins. 2002 Jun 1;47(4):409-43.
  • B. Hendrickson, "The Molecule Problem: Exploiting Structure in Global Optimization." Siam Journal of Computing, Vol. 5, No. 4, November 1995, pp. 835--857.
  • Temple F. Smith and Michael S. Waterman, Identification of Common Molecular Subsequences, J. Mol. Biol., 147:195-197, 1981. (PDF)
  • Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403-10. (PDF)
  • Zhang Y, Waterman MS. An Eulerian path approach to local multiple alignment for DNA sequences. Proc Natl Acad Sci U S A. 2005 Feb 1;102(5):1285-90. 2005 Jan 24. (PDF)
  • James L. Weber and Eugene W. Myers. Human Whole-Genome Shotgun Sequencing. Genome Research Vol. 7, No. 5, pp. 401-409, May 1997 (PDF)
  • Venter JC et al., "The sequence of the human genome.", Science, 2001 Feb 16;291(5507):1304-51. (PDF)
  • Mihai Pop, Steven L. Salzberg, Martin Shumway. Genome Sequence Assembly: Algorithms and Issues. IEEE Computer 35(7) 2002, pp. 47-54. seqsurvey.pdf
  • Pevzner, P., Tang, H., and Waterman, M.S. (2001), An Eulerian path approach to DNA fragment assembly, Proc. Natl. Acad. Sci. USA, 98 9748-9753. (PDF)
  • Stormo GD. DNA binding sites: representation and discovery. Bioinformatics. 2000 Jan;16(1):16-23. (PDF)
  • Keich U, Pevzner PA. Finding motifs in the twilight zone. Bioinformatics. 2002 Oct;18(10):1374-81. (PDF)
  • Lathrop RH, Smith TF. Global optimum protein threading with gapped alignment and empirical pair score functions. J Mol Biol. 1996 Feb 2;255(4):641-65.
  • Tatsuya Akutsu and Satoru Miyano, On the Approximability of Protein Threading, RECOMB 1997.
  • S. Wells, S. Menor, B.M. Hespenheide and M.F. Thorpe. Constrained geometric simulation of the diffusive motions in proteins. Phys. Bio., 2, S127 S136, 2005. (PDF)
  • Honig B. Protein folding: from the Levinthal paradox to structure prediction. J Mol Biol. 1999 Oct 22;293(2):283-93. (PDF)
  • Moult J. A decade of CASP: progress, bottlenecks and prognosis in protein structure prediction. Curr Opin Struct Biol. 2005 Jun;15(3):285-9. (PDF)
  • Lattman E. The state of the Protein Structure Initiative. Proteins. 2004 Mar 1;54(4):611-5. (PDF)
  • Rohl CA, Strauss CE, Misura KM, Baker D. Protein structure prediction using Rosetta. Methods Enzymol. 2004;383:66-93. (PDF)
  • Looger LL, Hellinga HW. Generalized dead-end elimination algorithms make large-scale protein side-chain structure prediction tractable: implications for protein design and structural genomics. J Mol Biol. 2001 Mar 16;307(1):429-45. (PDF)
  • Pierce NA, Winfree E. Protein design is NP-hard. Protein Eng. 2002 Oct;15(10):779-82. (PDF)
  • Park S, Yang X, Saven JG. Advances in computational protein design. Curr Opin Struct Biol. 2004 Aug;14(4):487-94.
  • Dahiyat BI, Mayo SL. De novo protein design: fully automated sequence selection. Science. 1997 Oct 3;278(5335):82-7. (
  • Looger LL, Dwyer MA, Smith JJ, Hellinga HW. Computational design of receptor and sensor proteins with novel functions. Nature. 2003 May 8;423(6936):185-90.
  • Dwyer MA, Looger LL, Hellinga HW. Computational design of a biologically active enzyme. Science. 2004 Jun 25;304(5679):1967-71.
  • Russ WP. Ranganathan R. (2002) Knowledge-based potential functions in protein design. Current Opinion in Structual Biology 12:447-52.
  • Grishaev A, Llinas M. Protein structure elucidation from minimal NMR data: the CLOUDS approach. Methods Enzymol. 2005;394:261-95.
  • Berger, B, Kleinberg J, Leighton FT. Reconstructing a Three-Dimensional Model with Arbitrary Errors Journal of the ACM, Vol. 46, No. 2, March 1999, pp. 212-235.
  • Herrmann T, Guntert P, Wuthrich K. Protein NMR structure determination with automated NOE assignment using the new software CANDID and the torsion angle dynamics algorithm DYANA. J Mol Biol. 2002 May 24;319(1):209-27. (PDF)
  • Zuiderweg ER. Mapping protein-protein interactions in solution by NMR spectroscopy. Biochemistry. 2002 Jan 8;41(1):1-7. (PDF)
  • M. A. McCoy and D. F. Wyss. Structures of protein-protein complexes are docked using only NMR restraints from residual dipolar couplings and chemical shift perturbations. Journal of the American Chemical Society, 124:2104-2105, 2002.
  • Apaydin MS, Guestrin CE, Varma C, Brutlag DL, Latombe JC. Stochastic roadmap simulation for the study of ligand-protein interactions. Bioinformatics. 2002;18 Suppl 2:S18-26.
  • Liang J, Edelsbrunner H, Fu P, Sudhakar PV, Subramaniam S. Analytical shape computation of macromolecules: I. Molecular area and volume through alpha shape. Proteins. 1998 Oct 1;33(1):1-17.
  • Liang J, Edelsbrunner H, Fu P, Sudhakar PV, Subramaniam S. Analytical shape computation of macromolecules: II. Inaccessible cavities in proteins. Proteins. 1998 Oct 1;33(1):18-29.
  • Liang J, Edelsbrunner H, Woodward C. Anatomy of protein pockets and cavities: measurement of binding site geometry and implications for ligand design. Protein Sci. 1998 Sep;7(9):1884-97.
  • I. V. Yap, D. Schneider, J. Kleinberg, D. Matthews, S. Cartinhour, S. R. McCouch. A Graph-Theoretic Approach to Comparing and Integrating Genetic, Physical and Sequence-Based Maps. Genetics, Vol. 165(2003). (PDF)
  • Nabieva E, Jim K, Agarwal A, Chazelle B, Singh M. Whole-proteome prediction of protein function via graph-theoretic analysis of interaction maps. Bioinformatics. 2005 Jun 1;21 Suppl 1:i302-i310.
  • Sharan R, Ideker T, Kelley B, Shamir R, Karp RM. Identification of protein complexes by comparative analysis of yeast and bacterial protein interaction data. J Comput Biol. 2005 Jul-Aug;12(6):835-46.
  • Lieberman E, Hauert C, Nowak MA. Evolutionary dynamics on graphs. Nature. 2005 Jan 20;433(7023):312-6.
  • L. Meyerguz, D. Kempe, J. Kleinberg, R. Elber. The Evolutionary Capacity of Protein Structures. Proc. ACM RECOMB Intl. Conference on Computational Molecular Biology, 2004.
  • Yu Xia, Michael Levitt. Simulating protein evolution in sequence and structure space. Current Opinion in Structural Biology 14: 202-207, 2004.

    • syllabus announcements schedule projects references

    Alper Üngör (ungor@cise.ufl.edu) January 2008