CAP5515: Computational Molecular Biology
Term: Spring 2008
Time: Tuesday 10:40am-12:35pm, Thursday 10:40am-11:30pm
Location: CSE 107
Office hours: Tuesday 13:30pm-15:30pm
Professor: Alper Üngör

syllabus announcements schedule projects references

Announcements

Schedule

Date Lecture Topic Speaker
Jan 8 Tu Introduction, syllabus, course structure, etc. A
Jan 10 Th Introduction to DNA, Dogma of Life, Shape and Function A
Jan 15 Tu Biomolecules, Chromosomes, DNA structure, Double Helix, Sequencing, Human Genome Project, RNA structure A
Jan 17 Th Biomolecules, Code of Life, Structure and Functionality, Protein Structure A
Jan 22 Tu Pop, Salzberg, Shumway. Genome Sequence Assembly: Algorithms and Issues. Saifullah
Jan 22 Tu Pierce NA, Winfree E. Protein design is NP-hard. Protein Eng. 2002 Oct;15(10):779-82. Subhajit
Jan 24 Th 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 Mathew
Jan 29 Tu Weber and Myers. Human Whole-Genome Shotgun Sequencing. Genome Research Vol. 7, No. 5, pp. 401-409, May 1997 Cheng-Wei
Jan 29 Tu Yu Xia, Michael Levitt. Simulating protein evolution in sequence and structure space. Current Opinion in Structural Biology 14: 202-207, 2004 Guan
Jan 31 Th Secondary Structure, alpha helices, beta strands, Ramachandran plots Alper
Feb 5 Tu 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. Chunchun
Feb 5 Tu Needleman and Wunsch (1970) A general method applicable to the search for similarities in the amino acid sequence of two proteins. Ai-Ti
Feb 7 Th Almost-Delaunay Tetrahedra for Analyzing Protein Structure Hale
Feb 12 Tu 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 Mayank
Feb 12 Tu Keich and Pevzner, Finding Motifs in the twilight zone , Bioinformatics, 2002. Sudan
Feb 14 Th Predicting protein function from sequence and structure. David Lee, Oliver Redfern and Christine Orengo Sona
Feb 19 Tu Karplus and McCammon. Molecular dynamics simulations of biomolecules. Cherry
Feb 19 Tu Park S, Yang X, Saven JG. Advances in computational protein design. Curr Opin Struct Biol. 2004 Aug;14(4):487-94 Bill
Feb 21 Th
Feb 26 Tu
Feb 28 Th Shapes Alper
Mar 4 Tu Stormo, G.D., DNA binding sites: representation and discovery, Bioinformatics, (16) 1:16-23, 2000. Sudan
Mar 6 Th Prediction of enzyme function based on 3D templates of evolutionarily important amino acids. Kristensen et al. BMC Bioinformatics 2008, 9:17 Sona
Mar 18-20 No Class (Due to DOE panel travel)
Mar 25 Tu Class Discussion
Mar 27 Th Protein Structure Prediction Using Rosetta. Carol A. Rohl , Charlie E. M. Strauss , Kira M. S. Misura and David Baker (Journal: Methods in Enzymology)
Advances in Rosetta protein structure prediction on massively parallel systems. S. Raman, B. Qian, D. Baker, R. C. Walker 		Cherry
Apr 1 Tu "Review: Protein Secondary Structure Prediction Continues to Rise", Rost, B. J. of Structural Biology, 2001. Chengwei
Apr 1 Tu Lieberman E, Hauert C, Nowak MA. Evolutionary dynamics on graphs. Nature. 2005 Guan
Apr 3 Th Pande et al. "Atomistic protein folding simulations on the submillisecond time scale using worldwide distributed computing". Biopolymers, Vol. 68, No. 1, 2003. pp. 91-109. Bill
April 8 Tu The Design, Implementation, and Evaluation ofmpiBLAST, Darling, Carey, Feng. Mayank
April 8 Tu "Automated Protein Structure Determination from NMR Spectra," Blanca Lopez-Mendez and Peter Guntert. AiTi
Apr 10 Th Computation of Tunnels in protein molecules using Delaunay triangulation. Medek Benes Sochor.
Visualization of Tunnels in Protein Molecules. Kozlikova, Andres, Sochor. 		Hale
Apr 15 Tu 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. Saifullah
Apr 15 Tu Fast protein folding in the hydrophobic-hydrophilic model within three-eights of optimal. William E. Hart ,Sorin Istrail. Subhajit
Apr 17 Th Probik: Protein Backbone Motion by Inverse Kinematics. Kimberly Noonan, David OżBrien and Jack Snoeyink Chunchun

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