Computer Science 296.4
Topics in Computational Structural Biology

Overview | Syllabus | Schedule | How to give a good talk
Supplemental Materials | Some Relevant WWW Links

Schedule and Readings

Please check this webpage, and schedule frequently, since I will post new papers and new readings and new assignments frequently, as we proceed through the term.

Please note: These dates and times might move some (see "The Queue", below), as we adapt to the time required to discuss the papers, or if I am unexpectedly called to Washington, etc.

*Papers that are not available online (below) have been handed out on paper.

*RECOMB papers (Proceedings of the Nth Annual International Conference on Computational Molecular Biology (N=1,2,3,4,...)) are available online via the ACM Digital Library.

In case the links at ACM, PNAS, etc. are down, Here is a local copy of many of the papers.

A few papers will be handed out in class. If you miss class, you can copy them from a classmate.

Announcements will be made in class. I will try to post them here, so consult this website.

Here is a useful bibliography of papers (and PDFs) in the area of this course.

Class Schedule

NOTE: Some PDF links may only work when accessed while on Duke's network!

  1. M 1/12
    Presenting: Bruce Donald.
    Overview and Administrivia
  2. F 1/16
    Talk: Pehr Harbury.
    Title TBA

    Everyone is encouraged to attend Pehr Harbury's talk as part of the 2009 Biochemistry seminar.

    Location: Friday at 12:00 noon in 147 Nanaline Duke Bldg.

  3. M 1/19
    No Class. Martin Luther King Day
  4. M 1/26
    Presenting: Anna Yershova.
    Kinematic Closure Constraints and RDCs
    [ Slides, Movie 1, Movie 2 ]
    Reading:
  5. M 2/2
    Presenting: Ivelin Georgiev.
    Novel Algorithms for Protein Design
    Reading:
  6. M 2/9
    Presenting: Nanjiang Shu.
    Dynamics of Phosphorylation and its implications for structural and systems biology
    Reading:
  7. M 2/16

    Reminder: Project proposals are due on Thursday, February 12. More information is available on the Syllabus page.

    Presenting: Kyle Roberts
    Rotamer optimization for protein design through MAP estimation and problem-size reduction
    Slides: [PDF] [PPT] [PPTX]
    Reading:

    1. Eun-Jong Hong et al., "Rotamer optimization for protein design through MAP estimation and problem-size reduction," Journal of Computational Chemistry (2008). (Epub ahead of print) [PDF]
  8. M 2/23
    Presenting: Pablo Gainza
    Accurate prediction for atomic-level protein design and its application in diversifying the near-optimal sequence space
    Slides: [PDF]
    Reading:
    1. Chen Yanover Menachem Fromer "Accurate prediction for atomic-level protein design and its application in diversifying the near-optimal sequence space," Proteins: Structure, Function, and Bioinformatics (2008). (Epub ahead of print) [HTML]
    2. Menachem Fromer and Chen Yanover "A computational framework to empower probabilistic protein design," Bioinformatics 24, no. 13 (2008): i214-222. [PDF]
    3. Hetunandan Kamisetty, Eric P. Xing, Christopher J. Langmead, "Free Energy Estimates of All-Atom Protein Structures Using Generalized Belief Propagation" Journal of Computational Biology. September 1, 2008, 15(7): 755-766. doi:10.1089/cmb.2007.0131. [PDF]
    Please focus on paper (1), but relate to papers (2) and (3); compare and contrast.
  9. M 3/9
    Spring Break
  10. M 3/16
    Presenting: Swati Jain
    HIV-1 Protease Inhibitors from Inverse Design in the Substrate Envelope Exhibit Subnanomolar Binding to Drug-Resistant Variants
    Slides: [PPTX]
    Reading:
    1. Michael D Altman et al., "HIV-1 Protease Inhibitors from Inverse Design in the Substrate Envelope Exhibit Subnanomolar Binding to Drug-Resistant Variants," Journal of the American Chemical Society 130, no. 19 (2008): 6099-6113. [PDF]
    2. David J. Huggins, Michael D. Altman, Bruce Tidor, "Evaluation of an inverse molecular design algorithm in a model binding site," Proteins: Structure, Function, and Bioinformatics (2008). (Epub ahead of print) [HTML]
    Please be sure to cover algorithm for pruning ligand rotamers during buildup.
  11. M 3/23
    Presenting: Desmond Moore
    NMR of invisible excited states
    Reading:
    1. Pramodh Vallurupalli, D. Flemming Hansen, and Lewis E Kay, "Structures of invisible, excited protein states by relaxation dispersion NMR spectroscopy," Proceedings of the National Academy of Sciences 105, no. 33 (2008): 11766-11771. [PDF]
    2. D. Hansen, Pramodh Vallurupalli, and Lewis Kay, "Using relaxation dispersion NMR spectroscopy to determine structures of excited, invisible protein states," Journal of Biomolecular NMR 41, no. 3 (July 1, 2008): 113-120, doi:10.1007/s10858-008-9251-5. [PDF]
    3. Pramodh Vallurupalli et al., "Measurement of bond vector orientations in invisible excited states of proteins," Proceedings of the National Academy of Sciences 104, no. 47 (2007): 18473-18477. [PDF]
    4. Dmitry M Korzhnev and Lewis E Kay, "Probing Invisible, Low-Populated States of Protein Molecules by Relaxation Dispersion NMR Spectroscopy: An Application to Protein Folding," Accounts of Chemical Research 41, no. 3 (2008): 442-451. [PDF]
  12. M 3/30
    Presenting: Shashidhara Ganjugunte
    Clustering and Matching Modulo a Group
    Slides: [PDF]
    Reading:
    1. Ryan H Lilien et al., "A subgroup algorithm to identify cross-rotation peaks consistent with non-crystallographic symmetry," Acta Crystallographica Section D 60, no. 6 (2004): 1057-1067. [PDF]
    2. Robert H O'Neil et al., "Phylogenetic Classification of Protozoa Based on the Structure of the Linker Domain in the Bifunctional Enzyme, Dihydrofolate Reductase-Thymidylate Synthase," J. Biol. Chem. 278, no. 52 (2003): 52980-52987. [PDF]
    3. Christopher James Langmead and Bruce Randall Donald, "An expectation/maximization nuclear vector replacement algorithm for automated NMR resonance assignments," Journal of Biomolecular NMR 29, no. 2 (June 1, 2004): 111-138, doi:10.1023/B:JNMR.0000019247.89110.e6. [PDF]
    4. Christopher James Langmead, Bruce Randall Donald, "3D Structural Homology Detection via Unassigned Residual Dipolar Couplings," csb,pp.209, IEEE Computer Society Bioinformatics Conference (CSB'03), 2003 [PDF]
    5. Christopher James Langmead et al., "A Polynomial-Time Nuclear Vector Replacement Algorithm for Automated NMR Resonance Assignments," Journal of Computational Biology 11, no. 2-3 (2004): 277-298. [PDF]
  13. M 4/6
    Presenting: Jonathan Jou
    Consistent blind protein structure generation from NMR chemical shift data
    Slides: [PPT]
    Reading:
    1. Yang Shen et al., "Consistent blind protein structure generation from NMR chemical shift data," Proceedings of the National Academy of Sciences 105, no. 12 (2008): 4685-4690. [PDF]
  14. M 4/13
    Presenting: John MacMaster
    NMR Structure Determination
    Slides: [PPT]
    Reading:
    1. Peter Güntert, "Automated NMR protein structure calculation," Progress in Nuclear Magnetic Resonance Spectroscopy 43, no. 3-4 (December 19, 2003): 105-125, doi:doi: DOI: 10.1016/S0079-6565(03)00021-9. [PDF]
    2. Amanda S Altieri and R Andrew Byrd, "Automation of NMR structure determination of proteins," Current Opinion in Structural Biology 14, no. 5 (October 2004): 547-553, doi:doi: DOI: 10.1016/j.sbi.2004.09.003. [PDF]
    3. Wolfram Gronwald and Hans Robert Kalbitzer, "Automated structure determination of proteins by NMR spectroscopy," Progress in Nuclear Magnetic Resonance Spectroscopy 44, no. 1-2 (April 16, 2004): 33-96, doi:doi: DOI: 10.1016/j.pnmrs.2003.12.002. [PDF]
    4. Martin Blackledge, "Recent progress in the study of biomolecular structure and dynamics in solution from residual dipolar couplings," Progress in Nuclear Magnetic Resonance Spectroscopy 46, no. 1 (March 17, 2005): 23-61, doi:doi: DOI: 10.1016/j.pnmrs.2004.11.002. [PDF]
    1, 2, and 3 are primary papers. 4 is a secondary paper.
  15. M 4/20

    Projects are due today! [Syllabus]
    Send your completed projects to Jeff for archiving and grading please.

    Presenting: Jianyang (Michael) Zeng
    Structure Determination using RDCs
    Reading:
    1. F. Fiorito, T. Herrmann, F.F. Damberger and K. Wüthrich. Automated amino acid side-chain NMR assignment of proteins using 13C- and 15N-resolved 3D [1H,1H]-NOESY. Journal of Biomolecular NMR; 2008; 42(1); pp 23-33. [PDF]
    2. J. Zeng, J. Boyles, C. Tripathy, L. Wang, A. Yan, P. Zhou and B.R. Donald. High-Resolution Protein Structure Determination Starting with a Global Fold Calculated from Exact Solutions to the RDC Equations. Journal of Biomolecular NMR. Submitted for review. [PDF]
  16. TBA
    Presenting: Chittaranjan Tripathy
    Structure Determination using RDCs
    Reading:
    1. S. Achuthan et al., "Continuity conditions and torsion angles from ssNMR orientational restraints," Journal of Magnetic Resonance 191, no. 1 (March 2008): 24-30, doi:doi: DOI: 10.1016/j.jmr.2007.11.018. [PDF]
    2. T. Asbury et al., "PIPATH: An optimized algorithm for generating [alpha]-helical structures from PISEMA data," Journal of Magnetic Resonance 183, no. 1 (November 2006): 87-95, doi:doi: DOI: 10.1016/j.jmr.2006.07.020. [PDF]
    3. J.R. Quine, M.T. Brenneman, and T.A. Cross, "Protein structural analysis from solid-state NMR-derived orientational constraints" 72, no. 5 (May 1, 1997): 2342-2348. [PDF]
  17. TBA
    Presenting: Cheng-Yu Chen
    Dynamic thiolation-thioesterase structure of a non-ribosomal peptide synthetase
    Reading:
    1. Tugarinov V, Muhandiram R, Ayed A, Kay LE. Four-dimensional NMR spectroscopy of a 723-residue protein: chemical shift assignments and secondary structure of malate synthase g. J Am Chem Soc. 2002 Aug 28;124(34):10025-35. [PDF]
    2. G. Tugarinov V, Kay LE. Quantitative NMR studies of high molecular weight proteins: application to domain orientation and ligand binding in the 723 residue enzyme malate synthase J Mol Biol. 2003 Apr 11;327(5):1121-33. [PDF]
    3. Tugarinov V, Kay LE. Ile, Leu, and Val methyl assignments of the 723-residue malate synthase G using a new labeling strategy and novel NMR methods. J Am Chem Soc. 2003 Nov 12;125(45):13868-78. [PDF]
    4. Tugarinov V, Hwang PM, Kay LE. Nuclear magnetic resonance spectroscopy of high-molecular-weight proteins. Annu Rev Biochem. 2004;73:107-46. [PDF]
    5. Tugarinov V, Choy WY, Orekhov VY, Kay LE. Solution NMR-derived global fold of a monomeric 82-kDa enzyme. Proc Natl Acad Sci U S A. 2005 Jan 18;102(3):622-7. Epub 2005 Jan 6. [PDF]
  18. TBA
    Presenting: Faisal Reza
    Title
    Reading:
    1. Coming Soon
  19. TBA
    Presenting: Ed triplett
    Epsilon-poly-L-lysine dispersity is controlled by a highly unusual nonribosomal peptide synthetase.
    Reading:
    1. Kazuya Yamanaka et al., "[epsi]-Poly-L-lysine dispersity is controlled by a highly unusual nonribosomal peptide synthetase," Nat Chem Biol 4, no. 12 (December 2008): 766-772, doi:10.1038/nchembio.125. [PDF]
    2. Jan C. M. van Hest, "Biochemistry: Flexible peptide assembly," Nature 456, no. 7219 (November 13, 2008): 186-187, doi:10.1038/456186a. [PDF]



  20. TBA
    Presenting: TBA
    Structure Determination using RDCs
    Reading:
    1. Fang Tian, Homayoun Valafar, and James H Prestegard, "A Dipolar Coupling Based Strategy for Simultaneous Resonance Assignment and Structure Determination of Protein Backbones," Journal of the American Chemical Society 123, no. 47 (2001): 11791-11796. [PDF]
    2. Kang Chen and Nico Tjandra, "Top-down approach in protein RDC data analysis: de novo estimation of the alignment tensor," Journal of Biomolecular NMR 38, no. 4 (2007): 303-313, doi:10.1007/s10858-007-9168-4. [PDF]
  21. TBA
    Presenting: Robert Gillespie
    Inositol Hexakisphosphate Is Bound in the ADAR2 Core and Required for RNA Editing
    Reading:
    1. Mark R Macbeth et al., "Inositol Hexakisphosphate Is Bound in the ADAR2 Core and Required for RNA Editing," Science 309, no. 5740 (2005): 1534-1539. [PDF]
    2. T. Renee Dawson, Christopher L Sansam, and Ronald B Emeson, "Structure and Sequence Determinants Required for the RNA Editing of ADAR2 Substrates," J. Biol. Chem. 279, no. 6 (2004): 4941-4951. [PDF]