Computer Science 590
Seminar on Computational Biology

To give you an idea about the kind of papers we will read, here is the schedule from last year.
Note that we will read different (but equally cool) papers this year!
This is just to give you an idea!

For each class, I assign primary reading (journal papers) which are the main thing to present. Background and introductory material is given in the textbook chapters to help you present. Do not present this textbook chapter material or write course notes about it, unless it is necessary for understanding the main papers.

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.

The Queue

NOTE: To accomodate all the talks this semester, some presenters may be asked to present on the same day. Keep checking the schedule for updates.

Student presentations will proceed in a strict rotation, ordered as a queue. The queue order is:
• February 19: Kelly H, Catherine E.
• February 26: Nate G, Sahba T.
• March 5: Siyu W, Andy Z, Kamyar Y.
• March 19: Graham H, Trenton B, Shaun L.
• March 26: Vivek S, Dina D, Kunal S.
• April 2: Elle D, Michael S, Zack M.
• April 9: Peter L, Azim D, Elizabeth S.
• April 16: Honglue S, Mala P, and Liane

These are not exact dates but a presentation ordering with estimated dates. This means that if you're planning ahead, your presentation might be moved to the next class, if our discussion takes longer. It will not be possible to plan to give your presentation on a precise day for this reason. However, the order of the presentations should be relatively stable, and, in general you will not be asked to present earlier than the order dictated by the queue. Moreover, in general, the paper you are presenting will be determined well ahead of time so you can prepare.

Because of the complexities of scheduling I cannot accommodate requests to move your presentation. No exceptions will be made for (e.g.) interviews, conferences, family trips, ballet classes, sports events.

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

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

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

The Textbook for this class is: Algorithms in Structural Molecular Biology (MIT Press, 2011), abbreviated as ASMB.
Order on Amazon. 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.

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Class Schedule

NOTE: Some PDF links may only work when accessed while on Duke's network, or by using the VPN!

1. Tues, Jan. 15 Room: North 311
   Presenting: Bruce Donald.
   Introductions and Administration
   A Brief Introduction to Computational Structural Biology and Drug Design
   [Get started]
   [Slides (PDF)]

   The Textbook for this class is: Algorithms in Structural Molecular Biology (MIT Press, 2011), abbreviated as ASMB.
   Order on Amazon.

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2. Tues, Jan. 22. North 311
   Presenting: Bruce Donald.
   Topic: Dead-End Elimination and Protein Design: Full Sequence Design
   
   Dear Students,
   For every class,
   before class starts, please do all the reading, including Supplementary Materials and Footnotes.*
   If you don't you will be lost.
   Be sure to also do the secondary, background, and "Also Read" assignments.
   
   *Why? See, for example, footnotes 8, 19, and 30 in the [assigned reading] below.
   Assignment --- Due 5:00 PM Monday
   Write three questions you would like answered, or comments you would like discussed, about the assigned reading material below.
   Post your questions on Piazza by the deadline.
   Answer at least one question posed by someone else.

   Primary Reading:
   Dahiyat and Mayo. De Novo Protein Design: Fully Automated Sequence Selection. Science 278, 82-87 (1997). [PDF]
   
   The Textbook for this class is: Algorithms in Structural Molecular Biology (MIT Press, 2011), abbreviated as ASMB.
   Order on Amazon.
   
   Also read:
   ASMB Chapter 11 (Algorithms in Structural Molecular Biology (MIT Press, 2011)). [PDF]
   PDB id 1FSD, Full sequence design 1 (FSD-1) of beta beta alpha motif, NMR Stucture
   And please try to read:
   ASMB Chapter 12 (Algorithms in Structural Molecular Biology (MIT Press, 2011)).

   Here are two helpul videos:

   • Force field comparison: Amber, GROMOS, CHARMM, OPLS (see also COMMENTS section)
   • Force Field Parameterization
   
   Background Reading: ASMB Chapters 10 and 9.
   
   Hint: you will find the Mayo paper above much easier to read if you read the ASMB textbook chapter 11 first.

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3. Tue Jan. 29
   
   Presenting: Bruce Donald
   Topic: Introduction to Biomolecular NMR for Protein Structure and Dynamics
   
   Assignment --- Due 5:00 PM Monday
   Write three questions you would like answered, or comments you would like discussed, about the assigned reading material below.
   Post your questions on Piazza by the deadline.
   Answer at least one question posed by someone else.

   
   useful video: [Fourier Transform, Fourier Series, and frequency spectrum]

   Primary Reading:
   ASMB: Chapters 1-5, 8, and 13.
   Structure calculation of biological macromolecules from NMR data, by Peter Guntert
   A brief introduction to NMR spectroscopy of proteins, by Flemming Poulsen
   NMR studies of protein structure and dynamics, by Lewis Kay.

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4. Tue Feb. 5
   
   Presenting: Bruce Donald
   Topic: RDCs and Structure Calculation
   

   Assignment --- Due 5:00 PM Monday
   Write three questions you would like answered, or comments you would like discussed, about the assigned reading material below.
   Post your questions on Piazza:
   Answer at least one question posed by someone else.

   Primary Reading:
   ASMB: Chapters 15-18, 5.
   ASMB: Chapters 4,13.
   Residual Dipolar Couplings in Structure Determination of Biomolecules, by James Prestegard
   Residual Dipolar Couplings: Measurements and Applications to Biomolecular Studies, by Lincong Wang
   
   Secondary reading:
   Lecture Notes in Computational Structural Biology- Volume II (LCSB-II) -- draft 2017, Chapter 16.
   Try LibProtNMR - Library for Protein NMR.
   LibProtNMR is a software platform and library of algorithms in structural molecular biology, and has many computational methods in Biomolecular NMR.

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5. Tue Feb. 12
   
   Presenting: Bruce Donald
   Topic: Protein Design Algorithms
   

   Assignment --- Due 5:00 PM Monday
   Write three questions you would like answered, or comments you would like discussed, about the assigned reading material below.
   Post your questions on Piazza:
   Answer at least one question posed by someone else. The question can be from this week, or last week.

   Primary Reading:
   ASMB Chapter 12, Review chapter 11.
   Algorithms for protein design, by Gainza et al.
   The Minimized Dead-End Elimination Criterion and Its Application to Protein Redesign in a Hybrid Scoring and Search Algorithm for Computing Partition Functions over Molecular Ensembles, by Georgiev et al.
   Secondary reading:
   Lecture Notes in Computational Structural Biology- Volume II (LCSB-II) -- draft 2017, Chapters 3,14.
   Computational structure-based redesign of enzyme activity, by Chen et al. [PDF]
   Video: Molecular Dynamics Simulation of self assembling Peptide
   (from: An amyloid inhibitor octapeptide forms amyloid type fibrous aggregates and affects microtubule motility *)
   *You do not have to read this paper before class.

   Additional Reading:
   Leach A R, Lemon A P. Exploring the conformational space of protein side chains using dead-end elimination and the A* algorithm[J]. Proteins Structure Function and Genetics, 1998, 33(2): 227-239. [PDF]
   

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6. Tues, Feb. 19
   
   Presenting: Kelly H, Catherine E.
   Topic: Presentations
   

   Assignment --- Due 5:00 PM Monday
   Write three questions you would like answered, or comments you would like discussed, about the assigned reading material below.
   Post your questions on Piazza:
   Answer at least one question posed by someone else. The question can be from this week, or last week.
   
   Project Proposal Due: A one-page written project proposal is due by the start of class.
   Primary Reading (for Kelly's presentation): [Slides]
   

   OuYang, B., Xie, S., Berardi, M. J., Zhao, X., Dev, J., Yu, W., ... & Chou, J. J. (2013). Unusual architecture of the p7 channel from hepatitis C virus. Nature, 498(7455), 521. [PDF]

   Oestringer, B. P., Bolivar, J. H., Hensen, M., Claridge, J. K., Chipot, C., Dehez, F., ... & Schnell, J. R. (2018). Re-evaluating the p7 viroporin structure. Nature, 562(7727), E8. [PDF]

   
   Secondary reading (for Kelly's presentation):
   

   Martin, J. W., Zhou, P., & Donald, B. R. (2015). Systematic solution to homo-oligomeric structures determined by NMR. Proteins: Structure, Function, and Bioinformatics, 83(4), 651-661. [PDF]

   Clarke, D., Griffin, S., Beales, L., Gelais, C. S., Burgess, S., Harris, M., & Rowlands, D. (2006). Evidence for the formation of a heptameric ion channel complex by the hepatitis C virus p7 protein in vitro. Journal of Biological Chemistry, 281(48), 37057-37068. [PDF]

   Martin, J. W., Yan, A. K., Bailey-Kellogg, C., Zhou, P., & Donald, B. R. (2011). A graphical method for analyzing distance restraints using residual dipolar couplings for structure determination of symmetric protein homo-oligomers. Protein Science, 20(6), 970-985. [PDF]

   Martin, J. W., Yan, A. K., Bailey-Kellogg, C., Zhou, P., & Donald, B. R. (2011). A geometric arrangement algorithm for structure determination of symmetric protein homo-oligomers from NOEs and RDCs. Journal of Computational Biology, 18(11), 1507-1523. [PDF]

   
   Primary Reading (for Catherine's presentation): [Slides]
   

   Stewart-Jones, G. B., Chuang, G. Y., Xu, K., Zhou, T., Acharya, P., Tsybovsky, Y., ... & Silacci-Fregni, C. (2018). Structure-based design of a quadrivalent fusion glycoprotein vaccine for human parainfluenza virus types 1-4. Proceedings of the National Academy of Sciences, 115(48), 12265-12270. [PDF]

   
   Secondary reading (for Catherine's presentation):
   

   Nogales, E., & Scheres, S. H. (2015). Cryo-EM: a unique tool for the visualization of macromolecular complexity. Molecular cell, 58(4), 677-689. [PDF]

   Waterhouse, A., Bertoni, M., Bienert, S., Studer, G., Tauriello, G., Gumienny, R., ... & Lepore, R. (2018). SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic acids research. [PDF]

   Elmlund, D., & Elmlund, H. (2015). Cryogenic electron microscopy and single-particle analysis. Annual Review of Biochemistry, 84, 499-517. [PDF]

   Bai, X. C., McMullan, G., & Scheres, S. H. (2015). How cryo-EM is revolutionizing structural biology. Trends in biochemical sciences, 40(1), 49-57. [PDF]

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7. Weds, Feb. 20 (11:30am; 4233 French Science Building)
   
   
   Guest Lecture: Siyu Wang
   Topic: Designing disease therapeutics using provable computational protein design algorithms
   

   Abstract: Computational protein design programs compute protein sequences that perform desired biochemical functions, such as strong binding affinity towards specific targets. My work focused on applying provable protein design algorithms to the design of novel therapeutics for important diseases. They include HIV antibodies, peptide inhibitors of cystic fibrosis transmembrane conductance regulator, and antibiotics targeting on Methicillin-resistant Staphylococcus aureus.

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8. Tues, Feb. 26
   
   Presenting: Nate G, Sahba T.
   Topic: Presentations
   

   Assignment --- Due 5:00 PM Monday
   Write three questions you would like answered, or comments you would like discussed, about the assigned reading material below.
   Post your questions on Piazza:
   Answer at least one question posed by someone else. The question can be from this week, or last week.

   Primary Reading (for Nate's presentation): [Slides]
   

   Georgiev, I., Lilien, R. H., & Donald, B. R. (2008). The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles. Journal of computational chemistry, 29(10), 1527-1542. [PDF]

   Bhowmick, A., Sharma, S. C., Honma, H., & Head-Gordon, T. (2016). The role of side chain entropy and mutual information for improving the de novo design of Kemp eliminases KE07 and KE70. Physical Chemistry Chemical Physics, 18(28), 19386-19396. [PDF] [PDF - Supplementary]

   Secondary Reading (for Nate's presentation):
   

   Dym, O., Albeck, S., Gallaher, J. L., Betker, J., Röthlisberger, D., Baker, D., . . . Althoff, E. A. (2008). Kemp elimination catalysts by computational enzyme design. Nature, 453(7192), 190-195. doi:10.1038/nature06879 [PDF]

   Leach, A. R., & Lemon, A. P. (1998). Exploring the conformational space of protein side chains using dead‐end elimination and the A* algorithm. Proteins: Structure, Function, and Bioinformatics, 33(2), 227-239. [PDF]

   Lilien, R., Stevens, B., Anderson, A., & Donald, B. (Mar 27, 2004). A novel ensemble-based scoring and search algorithm for protein redesign, and its application to modify the substrate specificity of the gramicidin synthetase A phenylalanine adenylation enzyme. Paper presented at the 46-57. doi:10.1145/974614.974622 Retrieved from http://dl.acm.org/citation.cfm?id=974622 [PDF]

   
   
   Primary Reading (for Sahba's presentation): [Slides]
   

   Hallen, M. A., Jou, J. D., & Donald, B. R. (2017). LUTE (Local unpruned tuple expansion): Accurate continuously flexible protein design with general energy functions and rigid Rotamer-Like efficiency. Journal of Computational Biology, 24(6), 536-546. [PDF]

   Hallen, M. A., Gainza, P., & Donald, B. R. (2015). Compact representation of continuous energy surfaces for more efficient protein design. Journal of chemical theory and computation, 11(5), 2292-2306. [PDF]

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9. Tues, March 5
   
   Presenting: Siyu W, Andy Z, Kamyar Y.
   Topic: Presentations
   

   Assignment --- Due 5:00 PM Monday
   Write three questions you would like answered, or comments you would like discussed, about the assigned reading material below.
   Post your questions on Piazza:
   Answer at least one question posed by someone else. The question can be from this week, or last week.

   Reading for Siyu's presentation [Slides] [Snapshot of whiteboard drawing.]
   

   Simoncini, D., Allouche, D., de Givry, S., Delmas, C., Barbe, S., & Schiex, T. (2015). Guaranteed discrete energy optimization on large protein design problems. Journal of chemical theory and computation, 11(12), 5980-5989. [PDF] [Supplementary] [Secondary: ASMB Ch. 11, 12]

   Reading for Andy's presentation [Slides][Notes] [Class feedback]
   

   Noguchi, H., Addy, C., Simoncini, D., Wouters, S., Mylemans, B., Van Meervelt, L., ... & Voet, A. R. D. (2019). Computational design of symmetrical eight-bladed beta-propeller proteins. IUCrJ, 6(1). [PDF] [Secondary: ASMB 17.5 & 18.1.4]

   Primary reading for Kamyar's presentation [Slides]
   

   Kaserer, T., & Blagg, J. (2018). Combining Mutational Signatures, Clonal Fitness, and Drug Affinity to Define Drug-Specific Resistance Mutations in Cancer. Cell chemical biology, 25(11), 1359-1371. [PDF] [Supplementary]

   Secondary reading for Kamyar's presentation
   

   Frey, K. M., Georgiev, I., Donald, B. R., & Anderson, A. C. (2010). Predicting resistance mutations using protein design algorithms. Proceedings of the National Academy of Sciences, 107(31), 13707-13712. [PDF]

   Reeve, S. M., Gainza, P., Frey, K. M., Georgiev, I., Donald, B. R., & Anderson, A. C. (2015). Protein design algorithms predict viable resistance to an experimental antifolate. Proceedings of the National Academy of Sciences, 112(3), 749-754. [PDF]

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10. Weds, March 6, LSRC D240 (Extra Lecture)
    
    Presenter: Dr. Donald
    Topic: Continuous Interdomain Orientation Distributions Reveal Components of Binding Thermodynamics
    
    Dr. Donald will present an extra lecture, for those that are interested, on a paper his lab wrote in conjunction with others on the "Continuous Interdomain Orientation Distributions Reveal Components of Binding Thermodynamics."
    
    Abstract: The flexibility of biological macromolecules is an important structural determinant of function. Unfortunately, the correlations between different motional modes are poorly captured by discrete ensemble representations. Here, we present new ways to both represent and visualize correlated interdomain motions. Interdomain motions are determined directly from residual dipolar couplings, represented as a continuous conformational distribution, and visualized using the disk-on-sphere representation. Using the disk-on-sphere representation, features of interdomain motions, including correlations, are intuitively visualized. The representation works especially well for multidomain systems with broad conformational distributions.This analysis also can be extended to multiple probability density modes, using a Bingham mixture model. We use this new paradigm to study the interdomain motions of staphylococcal protein A, which is a key virulence factor contributing to the pathogenicity of Staphylococcus aureus. We capture the smooth transitions between important states and demonstrate the utility of continuous distribution functions for computing the reorientational components of binding thermodynamics. Such insights allow for the dissection of the dynamic structural components of functionally important intermolecular interactions.
    
    Paper and other information [Here].

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11. Recitation: Monday, March 18
    A* Search

    Please read [this] paper in preparation for recitation. Also, please explore [this] webpage. Slides are [here].

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12. Recitation: Thursday, March 21
    A* Search

    Please read [this] paper in preparation for recitation. Also, please explore [this] webpage. Slides are [here].

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13. Tues, March 19
    
    Presenting: Graham H, Trenton B, and Shaun L.
    Topic: Presentations
    

    Assignment --- Due 5:00 PM Monday
    Write three questions you would like answered, or comments you would like discussed, about the assigned reading material below.
    Post your questions on Piazza:
    Answer at least one question posed by someone else. The question can be from this week, or last week.

    Reading for Graham's presentation [Slides]
    

    Simoncini, D., Barbe, S., Schiex, T., & Verel, S. (2018, July). Fitness landscape analysis around the optimum in computational protein design. In Proceedings of the Genetic and Evolutionary Computation Conference (pp. 355-362). ACM. [PDF]

    Jou, J., Holt, G., Lowgard, A., Donald, B. (2019). Minimization-Aware Recursive K-* (MARK*): A Novel, Provable Algorithm that Accelerates Ensemble-based Protein Design and Provably Approximates the Energy Landscape. Preprint, will be in RECOMB 2019. [PDF] [Supplementary Information]

    Primary Reading for Trenton's presentation [Slides] [Notes]
    

    Zhou, J., Panaitiu, A. E., & Grigoryan, G. (2018). A general-purpose protein design framework based on mining sequence-structure relationships in known protein structures. bioRxiv, 431635. [PDF]

    Secondary Reading for Trenton's presentation

    Mackenzie, C. O., Zhou, J., & Grigoryan, G. (2016). Tertiary alphabet for the observable protein structural universe. Proceedings of the National Academy of Sciences, 113(47), E7438-E7447. [PDF]

    Reading for Shaun's presentation [Slides][Notes]
    

    Yeates, T. O. (2017). Geometric principles for designing highly symmetric self-assembling protein nanomaterials. Annual review of biophysics, 46, 23-42. [PDF] [Secondary: ASMB 17.5 & 18.1.4]

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14. Tues, March 26
    
    Presenting: Vivek S, Dina D, and Kunal S.
    Topic: Presentations
    

    Assignment --- Due 5:00 PM Monday
    Write three questions you would like answered, or comments you would like discussed, about the assigned reading material below.
    Post your questions on Piazza:
    Answer at least one question posed by someone else. The question can be from this week, or last week.

    Primary reading for Vivek's presentation [Slides]
    

    Lou, Q., Dechter, R., & Ihler, A. T. (2017). Dynamic Importance Sampling for Anytime Bounds of the Partition Function. In Advances in Neural Information Processing Systems (pp. 3196-3204). [PDF]

    Secondary reading for Vivek's presentation
    

    Zhou, Y., Wu, Y., & Zeng, J. (2016). Computational protein design using AND/OR branch-and-bound search. Journal of Computational Biology, 23(6), 439-451. [PDF]

    Flerova, N., Marinescu, R., & Dechter, R. (2016). Searching for the m best solutions in graphical models. Journal of Artificial Intelligence Research, 55, 889-952. [PDF]

    Jou, J. D., Jain, S., Georgiev, I. S., & Donald, B. R. (2016). BWM*: A novel, provable, ensemble-based dynamic programming algorithm for sparse approximations of computational protein design. Journal of Computational Biology, 23(6), 413-424. [PDF]

    Jain, S., Jou, J. D., Georgiev, I. S., & Donald, B. R. (2017). A critical analysis of computational protein design with sparse residue interaction graphs. PLoS computational biology, 13(3), e1005346. [PDF]

    Georgiev, I., Lilien, R. H., & Donald, B. R. (2008). The minimized dead-end elimination criterion and its application to protein redesign in a hybrid scoring and search algorithm for computing partition functions over molecular ensembles. Journal of computational chemistry, 29(10), 1527-1542. [PDF]

    Roberts, K. E., Cushing, P. R., Boisguerin, P., Madden, D. R., & Donald, B. R. (2012). Computational design of a PDZ domain peptide inhibitor that rescues CFTR activity. PLoS computational biology, 8(4), e1002477. [PDF]

    [ASMB Ch. 12, 13]

    Primary reading for Dina's presentation [Video of presentation]
    

    Simoncini, D., Zhang, K. Y., Schiex, T., & Barbe, S. (2018). A structural homology approach for computational protein design with flexible backbone. Bioinformatics. [PDF] [Supplementary]

    Secondary reading for Dina's presentation
    

    Hallen, M. A., Keedy, D. A., & Donald, B. R. (2013). Dead-end elimination with perturbations (DEEPer): A provable protein design algorithm with continuous sidechain and backbone flexibility. Proteins: Structure, Function, and Bioinformatics, 81(1), 18-39. [PDF]

    Reading for Kunal's presentation [Slides]
    

    Ben-David, M., Huang, H., Sun, M. G., Corbi-Verge, C., Petsalaki, E., Liu, K., ... & Shifman, J. M. (2019). Allosteric Modulation of Binding Specificity by Alternative Packing of Protein Cores. Journal of molecular biology, 431(2), 336-350. [PDF] [Supplementary]

    Zhang, W., & Sidhu, S. S. (2018). Generating Intracellular Modulators of E3 Ligases and Deubiquitinases from Phage-Displayed Ubiquitin Variant Libraries. In The Ubiquitin Proteasome System (pp. 101-119). Humana Press, New York, NY. [PDF] [Secondary: ASMB Ch. 10]

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15. Mon, April 1 - Extra Lecture
    
    Time/Location: 10am LSRC B101 (Love Auditorium)
    Presenter: Anna Lowegard
    Topic: Novel Algorithms and Tools for Computational Protein Design with Applications
    
    Please join us to see CBB's very own Anna Lowegard defend her thesis in this PhD dissertation defense seminar.

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16. Tues, April 2
    
    Presenting: Elle D, Michael S, and Zack M.
    Topic: Presentations
    

    Assignment --- Due 5:00 PM Monday
    Write three questions you would like answered, or comments you would like discussed, about the assigned reading material below.
    Post your questions on Piazza:
    Answer at least one question posed by someone else. The question can be from this week, or last week.

    Primary reading for Elle's presentation [Slides]
    

    Brender, J. R., & Zhang, Y. (2015). Predicting the effect of mutations on protein-protein binding interactions through structure-based interface profiles. PLoS computational biology, 11(10), e1004494. [PDF] [Supplementary]

    Secondary reading for Elle's presentation
    

    Roberts, K. E., Cushing, P. R., Boisguerin, P., Madden, D. R., & Donald, B. R. (2012). Computational design of a PDZ domain peptide inhibitor that rescues CFTR activity. PLoS computational biology, 8(4), e1002477. [PDF]

    Rudicell, R. S., Do Kwon, Y., Ko, S. Y., Pegu, A., Louder, M. K., Georgiev, I. S., ... & Shi, W. (2014). Enhanced potency of a broadly neutralizing HIV-1 antibody in vitro improves protection against lentiviral infection in vivo. Journal of virology, JVI-02213. [PDF]

    Reading for Michael's presentation [Slides]
    

    van Zundert, G. C., Hudson, B. M., de Oliveira, S. H., Keedy, D. A., Fonseca, R., Heliou, A., ... & van den Bedem, H. (2018). qFit-ligand reveals widespread conformational heterogeneity of drug-like molecules in X-ray electron density maps. Journal of medicinal chemistry, 61(24), 11183-11198. [PDF] [Supplementary] [Secondary: ASMB Ch. 24]

    Reading for Zack's presentation [Slides]
    

    AlQuraishi, Mohammed. "AlphaFold @ CASP13: 'What Just Happened?'." Some Thoughts on a Mysterious Universe, 19 Dec. 2018, moalquraishi.wordpress.com/2018/12/09/alphafold-casp13-what-just-happened/. [Materials] [AlphaFold website] [Secondary: ASMB Ch. 45]

    Secondary reading for Zack's presentation
    

    Presentation from CASP13 [PDF]

    Abstract from website [PDF]

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17. Tues, April 9
    
    Presenting: Peter L, Azim D, and Elizabeth S.
    Topic: Presentations
    

    Assignment --- Due 5:00 PM Monday
    

    1. Please give us feedback on Nate's performance as a TA here!
    2. Please comment on Kamyar's Notes, Shauns's Notes, and Trenton's Notes. See the info on the syllabus for examples of good comments.
    3. Write three questions you would like answered, or comments you would like discussed, about the assigned reading material below. Post your questions on Piazza and answer at least one question posed by someone else. The question can be from this week, or last week.

    Reading for Peter's presentation [Slides]
    

    Garton, M., Nim, S., Stone, T. A., Wang, K. E., Deber, C. M., & Kim, P. M. (2018). Method to generate highly stable D-amino acid analogs of bioactive helical peptides using a mirror image of the entire PDB. Proceedings of the National Academy of Sciences, 201711837. [PDF]

    Garton, M., Sayadi, M., & Kim, P. M. (2017). A computational approach for designing D-proteins with non-canonical amino acid optimised binding affinity. PloS one, 12(11), e0187524. [PDF] [Secondary: ASMB Ch. 9]

    Primary reading for Azim's presentation [Slides]
    

    Studer, S., Hansen, D. A., Pianowski, Z. L., Mittl, P. R., Debon, A., Guffy, S. L., ... & Hilvert, D. (2018). Evolution of a highly active and enantiospecific metalloenzyme from short peptides. Science, 362(6420), 1285-1288. [PDF] [Supplementary]
    [Supplementary]

    Secondary reading for Azim's presentation
    

    Chen, C. Y., Georgiev, I., Anderson, A. C., & Donald, B. R. (2009). Computational structure-based redesign of enzyme activity. Proceedings of the National Academy of Sciences, 106(10), 3764-3769. [PDF]

    [ASMB Ch. 13]

    Reading for Elizabeth's presentation [Slides]
    

    Silva, D. A., Yu, S., Ulge, U. Y., Spangler, J. B., Jude, K. M., Labao-Almeida, C., ... & Biary, T. (2019). De novo design of potent and selective mimics of IL-2 and IL-15. Nature, 565(7738), 186. [PDF] [Supplementary]

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18. Tues, April 16
    
    Presenting: Honglue S, Mala P, and Liane
    Topic: Presentations
    

    Assignment --- Due 5:00 PM Monday
    

    1. Please comment on Kunal's Notes and Vivek's Notes. See the info on the syllabus for examples of good comments.
    2. Write three questions you would like answered, or comments you would like discussed, about the assigned reading material below. Post your questions on Piazza and answer at least one question posed by someone else. The question can be from this week, or last week.
    Answer at least one question posed by someone else. The question can be from this week, or last week.

    Reading for Honglue's presentation [Slides]
    

    Marcos, E., Basanta, B., Chidyausiku, T. M., Tang, Y., Oberdorfer, G., Liu, G., ... & Pereira, J. H. (2017). Principles for designing proteins with cavities formed by curved beta sheets. Science, 355(6321), 201-206. [PDF] [Supplementary]

    Reading for Mala's presentation [Slides]
    

    Verschueren, E., Vanhee, P., Rousseau, F., Schymkowitz, J., & Serrano, L. (2013). Protein-peptide complex prediction through fragment interaction patterns. Structure, 21(5), 789-797. [PDF] [Supplementary] [Secondary: ASMB Ch. 10]

    Reading for Liane's presentation
    

    Sankar, K., Krystek Jr, S. R., Carl, S. M., Day, T., & Maier, J. K. (2018). AggScore: Prediction of aggregation-prone regions in proteins based on the distribution of surface patches. Proteins: Structure, Function, and Bioinformatics, 86(11), 1147-1156. [PDF]

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19. Tues, April 23
    
    Presenting:
    Topic: Project presentations [Slides]
    

    Assignment
    

    1. HARD DEADLINE: 10 a.m. Monday, April 22. Send Nathan your slides (max 3 slides, in PDF format) for your 3 minute final project presentation. See syllabus for more details.
    2. By the beginning of class, please comment on Elle's Notes and Zack's Notes. See the info on the syllabus for examples of good comments.
    3. Submit your final project by 11:59 pm on April 23rd. If you have requested an extension and had it approved, submit by 11:59 pm on April 29. Remember you can request an extension until 11:59 pm on April 20th.

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NB: To give you an idea about this class,
here and
here is the schedule of papers we read in 2018, 2016, 2015, and 2013. We will read different papers this year!

Only one class meeting will have the same papers, and that one class meeting is a warm up.

2018 Schedule (To give you an idea:)
2016 Schedule (To give you an idea:)