Computer Science 590
Seminar on Computational Biology

NB: To give you an idea about this class,
this is the schedule of papers we read in 2016. 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.

2016 Schedule (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:
We will not assign exact dates to presentations but only an order in which the papers will be presented. 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. Weds, Jan. 13 Room TBA probably North 311
   Presenting: Bruce Donald.
   Introductions and Administration
   
2. Monday, Jan. 18 North 311
   No Class: MLK Day
   

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3. Monday, 1/25 North 311
   Presenting: Bruce Donald.
   Dead-End Elimination and Protein Design: Full Sequence Design
   
   Dear Students,
   For every class,
   Please do all the reading.
   If you don't you will be lost.
   Be sure to also do the secondary, background, and "Also Read" assignments.
   
   Primary Reading:
   Dahiyat, B. I. 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
   And please try to read:
   ASMB Chapter 12 (Algorithms in Structural Molecular Biology (MIT Press, 2011)).
   Background Reading: ASMB Chapters 10 and 9.
   

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4. February 1, 1:20 PM at North 311
   
   Presenting: Hunter Nisonoff
   Computational design of ligand-binding proteins with high affinity and selectivity
   [Slides PPTX] [Slides PDF]
   Primary Reading:
   Tinberg, C. E. et al. Computational design of ligand-binding proteins with high affinity and selectivity. Nature 501, 212-216 (2013) [PDF] SI: [PDF]
   
   Secondary Reading:
   
   1. Zanghellini, A. et al. New algorithms and an in silico benchmark for computational enzyme design. Protein Science 2006; 15(12) 2785-2794. [PDF]
      
   2. Fleishman, S. J. et al. Restricted sidechain plasticity in the structures of native proteins and complexes. Protein Science 2011; 20(4) 753-757. [PDF] SI: [PDF]
      

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5. February 8, 1:20 PM at North 311
   
   Presenting: Goke Ojewole
   Guaranteed Discrete Energy Optimization on Large Protein Design Problems
   [Slides PDF]
   Primary Reading:
   
   1. David Simoncini, David Allouche, Simon de Givry, Celine Delmas, Sophie Barbe, and Thomas Schiex. Guaranteed Discrete Energy Optimization on Large Protein Design Problems. Journal of Chemical Theory and Computation 2015 11 (12), 5980-5989. [PDF] SI: [PDF]
      
   2. Clement Viricel, David Simoncini, David Allouche, Simon de Givry, Sophie Barbe, Thomas Schiex. Approximate Counting with Deterministic Guarantees for Affinity Computation. [PDF]
      
   Secondary Reading:
   
   1. ASMB Ch. 12, 25, 45
      
   2. Ivelin Georgiev, Ryan H. Lilien, Bruce R. Donald. 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. J Comput Chem. 2008 Jul 30; 29(10): 1527-1542. [PDF]
      
   3. Pablo Gainza, Kyle E. Roberts, Bruce R. Donald. Protein Design Using Continuous Rotamers. PLoS Comput Biol. 2012 Jan; 8(1): e1002335. [PDF]
      SI: [SI 1] [SI 2]
      
   4. Gainza P, Roberts KE, Georgiev I, Lilien RH, Keedy DA, Chen CY, Reza F, Anderson AC, Richardson DC, Richardson JS, Donald BR. OSPREY: Protein Design with Ensembles, Flexibility, and Provable Algorithms. Methods Enzymol. 2013;523:87-107. doi: 10.1016/B978-0-12-394292-0.00005-9. [PDF]
      

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6. February 15, 1:20 PM at North 311
   
   Snow day!

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7. February 22, 1:20 PM at North 311
   
   Repeat Proteins
   
   Presenting: David Zhou
   Designing Repeat Proteins
   [Slides pdf]
   [Notes]
   Primary Reading:
   
   1. TJ Brunette, Fabio Parmeggiani, Po-Ssu Huang, Gira Bhabha, Damien C. Ekiert, Susan E. Tsutakawa, Greg L. Hura, John A. Tainer, & David Baker. Exploring the repeat protein universe through computational protein design. Nature 528, 580-584. [PDF] SI: [Link]
      
   2. Lindsey Doyle, Jazmine Hallinan, Jill Bolduc, Fabio Parmeggiani, David Baker, Barry L. Stoddard, & Philip Bradley. Rational design of alpha-helical tandem repeat proteins with closed architectures. Nature 528, 585-588. [PDF] SI: [PDF]
      
      
   Presenting: Bei Liu
   Principles of assembly reveal a periodic table of protein complexes
   [Slides ppt]
   [Slides pdf]
   [Notes]
   Primary Reading:
   Sebastian E. Ahnert, Joseph A. Marsh, Helena Hernandez, Carol V. Robinson, Sarah A. Teichmann. Principles of assembly reveal a periodic table of protein complexes. Science 2015; 350(6266), aaa2245. [PDF] SI: [Link]
   

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8. February 22, 4:15 at 437 Nanaline Duke
   
   SBB Seminar: Probing the Dynamic Contribution to Cephalosporin Resistance Conferred by Penicillin Binding Protein 2
   Presenting: Ben Fenton

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9. February 25, 1:00PM-2:00PM at LSRC D344
   Master's Defense: On Provable Algorithms for Determination of Continuous Protein Interdomain Motions from Residual Dipolar Couplings
   Presenting: Yang Qi

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10. February 29, 1:20 PM at North 311
    
    Presenting: Atul Rangadurai
    The dynamics of single protein molecules is non-equilibrium and self-similar over thirteen decades in time
    [Slides pdf]
    [Notes]
    Xiahou Hu, Liang Hong, Micholas Dean Smith, Thomas Neusius, Xiaolin Cheng, and Jeremy C. Smith. The dynamics of single protein molecules is non-equilibrium and self-similar over thirteen decades in time. Nature Physics (2015). [PDF] SI: [PDF]
    
    Presenting: JJ Jou
    iTreePack: Protein Complex Side-Chain Packing by Dual Decomposition
    [Slides ppt]
    Jain Peng, Raghavendra Hosur, Bonnie Berger, and Jinbo Xu. iTreePack: Protein Complex Side-Chain Packing by Dual Decomposition. arXiv:1504.05467v1. [PDF]

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11. March 1, 1:00PM at LSRC D344
    
    Ph.D. Defense: Protein and drug design algorithms using improved biophysical modeling
    Presenting: Mark Hallen

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12. March 7, 1:20 PM at North 311
    
    Presenting: Kevin Li
    Protein structure classification based on chaos game representation and multifractal analysis
    [Slides ppt]
    [Slides pdf]
    Primary Reading:
    
    1. Jian-Yi Yang; Zu-Guo Yu; Anh, V., Protein Structure Classification Based on Chaos Game Representation and Multifractal Analysis," in Natural Computation, 2008. ICNC '08. Fourth International Conference on , vol.4, no., pp.665-669, 18-20 Oct. 2008 doi: 10.1109/ICNC.2008.295 [PDF]
    Secondary Reading:
    
    1. Jeffrey, H Joel. Chaos game representation of gene structure. Nucleic Acids Res. 1990 Apr 25; 18(8): 2163–2170 [PDF]
    2. Jeffrey, H Joel. Chaos game visualization of sequences. Comput & Graphics Vol. 16 No. 1, pp 25-33. [PDF]
    3. Lila Kari, Kathleen A. Hill, Abu Sadat Sayem, Nathaniel Bryans, Katelyn Davis, Nikesh S. Dattani. Map of Life: Measuring and Visualizing Species' Relatedness with "Molecular Distance Maps". arXiv:1307.3755v1 [q-bio.GN] [PDF]
    4. Lila Kari, Kathleen A. Hill, Abu S. Sayem, Rallis Karamichalis, Nathaniel Bryans, Katelyn Davis, Nikesh S. Dattani. Mapping the Space of Genomic Signatures. PLoS ONE 10(5): e0119815. doi:10.1371/journal.pone.0119815 [PDF]
    5. Yingwei Wang, Kathleen Hill, Shiva Singh,Lila Kari. The spectrum of genomic signatures: from dinucleotides to chaos game representation. Gene. 2005 Feb 14;346:173-85. [PDF]
    Background Reading on LDA:
    
    1. Lilien RH, Farid H, Donald BR. Probabilistic disease classification of expression-dependent proteomic data from mass spectrometry of human serum. J Comput Biol. 2003;10(6):925-46. [PDF]
    
    Presenting: Elizabeth Dowd
    Computational Antibody Design
    [Slides ppt]
    Primary Reading:
    
    1. Shaun M Lippow, K Dane Wittrup, Bruce Tidor. Computational design of antibody- affinity improvement beyond in vivo maturation. Nature Biotechnology 25, 1171- 1176 (2007). [PDF] [SI]
    2. Azoitei ML, Correia BE, Ban YE, Carrico C, Kalyuzhniy O, Chen L, Schroeter A, Huang PS, McLellan JS, Kwong PD, Baker D, Strong RK, Schief WR. Computation-guided backbone grafting of a discontinuous motif onto a protein scaffold. Science. 2011 Oct 21;334(6054):373-6. [PDF] [SI]

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13. March 14 - No class due to Spring Break
    
    

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14. March 21, 1:20 PM at North 311
    
    Presenting: Anna Lowegard
    De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy.
    [Slides ppt]
    Primary Reading:
    
    1. Huang PS, Feldmeier K, Parmeggiani F, Fernandez Velasco DA, Hocker B, Baker D. De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy. Nat Chem Biol. 2016 Jan;12(1):29-34. [PDF] [SI]
    
    Presenting: Mark Hallen
    Computational Design of Symmetric Proteins
    [Slides ppt]
    Primary Reading:
    
    1. Mou Y, Huang PS, Hsu FC, Huang SJ, Mayo SL. Computational design and experimental verification of a symmetric protein homodimer. Proc Natl Acad Sci U S A. 2015 Aug 25;112(34):10714-9. [PDF] {SI]
    2. Voet AR, Noguchi H, Addy C, Simoncini D, Terada D, Unzai S, Park SY, Zhang KY, Tame JR. Computational design of a self-assembling symmetrical beta-propeller protein. Proc Natl Acad Sci U S A. 2014 Oct 21;111(42): 15102-7. [PDF] [SI]
    3. Zaccai NR, Chi B, Thomson AR, Boyle AL, Bartlett GJ, Bruning M, Linden N, Sessions RB, Booth PJ, Brady RL, Woolfson DN. A de novo peptide hexamer with a mutable channel. Nat Chem Biol. 2011 Oct 30;7(12):935-41. [PDF] [SI]

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15. March 28, 1:20 PM at North 311
    
    Project Progress Reports (1-2 pages) due today!
    
    Presenting: Thomas Li
    Computational analysis of anti-HIV-1 antibody neutralization panel data to identify potential functional epitope residues
    [Slides ppt]
    Primary Reading:
    
    1. West AP Jr, Scharf L, Horwitz J, Klein F, Nussenzweig MC, Bjorkman PJ. Computational analysis of anti-HIV-1 antibody neutralization panel data to identify potential functional epitope residues. PNAS 2013 Jun 25;110(26): 10598-603. [PDF] [SI]
    
    Presenting: Chanelle Simmons
    Redesign of a cross-reactive antibody to dengue virus with broad- spectrum activity and increased in vivo potency.
    [Slides ppt]
    [Slides pdf]
    Primary Reading:
    
    1. Robinson LN, Tharakaraman K, Rowley KJ, Costa VV, Chan KR, Wong YH, Ong LC, Tan HC, Koch T, Cain D, Kirloskar R, Viswanathan K, Liew CW, Tissire H, Ramakrishnan B, Myette JR, Babcock GJ, Sasisekharan V, Alonso S, Chen J, Lescar J, Shriver Z, Ooi EE, Sasisekharan R. Structure-Guided Design of an Anti-dengue Antibody Directed to a Non-immunodominant Epitope. Cell. 2015 Jul 30;162(3):493-504. doi: 10.1016/j.cell.2015.06.057. Epub 2015 Jul 16. [PDF + SI]
    Secondary Reading:
    
    1. Tharakaraman K, Robinson LN, Hatas A, Chen YL, Siyue L, Raguram S, Sasisekharan V, Wogan GN, Sasisekharan R. Redesign of a cross-reactive antibody to dengue virus with broad-spectrum activity and increased in vivo potency. Proc Natl Acad Sci U S A. 2013 Apr 23;110(17):E1555-64. doi: 10.1073/pnas.1303645110. Epub 2013 Apr 8. [PDF] [SI]

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16. April 4, 1:20 PM at North 311
    
    Presenting: Marcel Frenkel
    Design of Intracellular PPI Inhibitors
    Primary Reading:
    
    1. Pelay-Gimeno M, Glas A, Koch O, Grossmann TN. Structure-Based Design of Inhibitors of Protein-Protein Interactions: Mimicking Peptide Binding Epitopes. Angew Chem Int Ed Engl. 2015 Jul 27;54(31):8896-927. [PDF]
    2. Tsomaia N. Peptide therapeutics: Targeting the undruggable space. Eur J Med Chem. 2015 Apr 13;94:459-70. [PDF]
    Secondary Reading:
    
    1. Patgiri A, Yadav KK, Arora PS, Bar-Sagi D. An orthosteric inhibitor of the Ras-Sos interaction. Nat Chem Biol. 2011 Jul 17;7(9):585-7. [PDF] [SI]
    2. Verdine GL, Walensky LD. The challenge of drugging undruggable targets in cancer: lessons learned from targeting BCL-2 family members. Clin Cancer Res. 2007 Dec 15;13(24):7264-70. [PDF]
    
    Presenting: Chris Jernigan
    Escape from Prisoner's Dilemma in RNA phage phi6
    [Slides ppt]
    Primary reading:
    
    1. Turner PE, Chao L. Escape from Prisoner's Dilemma in RNA phage phi6. Am Nat, 2003 Mar;161(3):497-505. [PDF]

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17. April 11, 1:20 PM at North 311
    
    Presenting: Brian Petkov
    Specificity versus stability in computational protein design
    [Slides pdf]
    [Slides ppt]
    Primary Reading:
    
    1. Bolon DN, Grant RA, Baker TA, Sauer RT. Specificity versus stability in computational protein design. Proc Natl Acad Sci U S A. 2005 Sep 6;102(36): 12724-9. Epub 2005 Aug 29. [PDF]
    
    Presenting: Nisakorn Valyasevi
    Predicting the Effect of Mutations on Protein-Protein Binding Interactions through Structure-Based Interface Profiles.
    [Slides ppt]
    Primary Reading:
    
    1. Brender JR, Zhang Y. Predicting the Effect of Mutations on Protein- Protein Binding Interactions through Structure-Based Interface Profiles. PLoS Comput Biol. 2015 Oct 27;11(10):e1004494. [PDF] [SI]

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18. April 18, 1:20 PM at North 311
    
    Presenting: Francois Thelot
    Structure determination of helical filaments by solid-state NMR spectroscopy
    [Slides pdf]
    Primary Reading:
    
    1. He L, Bardiaux B, Ahmed M, Spehr J, Konig R, Lunsdorf H, Rand U, Luhrs T, Ritter C. Structure determination of helical filaments by solid-state NMR spectroscopy. PNAS USA. 2016 Jan 19;113(3):E272-81. [PDF]
       
    
    Presenting: Yang Qi
    Dynamic allostery governs cyclophilin A-HIV capsid interplay
    Primary Reading:
    
    1. Lu M, Hou G, Zhang H, Suiter CL, Ahn J, Byeon IJ, Perilla JR, Langmead CJ, Hung I, Gor'kov PL, Gan Z, Brey W, Aiken C, Zhang P, Schulten K, Gronenborn AM, Polenova T. Dynamic allostery governs cyclophilin A-HIV capsid interplay. PNAS 2015 Nov 24;112(47):14617-22. [PDF + SI]
       

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19. April 25 - Last Class
    
    Project Presentations
    

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20. Computational Immunology - Background Reading
    
    
    1. Wu, X., Yang, Z. Y., Li, Y., Hogerkorp, C. M., Schief, W. R., Seaman, M. S., ... & Mascola, J. R. (2010) Rational design of envelope identifies broadly neutralizing human monoclonal antibodies to HIV-1. Science, 329(5993), 856-681. [PDF] SI: [PDF]
       
       
    2. Zhou, T., Georgiev, I., Wu, X., Yang, Z. Y., Dai, K., Finzi, A., ... & Kwong, P. D. (2010). Structural basis for broad and potent neutralization of HIV-1 by antibody VRC-01. Science, 329(5993), 811-817. [PDF] SI: [PDF]
       
       
    3. Wu, X., Zhou, T., Zhu, J., Zhang, B., Georgiev, I., Wang, C., ..., & Mascola, J. R. (2011). Focused evolution of HIV-1 neutralizing antibodies revealed by structures and deep sequencing. Science, 333(6049), 1593-1602. [PDF] SI: [PDF]
       
       
    4. McLellan, J. S., Chen, M., Joyce, M. G., Sastry, M., Stewart-Jones, G. B., Yang, Y., ... & Kwong, P. D. (2013). Structure-based design of a fusion glycoprotein vaccine for respiratory syncytial virus. Science, 342(6158), 592-598. [PDF] SI: [PDF]
       
       
    5. Wu, X., Zhang, Z., Schramm, C. A., Joyce, M. G., Do Kwon, Y., Zhou, T., ... & NISC Comparative Sequencing Program. (2015). Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection. Cell, 161(3), 470-485. [PDF]
       
       
    6. Zhou, T., Lync, R. M., Chen, L., Acharya, P., Wu, X., Doria-Rose, N. A., ... & Shapiro, L. (2015). Structural Repertoire of HIV-1-Neutralizing Antibodies Targeting the CD4 Supersite in 14 Donors. Cell. [PDF]
       
       
    7. Ngwuta, J. O., Chen, M., Modjarrad, K., Joyce, M. G., Kanekiyo, M., Kumar, A., ... & Graham, B. S. (2015). Prefusion F-specific antibodies determine the magnitude of RSV neutralizing activity in human sera. Science Translational Medicine, 7(309), 309ra162-309ra162. [PDF] SI: [PDF]
       
       
    8. Georgiev, I. S., Doria-Rose, N. A., Zhou, T., Do Kwon, Y., Staupe, R. P., Moquin, S., ... & Kwong, P. D. (2013). Delineating Antibody Recognition in Polyclonal Sera from Patterns of HIV-1 Isolate Neutralization. Science, 340(6133), 751-756. [PDF] SI: [PDF]
       
       
    9. Rudicell, R. S., Do Kwon, Y., Ko, S. Y., Pegu, A., Louder, M. K., Georgiev, I. S., ... & Nabel, G. J. (2014). Enhanced Potency of a Broadly Neutralizing HIV-1 Antibody In Vitro Improves Protection against Lentiviral Infection In Vivo. Journal of virology, 88(21), 12669-12682. [PDF] SI: [PDF]
       
       
    10. Do Kwon, Y., Pancera, M., Acharya, P., Georgiev, I. S., Crooks, E. T., Gorman, J., ... & Bindley, J. M. (2015). Crystal structure, conformational fixation and entry-related interactions of mature ligand-free HIV-1 Env. Nature structural & molecular biology, 22(7), 522-531. [PDF] SI: [PDF 1] [PDF 2]
        
        

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21. Supplemental Readings
    
    
    Computational design of the affinity and specificity of a therapeutic T cell receptor.
    Primary Reading:
    
    1. Pierce BG, Hellman LM, Hossain M, Singh NK, Vander Kooi CW, Weng Z, Baker BM. Computational design of the affinity and specificity of a therapeutic T cell receptor. PLoS Comput Biol. 2014 Feb 13;10(2):e1003478 [PDF] [SI]
    
    
    Antibody humanization by structure-based computational protein design.
    Primary Reading:
    
    1. Choi Y, Hua C, Sentman CL, Ackerman ME, Bailey-Kellogg C. Antibody humanization by structure-based computational protein design. MAbs. 2015;7(6):1045-57. [PDF]
    
    
    Precise assembly of complex beta sheet topologies from de novo designed building blocks.
    Primary Reading:
    
    1. King IC, Gleixner J, Doyle L, Kuzin A, Hunt JF, Xiao R, Montelione GT, Stoddard BL, DiMaio F, Baker D. Precise assembly of complex beta sheet topologies from de novo designed building blocks. Elife. 2015 Dec 9;4. pii: e11012. [PDF]
    
    
    Prediction of Stable Globular Proteins Using Negative Design with Non-native Backbone Ensembles.
    Primary Reading:
    
    1. Davey JA, Damry AM, Euler CK, Goto NK, Chica RA. Prediction of Stable Globular Proteins Using Negative Design with Non-native Backbone Ensembles. Structure. 2015 Nov 3;23(11):2011-21. [PDF] [SI]
    
    
    Large-scale characterization of peptide-MHC binding landscapes with structural simulations.
    Primary Reading:
    
    1. Yanover C, Bradley P. Large-scale characterization of peptide-MHC binding landscapes with structural simulations. Proc Natl Acad Sci U S A. 2011 Apr 26;108(17):6981-6. [PDF] [SI]
    
    
    Global landscape of HIV-human protein complexes.
    Primary Reading:
    
    1. Jager S, Cimermancic P, Gulbahce N, Johnson JR, McGovern KE, Clarke SC, Shales M, Mercenne G, Pache L, Li K, Hernandez H, Jang GM, Roth SL, Akiva E, Marlett J, Stephens M, D'Orso I, Fernandes J, Fahey M, Mahon C, O'Donoghue AJ, Todorovic A, Morris JH, Maltby DA, Alber T, Cagney G, Bushman FD, Young JA, Chanda SK, Sundquist WI, Kortemme T, Hernandez RD, Craik CS, Burlingame A, Sali A, Frankel AD, Krogan NJ. Global landscape of HIV-human protein complexes. Nature. 2011 Dec 21;481(7381):365-70. [PDF] [SI]
    
    
    Boosting protein stability with the computational design of beta- sheet surfaces.
    Primary Reading:
    
    1. Kim DN, Jacobs TM, Kuhlman B. Boosting protein stability with the computational design of beta-sheet surfaces. Protein Sci. 2015 Dec 23. [PDF] [SI]
    2. Murphy GS, Sathyamoorthy B, Der BS, Machius MC, Pulavarti SV, Szyperski T, Kuhlman B. Computational de novo design of a four-helix bundle protein--DND_4HB. Protein Sci. 2015 Apr;24(4):434-45. [PDF] [SI]
    
    
    Computational design of self-assembling protein nanomaterials with atomic level accuracy.
    Primary Reading:
    
    1. King NP, Sheffler W, Sawaya MR, Vollmar BS, Sumida JP, Andre I, Gonen T, Yeates TO, Baker D. Computational design of self-assembling protein nanomaterials with atomic level accuracy. Science. 2012 Jun 1;336(6085):1171-4. [PDF] [SI]
    
    
    Application of asymmetric statistical potentials to antibody- protein docking.
    Primary Reading:
    
    1. Brenke R, Hall DR, Chuang GY, Comeau SR, Bohnuud T, Beglov D, Schueler- Furman O, Vajda S, Kozakov D. Application of asymmetric statistical potentials to antibody-protein docking. Bioinformatics. 2012 Oct 15;28(20):2608-14. [PDF] [SI]
    
    
    Engineering a therapeutic lectin by uncoupling mitogenicity from antiviral activity.
    Primary Reading:
    
    1. Swanson MD, Boudreaux DM, Salmon L, Chugh J, Winter HC, Meagher JL, Andre S, Murphy PV, Oscarson S, Roy R, King S, Kaplan MH, Goldstein IJ, Tarbet EB, Hurst BL, Smee DF, de la Fuente C, Hoffmann HH, Xue Y, Rice CM, Schols D, Garcia JV, Stuckey JA, Gabius HJ, Al-Hashimi HM, Markovitz DM. Engineering a therapeutic lectin by uncoupling mitogenicity from antiviral activity. Cell. 2015 Oct 22;163(3):746-58. [PDF] [SI 1] [SI 2]
    
    
    Rational design of a meningococcal antigen inducing broad protective immunity.
    Primary Reading:
    
    1. Scarselli M, Arico B, Brunelli B, Savino S, Di Marcello F, Palumbo E, Veggi D, Ciucchi L, Cartocci E, Bottomley MJ, Malito E, Lo Surdo P, Comanducci M, Giuliani MM, Cantini F, Dragonetti S, Colaprico A, Doro F, Giannetti P, Pallaoro M, Brogioni B, Tontini M, Hilleringmann M, Nardi-Dei V, Banci L, Pizza M, Rappuoli R. Rational design of a meningococcal antigen inducing broad protective immunity. Sci Transl Med. 2011 Jul 13;3(91):91ra62. [PDF] [SI]
    
    
    Computational design of antibodies
    Primary Reading:
    
    1. Weitzner BD, Dunbrack RL Jr, Gray JJ. The origin of CDR H3 structural diversity. Structure. 2015 Feb 3;23(2):302-11. [PDF] [SI]
    Secondary Reading:
    
    1. Sircar A, Kim ET, Gray JJ. RosettaAntibody: antibody variable region homology modeling server. Nucleic Acids Res. 2009 Jul;37(Web Server issue):W474-9. [PDF]
    2. Weitzner BD, Kuroda D, Marze N, Xu J, Gray JJ. Blind prediction performance of RosettaAntibody 3.0: grafting, relaxation, kinematic loop modeling, and full CDR optimization. Proteins. 2014 Aug;82(8):1611-23. [PDF]
    
    

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As of 2/2/2016, this schedule is accurate through March 14.

What happens beyond that?

To give you an idea about the class, below please find the schedule from the last seminars, in 2015 and 2013. We will read entirely different papers this time. Only one class meeting will have the same papers, and that one class meeting is a warm up.

• Schedule for 2015 class
• Schedule for 2013 class