Computer Science 590
Seminar on Computational Biology

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.

Piazza

Piazza for this class.

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. 10 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. Monday, Jan. 15
   No Class: MLK Day
   

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3. Tuesday, Jan. 16, 2:00 - 3:00pm, 147 Nanaline Duke Building
   
   Note unusual time and place
   Presenting: Guest Lecture by Priyamvada Acharya, Research Scientist, Simons Electron Microscopy Center New York Structural Biology Center, and Structural Biology Center, Vaccine Research Center
   Topic: "Structural biology of HIV-1 entry and its application to vaccine design"
   

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4. Recitation: 5-7pm Jan. 18 Thursday, LSRC D-wing room D344.
   
   Presenting: Siyu Wang.
   The topic of the first recitation will be the installation and basic use of Pymol, a very useful protein structure visualization software (https://pymol.org/2/, https://en.wikipedia.org/wiki/PyMOL).

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5. Monday, 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 8:00 AM today
   Write three questions you would like answered, or comments you would like discussed, about the assigned reading material below.
   Turn in your questions on Sakai by the deadline, in PDF.
   We will never accept any proprietary format, such as .docx

   [Slides (PDF)]

   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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6. On Monday, 1/29, we will have a guest lecture at 12:00, plus class as usual at 1:20.

   Topic: "From Robots to Biomolecules: Computing meets the Physical World"
   Reading: ASMB: Chapter 24..
   Guest Lecture
   Speaker: Lydia E. Kavraki, Noah Harding Professor of Computer Science, Rice University
   Date: Monday, January 29, 2018
   Time: 12:00pm - 1:00pm
   Location: D106 LSRC
   (lunch served at 11:45)
   

   Note unusual time and place
   
   

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7. Jan. 29, 1:20 PM at North 311
   Class meets at usual time
   
   Presenting: Bruce Donald
   Topic: Introduction to Biomolecular NMR for Protein Structure and Dynamics
   
   Assignment --- Due 8:00 AM today
   Write three questions you would like answered, or comments you would like discussed, about the assigned reading material below.
   Turn in your questions on Sakai by the deadline, in PDF.
   We will never accept any proprietary format, such as .docx

   [Slides part 1 (PDF)]
   [Slides part 2 (PDF)]
   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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8. Feb. 4, 1:20 PM at North 311
   
   Presenting: Bruce Donald
   Topic: RDCs and Structure Calculation
   

   Assignment --- Due 8:00 AM today
   Write three questions you would like answered, or comments you would like discussed, about the assigned reading material below.
   Post your questions on Piazza: https://piazza.com/class/jcaqa7qazj433r
   Answer at least one question posed by someone else.

   [Slides (PDF)]

   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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9. Date Feb. 12, 1:20 PM at North 311
   
   Presenting: Bruce Donald
   Topic: Protein Design Algorithms
   

   Assignment --- Due 8:00 AM today
   Write three questions you would like answered, or comments you would like discussed, about the assigned reading material below.
   Post your questions on Piazza: https://piazza.com/class/jcaqa7qazj433r
   Answer at least one question posed by someone else. The question can be from this week, or last week.

   [Slides]

   Primary Reading:
   ASMB Chapter 12, Review chapter 11.
   Algorithms for protein design, by Gainza et al.
   The Minimized Dead-End Elimination Criterion and the K* Algorithm, 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, HTML]
   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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10. Monday Feb. 19, 1:20 PM at North 311
    
    A one-page written project proposal is due on Feb 19.

    Assignment --- Due 8:00 AM today
    Write three questions you would like answered, or comments you would like discussed, about the assigned reading material below.
    Post your questions on Piazza: https://piazza.com/class/jcaqa7qazj433r
    Answer at least one question posed by someone else. The question can be from this week, or last week.

    Presenting: Marcel Frenkel
    Computationally-driven identification of antibody epitopes
    [Slides]
    Primary Reading:
    Hua C K, Gacerez A T, Sentman C L, et al. Computationally-driven identification of antibody epitopes. eLife, 2017, 6. [PDF]
    Secondary reading:
    Lecture Notes in Computational Structural Biology- Volume II (LCSB-II) -- draft 2017, Chapters 2,6,8,18.
    

    Presenting: Joshua Pajak
    Direct-coupling analysis of residue coevolution captures native contacts across many protein families
    [Slides] [Notes]
    Primary Reading:
    Morcos F, Pagnani A, Lunt B, et al. Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proceedings of the National Academy of Sciences, 2011, 108(49): E1293-E1301. [PDF] [SI]
    Secondary reading:
    Lecture Notes in Computational Structural Biology- Volume II (LCSB-II) -- draft 2017, Chapter 32, 19.
    

    Additional Reading Based on Questions:
    Read ASMB Chapter 25 - On Markov Random Fields
    Self-consistent mean field (local copy)
    HMM Handout -- You may do the problems given here for extra credit if you like.
    

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11. Monday Feb. 26, 1:20 PM at North 311
    
    A one-page written project proposal was due on Feb 19.
    Revised written project proposals are due today. Use PDF and put your name on the proposal.

    Assignment --- Due 8:00 AM today
    

    For this assignment, you may discuss with anyone you like, and consult any books, articles, online resources, etc., Provided that you acknowledge them (people or resources) in your answer. You may also discuss freely on Piazza with your classmates.

    For the paper by Salmon et al., below, please answer the following questions:

    (i) Please consult figure 2.* The second Euler angle usually only goes between 0° and 90°. But in the figure, all the Euler angles go between -180° and 180°. What is going on?
    (ii) Please consult figure 2.* It looks like 2(C) is the same distribution as 2(B), just undersampled. What is going on?
    Notes:
    *Also see figure S7 in the SI.
    Post your answers on Piazza, and discuss with the class: https://piazza.com/class/jcaqa7qazj433r
    Answer at least one question/answer/comment posed on Piazza by someone else. The question can be from this week, or last week.

    For extra credit, or, if you are interested:

    Write three questions you would like answered, or comments you would like discussed, about the assigned reading material below.
    Post your questions on Piazza: https://piazza.com/class/jcaqa7qazj433r

    Presenting: Graham Holt
    HIV Envelope Glycoform Heterogeneity and Localized Diversity Govern the Initiation and Maturation of a V2 Apex Broadly Neutralizing Antibody Lineage
    [Slides] [Notes]
    Primary Reading:
    Landais E, Murrell B, Briney B, et al. HIV Envelope Glycoform Heterogeneity and Localized Diversity Govern the Initiation and Maturation of a V2 Apex Broadly Neutralizing Antibody Lineage. Immunity, 2017, 47(5): 990-1003. e9. [PDF+SI]
    Secondary reading:
    Lecture Notes in Computational Structural Biology- Volume II (LCSB-II) -- draft 2017, Chapters 24,18,8,15,6.
    

    Presenting: Catherine Ehrhart
    A general method for constructing atomic-resolution RNA ensembles using NMR residual dipolar couplings: the basis for interhelical motions revealed
    [Slides]
    Primary Reading:
    Salmon L, Bascom G, Andricioaei I, et al. A general method for constructing atomic-resolution RNA ensembles using NMR residual dipolar couplings: the basis for interhelical motions revealed. Journal of the American Chemical Society, 2013, 135(14): 5457-5466. [PDF] [SI]
    Secondary reading:
    ASMB: Chapters 24, 15-18, 5.
    ASMB: Chapters 4,13.
    [Salamin on Quaternions (PDF)]
    Lecture Notes in Computational Structural Biology- Volume II (LCSB-II) -- draft 2017, Chapters 9, 26.
    

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12. Monday, March 5, 10:00am
    North Building, Room 311
    
    Note unusual time and place
    Please note we will also have our usual class today at 1:20 PM as well (See below).
    Presenting: Guest Lecture by Adegoke Ojewole.
    Topic: " Efficient New Computational Protein Design Algorithms, with Applications to Drug Resistance Prediction and HIV Antibody Design"
    

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13. Monday Mar. 5, 1:20 PM at North 311
    
    

    Assignment --- Due 8:00 AM today
    Write three questions you would like answered, or comments you would like discussed, about the assigned reading material below.
    Post your questions on Piazza: https://piazza.com/class/jcaqa7qazj433r
    Answer at least one question posed by someone else. The question can be from this week, or last week.

    Presenting: Anna Lowegard
    Tertiary alphabet for the observable protein structural universe
    [Slides]
    Primary Reading:
    Mackenzie C O, Zhou J, Grigoryan G. Tertiary alphabet for the observable protein structural universe. Proceedings of the National Academy of Sciences, 2016, 113(47): E7438-E7447. [PDF] [SI]
    Zhou J., Grigoryan G., "Rapid Search for Tertiary Fragments Reveals Protein Sequence-Structure Relationships", Protein Science, 24(4): 508-524, 2015. [PDF]
    Secondary reading:
    Lecture Notes in Computational Structural Biology- Volume II (LCSB-II) -- draft 2017, Chapters 27,32.
    Method of Accelerated Search for Tertiary Ensemble Representatives
    

    Presenting: Yuze Hou
    Comprehensive computational design of ordered peptide macrocycles
    [Slides]
    Primary Reading:
    Hosseinzadeh P, Bhardwaj G, Mulligan V K, et al. Comprehensive computational design of ordered peptide macrocycles. Science, 2017, 358(6369): 1461-1466. [PDF] [SI]
    Secondary reading:
    ASMB: Chapter 45.
    Lecture Notes in Computational Structural Biology- Volume II (LCSB-II) -- draft 2017, Chapter 17.
    

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14. Wednesday, March 7, 2:00 PM
    Levine Science Research Center (LSRC), Room D344
    
    Note unusual time and place
    
    Presenting: Guest Lecture by Jonathon Dragon Jou.
    Topic: "Novel Computational Protein Design Algorithms with Sparse Residue Interaction Graphs, Ensembles, and Mathematical Guarantees, and their Application to Antibody Design"
    

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15. Monday March 12. Duke Spring Break. No Class.
    Next class will be Monday March 19.
    

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16. Monday Mar. 19, 1:20 PM at North 311
    
    

    Assignment --- Due 8:00 AM today
    Write three questions you would like answered, or comments you would like discussed, about the assigned reading material below.
    Post your questions on Piazza: https://piazza.com/class/jcaqa7qazj433r
    Answer at least one question posed by someone else. The question can be from this week, or last week.

    Presenting: Siyu Wang
    [Slides]
    EpiSweep: Computationally driven reengineering of therapeutic proteins to reduce immunogenicity while maintaining function
    Primary Reading:
    Choi, Yoonjoo, et al. "EpiSweep: Computationally driven reengineering of therapeutic proteins to reduce immunogenicity while maintaining function." Computational Protein Design. Humana Press, New York, NY, 2017. 375-398. [PDF]
    Salvat R S, Choi Y, Bishop A, et al. Protein deimmunization via structure-based design enables efficient epitope deletion at high mutational loads. Biotechnology and bioengineering, 2015, 112(7): 1306-1318. [PDF]
    Parker A S, Choi Y, Griswold K E, et al. Structure-guided deimmunization of therapeutic proteins. Journal of Computational Biology, 2013, 20(2): 152-165. [PDF]
    

    Presenting: John Decker
    Rational design of proteins that exchange on functional timescales
    [Slides]
    Primary Reading:
    Davey J A, Damry A M, Goto N K, et al. Rational design of proteins that exchange on functional timescales. Nature chemical biology, 2017, 13(12): 1280. [PDF] [SI]
    Chemical Exchange. Pramodh Vallurupalli. February 24, 2009. Workshop Series on NMR and Related Topics. [PDF]
    Secondary Reading:
    Kristoffer E Johansson and Kresten Lindorff-Larsen. Structural heterogeneity and dynamics in protein evolution and design. Current Opinion in Structural Biology 2018, 48:157-163. [PDF]

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17. Thursday Mar. 22, 5:00 PM at LSRC D344
    
    

    Presenting: Brian Lee
    The Rosetta all-atom energy function for macromolecular modeling and design
    [Slides] [Notes]
    Primary Reading:
    Alford R F, Leaver-Fay A, Jeliazkov J R, et al. The Rosetta all-atom energy function for macromolecular modeling and design. Journal of chemical theory and computation, 2017, 13(6): 3031-3048. [PDF] [SI]
    

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18. Monday Mar. 26, 1:20 PM at North 311
    
    

    Assignment --- Due 8:00 AM today
    Write three questions you would like answered, or comments you would like discussed, about the assigned reading material below.
    Post your questions on Piazza: https://piazza.com/class/jcaqa7qazj433r
    Answer at least one question posed by someone else. The question can be from this week, or last week.

    Presenting: Sean Doherty
    DINC 2.0: A New Protein-Peptide Docking Webserver Using an Incremental Approach
    [Slides] [Notes]
    Primary Reading:
    Antunes D A, Moll M, Devaurs D, et al. DINC 2.0: A New Protein-Peptide Docking Webserver Using an Incremental Approach. Cancer research, 2017, 77(21): e55-e57. [PDF]
    Dhanik A, McMurray J S, Kavraki L E. DINC: A new AutoDock-based protocol for docking large ligands. BMC structural biology, 2013, 13(1): S11. [PDF]
    Secondary reading:
    Raveh B, London N, Zimmerman L, et al. Rosetta FlexPepDock ab-initio: simultaneous folding, docking and refinement of peptides onto their receptors. PloS one, 2011, 6(4): e18934. [PDF]
    Alam N, Goldstein O, Xia B, et al. High-resolution global peptide-protein docking using fragments-based PIPER-FlexPepDock. PLOS Computational Biology, 2017, 13(12): e1005905. [PDF]
    

    Presenting: Hong Niu
    Computational design of self-assembling cyclic protein homo-oligomers
    [Slides] [Notes]
    Primary Reading:
    Fallas J A, Ueda G, Sheffler W, et al. Computational design of self-assembling cyclic protein homo-oligomers. Nature chemistry, 2017, 9(4): 353. [PDF] [SI]
    

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19. Recitation: 5-7pm Mar. 29 Thursday, LSRC D-wing room D344.
    
    Presenting: Siyu Wang.
    Topic: the installation and basic usage of Osprey.
    Osprey download link on Github: https://github.com/donaldlab/OSPREY_refactor/releases
    Toturial: [Slides]
    

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20. Monday Apr. 2, 1:20 PM at North 311
    
    

    Assignment --- Due 8:00 AM today
    Write three questions you would like answered, or comments you would like discussed, about the assigned reading material below.
    Post your questions on Piazza: https://piazza.com/class/jcaqa7qazj433r
    Answer at least one question posed by someone else. The question can be from this week, or last week.

    Presenting: Madhurima Vardhan
    Dissecting Interfaces of Antibody-Antigen Complexes: from Ligand Specific Features to Binding Affinity Predictions
    [Slides]
    Primary Reading:
    Marillet S, Lefranc M P, Boudinot P, et al. Dissecting Interfaces of Antibody-Antigen Complexes: from Ligand Specific Features to Binding Affinity Predictions[D]. Inria Sophia Antipolis, 2015. [PDF+SI]
    

    Presenting: David Wang
    Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening
    [Slides]
    Primary Reading:
    Cang Z, Mu L, Wei G W. Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening. PLoS computational biology, 2018, 14(1): e1005929. [PDF] [SI]
    Cang Z, Wei G. TopologyNet: Topology based deep convolutional and multi-task neural networks for biomolecular property predictions. PLOS Computational Biology, 2017, 13(7): e1005690. [PDF]
    Secondary reading:
    H. Edelsbrunner and P. Koehl. Computational topology for structural molecular biology. Chapter 68 in Handbook of Computational Geometry. [PDF]
    ASMB: Chapter 50.
    
    

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21. Monday Apr. 9, 1:20 PM at North 311
    
    

    Assignment --- Due 8:00 AM today
    Write three questions you would like answered, or comments you would like discussed, about the assigned reading material below.
    Post your questions on Piazza: https://piazza.com/class/jcaqa7qazj433r
    Answer at least one question posed by someone else. The question can be from this week, or last week.

    Presenting: Fang Liu
    The role of side chain entropy and mutual information for improving the de novo design of Kemp eliminases KE07 and KE70
    [Slides]
    Primary Reading:
    Bhowmick A, Sharma S C, Honma H, et al. 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, 2016, 18(28): 19386-19396. [PDF]
    

    Presenting: Sudarshan Balaji
    Data driven flexible backbone protein design
    [Slides]
    Primary Reading:
    Sun M G F, Kim P M. Data driven flexible backbone protein design. PLoS Computational Biology, 2017, 13(8): e1005722. [PDF]
    

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22. Thursday Apr. 12, 8:30am-9:30am at 147 Nanaline Duke
    
    Note unusual time and place
    Presenting: Guest Lecture by Ivelin Georgiev Assistant Professor, Vanderbilt Vaccine Center Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center Department of Electrical Engineering and Computer Science, Vanderbilt University
    Topic: "Toward Population-Level Analysis of Antibody Responses to HIV-1 Infection"
    

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23. Thursday Apr. 12, 5:00 PM at LSRC D344
    
    

    Presenting: Nancy Wiebelhaus
    Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations
    [Slides]
    Primary Reading:
    Cournia Z, Allen B, Sherman W. Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations. Journal of chemical information and modeling, 2017. [PDF]
    

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24. Monday Apr. 16, 1:20 PM at North 311
    
    Presenting: Bruce Donald
    Topic: A peek at some current research in this field
    [Abstract (PDF)]
    [Reading (PDF on BioarXiv) ]
    Summary: I will describe new ways to represent and visualize correlated interdomain protein motions. Interdomain motions are determined directly from residual dipolar couplings (RDCs), represented as a continuous conformational distribution. Connections to modeling continuous flexibility in computational protein design will be mooted.
    

    Assignment --- Due 8:00 AM today
    Write three questions you would like answered, or comments you would like discussed, about the assigned reading material below.
    Post your questions on Piazza: https://piazza.com/class/jcaqa7qazj433r
    Answer at least one question posed by someone else. The question can be from this week, or last week.

    Primary Reading:
    Yang Qi, Jeffrey W Martin, Adam W Barb, Francois Thelot, Anthony Yan, Bruce R Donald,* Terrence G Oas*. Continuous interdomain orientation distributions reveal components of binding thermodynamics. bioRxiv, doi: 10.1101/200238. Cold Spring Harbor Laboratory.
    [PDF]
    or: https://www.biorxiv.org/content/early/2018/01/29/200238,
    and https://www.biorxiv.org/content/early/2018/01/29/200238.full.pdf.

    Important Background Reading:
    [Salamin on Quaternions (PDF)]
    ASMB: Chapters 15-18, 5.
    ASMB: Chapters 4,13.
    RDC lecture

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25. Monday Apr. 23 (last day of class), 1:20 PM at North 311
    
    

    Assignment --- Due Noon 4/22
    Send Siyu 3 slides as per below. Prepare a 3-minute talk on your project.

    Assignment --- Due 8:00 AM today
    Class Projects are Due Today. Turn in on Sakai.

    Assignment --- Due 8:00 AM today
    Write three questions you would like answered, or comments you would like discussed, about the assigned reading material below.
    Post your questions on Piazza: https://piazza.com/class/jcaqa7qazj433r
    Answer at least one question posed by someone else. The question can be from this week, or last week.

    Presenting: Vincentius Martin
    Elfin: An algorithm for the computational design of custom three-dimensional structures from modular repeat protein building blocks
    Primary Reading:
    Yeh C T, Brunette T J, Baker D, et al. Elfin: An algorithm for the computational design of custom three-dimensional structures from modular repeat protein building blocks. Journal of structural biology, 2017. [PDF]
    

    Presenting: Everyone
    Speed Science/Lightning Advertisements for Class Projects
    Tell the class about your Course Projects (3 minutes each).
    You must send Siyu 3 slides in pptx format by Sunday April 22, Noon.
    Prepare to tell the class what you are doing in 3 minutes.
    Your slides should also show what you learned: results/conclusions/progress.
    

    This is the last day of class.

    We have learned a lot, yes?

    But wait! There is more to learn. See below.

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26. Summer seminars
    Have a good summer!
    Don't forget to Keep going to seminars and talks in the summer, to keep current on the scientific literature!
    For example:
    
    

    Monday, April 30, 2018 12:00 pm - 1:00 pm
    North 311
    Quantitative equational reasoning
    Duke Computer Science Colloquium
    Prakash Panangaden
    Lunch will be served at 11:45.
    Abstract: Reasoning with equations is a central part of mathematics. Typically we think of solving equations but another role they play is to define algebraic structures like groups or vector spaces. Equational logic was formalized and developed by Birkhoff in the 1930s and led to a subject called universal algebra. Universal algebra was used in formalizing concepts of data types in computer science. In this talk I will present a quantitative analogue of equational logic: we write expressions with the intended interpretation "s is within epsilon of t". It turns out that the metatheory of equational logic can be redeveloped in this setting. Perhaps this seems like sterile theory but what makes it come alive is some striking examples. A notion of distance between probability distributions called the Kantorovich metric (frequently called the Wasserstein metric) has become important in the theory of probabilistic systems and in parts of machine learning. It turns out that this metric emerges naturally as the "free algebra" of some simple equational axioms in our extended sense. My presentation will be elementary and does not require the audience to be familiar with all the words that appear above. This is joint work with Radu Mardare and Gordon Plotkin.

    Short Biography
    Prakash Panangaden is a professor of computer science at McGill University where he works on probabilistic systems and related topics. He obtained his undergraduate degree from IIT Kanpur in India, an MS in physics from the University of Chicago, a PhD in physics from the University of Wisconsin-Milwaukee and an MS in computer science from the University of Utah. He was formerly at Cornell University before moving to McGill University in 1990 where he has been ever since. He was elected a Fellow of the Royal Society of Canada in 2013 and was awarded the Test of Time from LICS in 2017.

    Video: https://compsci.capture.duke.edu/Panopto/Pages/Viewer.aspx?id=b265426f-39df-4d89-894b-4b1c8020f0bf

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27. Summer reading
    Have a good summer!
    Don't forget to Keep Reading, to keep current on the scientific literature!
    For example:
    
    

    Enriching peptide libraries for binding affinity and specificity through computationally directed library design
    Primary Reading:
    Foight G W, Chen T S, Richman D, et al. Enriching peptide libraries for binding affinity and specificity through computationally directed library design. Modeling Peptide-Protein Interactions: Methods and Protocols, 2017: 213-232. [PDF]
    Araghi R R, Keating A E. Designing helical peptide inhibitors of protein-protein interactions. Current opinion in structural biology, 2016, 39: 27-38. [PDF]
    Potapov V, Kaplan J B, Keating A E. Data-driven prediction and design of bZIP coiled-coil interactions. PLoS computational biology, 2015, 11(2): e1004046. [PDF]
    

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

2016 Schedule (To give you an idea:)