We will be reviewing initially one paper a week, then two once we have completed the lectures. These papers will focus on protein bioinformatics and structure related questions and will be drawn from papers published in highly ranked journals in the past year. Links to the papers are posted at the end of the document. Students are responsible for retrieving the papers (copyright issues).
Discussion of the papers will be led by groups of two or three students, who are expected to co-ordinate their efforts. All other students are expected to participate in the discussion. Discussions will run roughly 1 hr per paper. All students are required to post a short reflection on courselink by no later than the night before the journal club class. You are required to have read all of the papers carefully and thoughtfully; this includes the main text and supplement (modern papers tend to have a lot of important figures in the supplementary files). If anything is unfamiliar (e.g. a technique, a term) look it up and familiarize yourself with it. Make sure you look at any supplementary data in addition to the main text. Please read the paper well ahead of the time, give yourself a day or so to think it over, then read it again.
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The expectation is that the presenters will have familiarized themselves with the paper plus all context, including possibly reading additional materials (e.g. in reviews or related papers) requires to understand the context. Students not presenting will need, at minimum, have read the paper carefully at least once. While reading the paper, pay attention to the way that a structure-focussed paper is constructed. E.g. the phrasing used, the way larger arguments are constructed, the relationship between text and figures. You want to be able to use the idiom and conventions of structural biology correctly when writing the major project at the end of the course. Things that you might want to look out for, and be prepared to discuss: Scientific ideas: This should be the primary focus of the discussion.
What is the scientific problem, and what methods are the authors using to address it? Is this study a specific and narrow investigation of one system using well-established methods, or are their insights adding perspective to a wider set of problems? How does this paper reflect, reinforce, expand upon or question key ideas that we have discussed during the lectures?
How are the methods, especially structural, modelling or bioinformatics methods, implemented (e.g. what specific sub-methods are used; often the supplement is key to the details)? What aspects of these techniques and ideas become clearer when embodied in a concrete example? What ideas, terminology and concepts are new (to you), and might need explication? How do the different methods used synergise? What is the role of each experiment within the bigger-picture story? Do the authors say anything in the text that is striking, that made you think, or you did not understand?
Relevant methods: Please focus on the more structural/bioinformatics aspects of the paper. If there is supporting non-structural data (from cell biology, biochemistry, enzymology etc.) note the main findings, but don’t dwell on them except to the extent that they are important to understanding or validating the structural/bioinformatics insights. Note any pertinent methods, approaches, or tools used in the paper that were not covered in class. If there are, make sure you understand them, and can explain them to others. If methods were covered in class, are the authors simply using it in a completely standard way, or do they have an interesting twist? Potential limitations of the paper (not always relevant, and not the primary focus): Is there any place you feel the authors are drawing conclusions without having the data to fully justify these? Where there are potential issues or limitations, are they being addressed forthrightly, or papered over?
Along the same vein, any place where the authors are missing an alternative explanation for their observations. Would the conclusions being presented be considered controversial, or contradicting existing models. Looking at some other papers in the area might help give some insights here. If new structures were reported, possibly have a look at them in pymol. Are they omitting inconvenient details from their story? Communication skills (worth drawing attention to highlights and lowlights, this should be a minor focus): How the information is being presented visually? Are the figures getting the key ideas across? Do the figures draw you in, make you want to read the paper? Is there anything the authors are doing that is noteworthy in how they convey information. How are they connecting different figures and panels to one another so that the reader does not have to continuously re-orient themselves? Did you find this paper easy and clear to read? Why or why not? In addition, please pay attention to how specific arguments and points are organized and worded. Take these papers as possible models for your own future writings. When leading journal club discussions.
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For the journal club presentation, you generally do not need to prepare any visual aids. You don’t need a power point presentation, but you are welcome to use the projector if you would like to show some detail of a structure in Pymol, or play a video from the paper that you think is especially informative. But largely, presenters remain seated, and direct the class’s attention to specific aspects of the paper as they arise. If you are leading the discussion, the idea is to lead a dynamic conversation, not engage in a protracted monologue. It is often a good idea to use the figures and tables (including those in the supplement) as a framework for walking through the paper as they present many of the key ideas. Do not ignore the text itself though, as many ideas will not be apparent in the figures. Make sure you communicate the logic of how the authors are approaching and solving the problems in the paper. Draw your classmates into a multi-way conversation; try to not to be the only person in the room speaking, but also avoid protracted silences. Note that you need your classmates to be prepared for this to work; give them the same consideration. Note that anyone can introduce their own questions, or topics of discussion. I encourage students to speak up especially where they have personal expertise in an area or method. From what I’ve seen in the past, too non-specific questions (“What did you think of figure 4a?”) struggle to get a discussion going. Questions that invite a straightforward answer can also peter out quickly (“Does anyone else agree that the phylogenetic tree in figure 4a is just too busy and hard to follow?”). More useful are questions that draw attention to something non-obvious, but invite others to think about what it means (“In connection with this figure, the authors make an intriguing observation, saying ‘of note, this density in the active site is present even when no ligands were introduced into the crystallization solution’. What does this observation imply? Why are the authors emphasizing this specific point? And what idea later in the paper this statement serve to set up?” which would lead the discussion back to the key ideas in the paper, and highlighting an important point that might be missed in a quick reading). Its best if you have a possible answer in mind to prompt people further if needed, but also be willing to give others room to present their own viewpoint. If you disagree, do so in a respectful way. I am looking for substantive discussion where everyone walks away feeling that they have learned something useful. It is up to you to figure out what you find to be most instructive and interesting about the paper, and to find the best way to communicate it. I will be grading student’s preparedness, insight into the material, ability to engage other students. In general, it can work well for everyone to look at the relevant section of their paper on their own screens. If you feel it would be helpful to have access to the projector (e.g. to share a Pymol session) this can be arranged, but please remember that this is intended to be a group discussion, rather than a presentation. Journal club pre-discussion written reflection. You are required to submit your thoughts on each paper to be presented, in writing, by the night before class.
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Please summarize the main idea of the paper in a couple of sentences, and highlight a few questions you have or points found interesting and would like to discuss with your classmates. If you are not presenting, a half page or so paragraph would be plenty. If you are presenting, you probably will have more to say. The main purpose of this exercise is to ensure that you read and reflected on the paper ahead of time, and to ensure that you come to class with some ideas you can contribute to the discussion. This written portion, as well as your participation in discussions, will be taken into consideration when grading the journal club.