Monthly Archives: May 2015

Submitting your thesis!

Writing and submitting your thesis is (almost) the final stage of completing your PhD. It can be the most stressful and unpleasant part of the process… but it can also be rewarding to see the story of your last three years’ work fall into place.

 "Piled Higher and Deeper" by Jorge Cham (

All I want for christmas is… “Piled Higher and Deeper” by Jorge Cham (

This post is a miscellaneous collection of advice and resources about the submission process, most of which have been passed down from the very first members of OPIG. Hopefully it will be useful to have it all in the same place for present and future members. Feel free to comment here if you have any tips I have missed!

All information and links that I’ve included are correct at the time of writing (for Oxford University Statistics students) but you should always use the university’s guidelines as your primary resource.

The very beginning: the plan

Don’t spend too long on this! But you should have an idea of your planned chapter titles and an overall story for your book. Also useful is a timeline for when you will finish drafts of chapters by. Try to be realistic with this. If you decide to change your thesis title you should fill out an application for change of thesis title form (GSO.6). Make sure you look up any restrictions (word/page limits etc.) which may apply, and confirm your hand-in date.

Starting writing

It’s a good idea to decide what you will use to write your thesis. Most OPIG members use LaTeX. There are some great thesis templates out there but the one most people tend to use is one from Cambridge’s Engineering department. You can do a fair bit of customisation within that template… changing fonts, headers, titles and more, but it’s a great starting point.

When the finish line’s in sight: choosing examiners

A couple of months before you are planning to submit your thesis you should discuss with your supervisor(s) potential examiners. Your supervisor can informally check with them if they are happy to examine you and then you should fill out an appointment of examiners form (GSO.3). You can also change your thesis title on this form without filling in GSO.6.

Finishing writing

Your final document is likely to be over 100 pages with thousands of words (or potential typos as you might come to call them). A great LaTeX spell checker is aspell which should already be installed on your work machine. To spell check a .tex file (ignoring all TeX notation… apart from multiple citations I found!) using a British dictionary simply type:

aspell --lang=en_GB -t -c filename.tex

You’re absolutely guaranteed to still have typos floating around but it’s a decent start. You (and others if you can get them) should manually proof-read as well!

Final Formatting

Your thesis should be set out on numbered, portrait A4 pages. It should be double spaced and the inner (bound) margin should be 3-3.5cm. For more details on the formatting required check out the university’s regulations.

Printing and binding

When you’re happy with your proof-reading (you’re still almost guaranteed to have remaining typos) you’ll have to print and bind your finished book! To comply with university guidelines you will need to submit two copies, for each of your examiners, to the exam schools. You may also like to print a copy for yourself (you will need one to take with you into your viva). Before you start, if you are printing in colour at the department make sure you have enough printer credit by emailing IT (let them know the printer and your Bod card number and they will top you up if necessary).

If you are planning to print your copies double sided you may want to buy your own paper of higher quality than that provided by the department (at least 100gsm). As of October 2014, the Oxford Print Centre was selling the cheapest packs of 100gsm paper we could find but sold out close to deadline day! Also check out WHSmiths or Ryman’s.

You might want to do a test run of a few colour pages of your thesis before you send the whole file to be printed. Printing at 1200dpi (instead of the default 600dpi) can improve the appearance of your figures considerably. You may want to stay late at the office to print so you are not disturbed by other print jobs during office hours.

Your thesis should be securely bound in either hard or soft cover. Loose-leaf or spiral binding won’t be accepted. There are several binding facilities through Oxford but I used the Oxford Print Centre just down the road, which also guarantees a one hour service for soft binding even on submission days.


Submit your completed copies to the exam schools, noting their opening hours (08.30-17:00, Monday to Friday), take the traditional photo, and bask in your newly found FREEDOM (try to forget about the viva!).

Journal Club: The Origin of CDR H3 Structural Diversity

Antibody binding site is broadly composed of the six hypervariable loops, the CDRs. There are three loops on the antibody light chain (L1, L2 and L3) and three loops on the antibody heavy chain (H1, H2 and H3).

Out of the six loops, five appear to adopt a constrained set of structural conformations (L1, L2, L3, H1 and H2). The conformations of H3 appear much less constrained, which was suggested to be the result of its higher relative importance in antigen recognition (however it is not a necessary condition). The only observations to date about the shapes of CDR-H3 is the existence of the extended and kinked conformations of its anchor.

The function of the kink was investigated recently by Weitzner et al. Here, the authors contrasted the geometry found in the antibody CDR-H3 loops to a set of 15k non-antibody polypeptides. They found that even though the extended conformation appears to be more favorable, the kinked one can also be found in many cases, particularly in the PDZ domains.

Weitzner et al. find that the extended conformation is much more common in non-antibody loops. However, the kinked conformation, even though less frequent is not outright rare. The situation is the opposite in antibodies where the majority of H3 conformations are kinked rather than extended.

The authors contrasted the sequence patterns of kinked antibody loops and kinked non-antibody loops and did not find anything predictive of the kinked conformation — suggesting that the effect might be non-local. Nonetheless, the secondary structure pattern of the kinked H3 and the kinked non-antibody loops appears similar.

Even though there might be no sequence-kink link, the authors indicate how their findings might improve H3 structure prediction. They demonstrate that admixing the kinked non-antibody loops into a template dataset for an H3 modeling software might provide more relevant templates.

In conclusion, the main message of the paper (selon moi) is putting forward of the hypothesis as to the role of the H3 kink. Since the kink is much more prevalent in H3 than in non-antibody proteins, there is a strong suggestion that there might be a special role for it. The authors suggest that the kinked conformation allows for more structural diversity, that would otherwise be restricted in the more rigid beta-stranded extended conformation. Thus, antibodies might have opted for a system wherein, they do not need to add dramatic mutations to their H3 in order to get more structural flexibility.


Hierachical Natural Move Monte Carlo using MOSAICS

After having recently published a large scale Molecular Dynamics simulations project of TCRpMHC [1,2] interaction I have extended my research to another technique of spatial sampling. At this week’s group meeting I presented the first results of my first MOSAICS [3] project.

The MOSAICS package is a software that allows for so called hierarchical natural Monte Carlo moves. That means that the user can specify regions in the protein of interest. These regions are indented to reflect “natural” sets of atoms and are expected to move together. An example would be a stable alpha-helix. “Hierarchical” means that region can be grouped together to super-regions. For example a helix that is broken by a kink [4] in its middle could have a region for the helix parts on both sides of the kink as well as for the overall helix. An example for peptide/MHC is illustrated below.


MOSAICS uses Monte Carlo moves to rearrange these region with respect to each other. A stochastic chain closure algorithm ensures that no chain breaks occur. An example of such movements in comparison to classical all-atom Molecular Dynamics is shown below.


In this study we used MOSAICS to simulate the detachment of peptides from MHCs for experimentally known binder and non-binder. An example of such a detaching peptide is shown below


Our results show that experimentally known non-binding peptides detach significantly faster from MHC than experimentally known binding peptides (results to be reported soon).

As a first conclusion of this project:
After having worked with both MOSAICS and Molecular Dynamics simulations, I think that both techniques have their advantages and disadvantages. They are summarized below:


Which technique should be chosen for which project depends mainly on what the aims of these projects are. If large moves of well defined segments are expected then MOSAICS might be the method of choice. If the aim is to investigate fine changes and detailed dynamics Molecular Dynamics simulations might be the better choice.


1.    Knapp B, Demharter S, Esmaielbeiki R, Deane CM (2015) Current Status and Future Challenges in T-cell receptor / peptide / MHC Molecular Dynamics Simulations. Brief Bioinform accepted.
2.    Knapp B, Dunbar J, Deane CM (2014) Large Scale Characterization of the LC13 TCR and HLA-B8 Structural Landscape in Reaction to 172 Altered Peptide Ligands: A Molecular Dynamics Simulation Study. PLoS Comput Biol 10: e1003748.
3.    Sim AY, Levitt M, Minary P (2012) Modeling and design by hierarchical natural moves. Proc Natl Acad Sci U S A 109: 2890-2895.
4.    Wilman HR, Ebejer JP, Shi J, Deane CM, Knapp B (2014) Crowdsourcing yields a new standard for kinks in protein helices. J Chem Inf Model 54: 2585-2593.