Author Archives: Clare West

Latexing with gvim

Here I’ll share my set-up for writing Latex with gvim instead of a separate Latex editor. If you are text-editor averse, this blog post is not for you. But if, like me, you love vim and hate useless GUIs, this might be helpful.

We’re lucky to have nice big screens in the Stats Department, but I tend to prefer writing on my MacBook (I find it’s easier to transport to e.g. a cafe, my home, etc). Until now, I’ve been happily using TexMaker for writing, but during a recent period of intense Latexing I started to find the useable screen space oppressively small. The unnecessary GUI had to go.   

No offence TexMaker but I don’t like you

One of our good friends in Statistical Genetics recommended some things to help me with the transition to just using good old (g)vim, which I will now recommend to you.

The key thing is the LaTex-Box plug-in for vim, which gives you the compilation commands, as well as the essentials such as smart indentation, highlight matching, command completion, etc. I used pathogen to install it (see the GitHub for instructions).

Of course, you can then customise your .vimrc file to add more helpful things. This can be the simple preferences, such as using a light background when using gvim:

 

if has(“gui_running”)

        set background=light

endif

You can also do more complicated magic like tabbing through available commands, and the ability to minimise sections, etc. Sidenote: to make working with paragraphs easier, I recommend setting the up/down arrows to move the cursor to the next line in the GUI rather than the next actual line. I prefer overriding this behaviour only in gvim, while leaving the normal behaviour in vim (for actual coding). But each to their own.

To get started, open a .tex file, then compile and view the document with the command Latexmk.

Command suggestions are an example of a magical feature added in .vimrc

The configurations for this command are set in the file .latexmkrc. Mine looks like this:

 

$recorder = 1;
$pdf_mode = 1;
$bibtex_use = 2;
$pdflatex = "pdflatex --shell-escape %O %S";
$pdf_previewer = "start open -a skim %O %S";

My pdf viewer of choice on Mac is Skim, which autoupdates. I view the source and preview at the same time using split view. Please admire the beauty below:

Wow what a beautiful screen

My favourite part is that whenever you save (w), it recompiles and updates the preview. As someone who accidentally types :w everywhere that isn’t vim, it’s nice that this is now productive. It also recompiles automatically if the .bib file is updated. Note that if you have errors at compilation (I’m sure you don’t), you can view them with the command LatexErrors.

Now you too can be a (nearly) GUI-free lightweight Latexer. Enjoy!

 

Protein Structure Classification: Order in the Chaos

The number of known protein structures has increased exponentially over the past decades; there are currently over 127,000 structures deposited in the PDB [1]. To bring order to this large volume of data, and to further our understanding of protein function and evolution, these structures are systematically classified according to sequence and structural similarity. Downloadable classification data can be used for annotating datasets, exploring the properties of proteins and for the training and benchmarking of new methods [2].

Yearly growth of structures in the PDB (adapted from [1])

Typically, proteins are grouped by structural similarity and organised using hierarchical clustering. Proteins are sorted into classes based on overall secondary structure composition, and grouped into related families and superfamilies. Although this process could originally be manually curated, as with Structural Classification of Proteins (SCOP) [3] (last updated in June 2009), the growing number of protein structures now requires semi- or fully-automated methods, such as SCOP-extended (SCOPe) [4] and Class, Architecture, Topology, Homology (CATH) [5]. These resources are comprehensive and widely used, particularly in computational protein research. There is a large proportion of agreement between these databases, but subjectivity of protein classification is to be expected. Variation in methods and hierarchical structure result in differences in classifications.  For example, different criteria for defining and classifying domains results in inconsistencies between CATH and SCOPe.

The arrangements of secondary structure elements in space are known as folds. As a result of evolution, the number of folds that exist in nature is thought to be finite, predicted to be between 1000-10,000 [6]. Analysis of currently known structures appears to support this hypothesis, although solved structures in the PDB are likely to be a skewed sample of all protein structures space. Some folds are extremely commonly observed in protein structures.

In his ‘periodic table for protein structures’, William Taylor went one step further in his goal to find a comprehensive, non-hierarchical method of protein classification [7]. He attempted to identify a minimal set of building blocks, referred to as basic Forms, that can be used to assemble as many globular protein structures as possible. These basic Forms can be combined systematically in layers in a way analogous to the combination of electrons into valence shells to form the periodic table. An individual protein structure can then be described as the closest matching combination of these basic Forms.  Related proteins can be identified by the largest combination of basic Forms they have in common.

The ‘basic Forms’ that make up Taylor’s ‘periodic table of proteins’. These secondary structure elements accounted for, on average, 80% of each protein in a set of 2,230 structures (all-alpha proteins were excluded from the dataset) [7]

The classification of proteins by sequence, secondary and tertiary structure is extensive. A relatively new frontier for protein classification is the quaternary structure: how proteins assemble into di-, tri- and multimeric complexes. In a recent publication by an interdisciplinary team of researchers, an analysis of multimeric protein structures in combination with mass spectrometry data was used to create a ‘periodic table of protein complexes’ [8]. Three main types of assembly steps were identified: dimerisation, cyclisation and heteromeric subunit addition. These types are systematically combined to predict many possible topologies of protein complexes, within which the majority of known complexes were found to reside. As has been the case with tertiary structure, this classification and exploration of of quaternary structure space could lead to a better understanding of protein structure, function and evolutionary relationships. In addition, it may inform the modelling and docking of multimeric proteins.

 

  1. RCSB PDB Statistics
  2. Fox, N.K., Brenner, S.E., Chandonia, J.-M., 2015. The value of protein structure classification information-Surveying the scientific literature. Proteins Struct. Funct. Bioinforma. 83, 2025–2038.
  3. Murzin AG, Brenner SE, Hubbard T, Chothia C., 1995. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol. 247, 536–540.
  4. Fox, N.K., Brenner, S.E., Chandonia, J.-M., 2014. SCOPe: Structural Classification of Proteins–extended, integrating SCOP and ASTRAL data and classification of new structures. Nucleic Acids Res. 42, 304-9.
  5. Dawson NL, Lewis TE, Das S, et al., 2017. CATH: an expanded resource to predict protein function through structure and sequence. Nucleic Acids Research. 45, 289-295.
  6. Derek N Woolfson, Gail J Bartlett, Antony J Burton, Jack W Heal, Ai Niitsu, Andrew R Thomson, Christopher W Wood,. 2015. De novo protein design: how do we expand into the universe of possible protein structures?, Current Opinion in Structural Biology, 33, 16-26.
  7. Taylor, W.R., 2002. A “periodic table” for protein structures. Nature. 416, 657–660.
  8. Ahnert, S.E., Marsh, J.A., Hernandez, H., Robinson, C. V., Teichmann, S.A., 2015. Principles of assembly reveal a periodic table of protein complexes. Science. 80, 350

Start2Fold: A database of protein folding and stability data

Hydrogen/deuterium exchange (HDX) experiments are used to probe the tertiary structures and folding pathways of proteins. The rate of proton exchange between a given residue’s backbone amide proton and the surrounding solvent depends on the solvent exposure of the residue. By refolding a protein under exchange conditions, these experiments can identify which regions quickly become solvent-inaccessible, and which regions undergo exchange for longer, providing information about the refolding pathway.

Although there are many examples of individual HDX experiments in the literature, the heterogeneous nature of the data has deterred comprehensive analyses. Start2Fold (Start2Fold.eu) [1] is a curated database that aims to present protein folding and stability data derived from solvent-exchange experiments in a comparable and accessible form. For each protein entry, residues are classified as early/intermediate/late based on folding data, or strong/medium/weak based on stability data. Each entry includes the PDB code, length, and sequence of the protein, as well as details of the experimental method. The database currently includes 57 entries, most of which have both folding and stability data. Hopefully, this database will grow as scientists add their own experimental data, and reveal useful information about how proteins refold.

The folding data available in Start2Fold is visualised in the figure below, with early, intermediate and late folding residues coloured light, medium and dark blue, respectively.

start2foldpng

[1] Pancsa, R., Varadi, M., Tompa, P., Vranken, W.F., 2016. Start2Fold: a database of hydrogen/deuterium exchange data on protein folding and stability. Nucleic Acids Res. 44, D429-34.