Author Archives: jp

And the Oscar goes to …

08:44

I have a bet I can write a blog post in under 20 mins.  Last week I asked Leila Tamara where her blog post was (we aim to have one up every week) and she replied that “It was ready but hadn’t been proof-read yet“.  I guess it goes to show the diligence of the students here at Oxford.  (Some of them, anyway).

So as a Marie Curie Stars ITN Fellow, my time is coming to an end (in mid-September).  Part of my D.Phil was about finding novel anti-malarial inhibitors using computational methods (virtual screening).  No, we haven’t cured it yet.

During a conference in Riga we made a video about the project – I find it funny to see myself on screen, (and to hear my heavily accented commentary).  Pity the Oscars have already been dished out this year!

And a “making of” still

JP make-up

08:52.

Warning: this post hasn’t been proof-read yet!

 

[Publication] Memoir: template-based structure prediction for membrane proteins

Congratulations to all involved in the Memoir publication in Nucleic Acids Research! 

Memoir is a web server which builds homology models for membrane proteins.  It is a web-enabled workflow combining some of OPIG’s software; MP-T, IMembrane, Medeller & Fread.  The inputs are a sequence of the membrane protein you wish to model (target) and a PDB file to use as template.

Memoir may be found here and there is also a video tutorial narrated by Jamie.  There is even a funny blooper of him practising, which I kept to celebrate this moment.

Happy modelling!

 

Free food!

Yesterday I walked into Group Meeting not having read Bernhard‘s paper (shameful, I know), and I was immediately asked “Where is the Daleks post on the blog?”.  To which I mumbled something unconstrued, because I am not sure what a Dalek is and because I didn’t know we were doing post requests.

Anyway, at every group meeting one of us is responsible to organise the talk and another to supply food.  The only current rule (since the well-received demise of the “No alcohol” one)  is: “No tomatoes“.  We’ve had a number of original and tasty contributions: Dominos pizza, Ben’s and Millies cookies, truckloads of Haribos, Krispy Kreme Doughnuts, Sushi, Nutella baguettes and home-baked delights.

But Eoin‘s contribution takes the prize this round (a small trophy in Lab Room #1).

drwho-daleks-food

Eoin’s Dr. Who Daleks sugar rush inducing cakes (click for the juicy detail).

So, a small pointer to OPIG prospective students – “baking” and “creative thinking” skills are really well appreciated and look good on your CV!

 

How to install RDKit on Ubuntu 12.04 / 12.10 / 13.04 / 13.10 / 14.04 / 14.10 (with InChI support)

I make extensive use of this brilliant piece of cheminformatics software (RD)kit, and it has saved me writing my own Molecule, Atom, Bond, Conformer, Fingerprint, SimilarityMetric, Descriptor etc. classes time and time again.  It is really neat, and works with C++ and python (and Java I think).  Here are the instructions on how to install it on a relatively recent Ubuntu version (12.04 / 12.10 / 13.04 / 13.10 / 14.04 / 14.10).

Pre-requisite software (this is why I love Debian based systems)

sudo apt-get install flex bison build-essential python-numpy cmake python-dev sqlite3 libsqlite3-dev libboost-dev  libboost-python-dev libboost-regex-dev

Get the latest RDKit goodie from here (watch out – version number has been replaced by ‘X’ below)

wget http://downloads.sourceforge.net/project/rdkit/rdkit/QX_20XX/RDKit_20XX_XX_X.tgz

Unzip the beast, save it to /opt

sudo tar xzvf RDKit_20XX_XX_X.tgz -C /opt

Add some environment salt, vim ~/.bashrc

export RDBASE=/opt/RDKit_20XX_XX_X
export LD_LIBRARY_PATH=$RDBASE/lib:$LD_LIBRARY_PATH
export PYTHONPATH=$RDBASE:$PYTHONPATH

Resource your .bashrc

. ~/.bashrc

if you want the InChI stuff (trust me you do), first:

cd $RDBASE/External/INCHI-API/
./download-inchi.sh

Build (compile), install & test

cd $RDBASE
mkdir build
cd build
cmake .. # if you do not care for InChI support OR
cmake -DRDK_BUILD_INCHI_SUPPORT=ON .. # to install InChI generation code 
make # -j 4 to use multiple processors
make install
ctest

If all your tests passed successful you are good to go.  Otherwise, get in touch via the post comments below.