Friday, 24 February 2012

Internship Project - A fully Open Chemically Searchable ChEMBL

For a long time now we have been keen to release a full and freely deployable version of the ChEMBL database with compound search capabilities built in. This has been possible in the past, but complicated by commercial licenses associated with either the databases or the chemical cartridges. There are now a number mature Open Source chemical toolkits available, such as the excellent CDK, and RDKit.

So with that brief bit of background there is now an opportunity for an intern to work in the ChEMBL group on the project for 2-3 months. The idea is will be to setup a process which:

  1. Creates a PostgreSQL version of the ChEMBL database (database required by RDKit).
  2. Install the RDKit chemical cartridge.
  3. Migrate this setup to Amazon Web Service public image.
  4. Migrate existing (or new) ChEMBL interface to run off new database and package this up into AWS image.
  5. Develop scripts to allow new releases of ChEMBL to be processed and uploaded as a new AWS image.
Actually some work has already been done in the public domain, and this will act as a good starting point for someone wanting to learn more about the data and technologies.

If you are looking for internship this year and have interest in the area of cheminformatics tools and some relevant experience please get in touch (as potential interns, we appreciate you may not have years of industry experience, but we would require you to have previous experience with relational databases and be competent in at least one programming language).

Friday, 17 February 2012

Molecular Modeller (HAR-605)

Molecular Modeller (HAR-605)

We have an opportunity for a molecular modeller with industrial experience and a track record of excellence to join our Computer-aided Drug Design (CADD) group.
The main responsibilities associated with the role are as follows:
  • To work in interdisciplinary teams and actively contribute to all stages of our clients’ drug discovery projects from hit identification to candidate nomination
  • To perform structure- and ligand-based molecular design including protein modelling and virtual screening
  • To evaluate, implement or acquire, and apply new CADD methodologies and techniques
You should possess the following qualifications:
  • A first degree in chemistry or a closely related subject
  • A PhD in a field of relevance to molecular modelling
  • At least 5 years of molecular modelling experience within the pharmaceutical or biotech industries
  • A sound knowledge of molecular modelling software, data pipelining tools and Linux (experience of Schrödinger’s software would be advantageous)
  • Some programming/scripting skills (e.g., C/Java, Python) would be desirable
  • Strong interpersonal, communication and presentation skills
At Galapagos and Argenta, we aim to recruit the best people, who stand out among their peers, with integrity and excellent interpersonal and organizational skills. Our employees are the strength behind Galapagos, a highly motivated team, eager to maintain Galapagos’ leading position and achieve breakthroughs in pharmaceutical research. Galapagos offers a competitive remuneration package and a dynamic work environment.
Do you have the qualifications for this job opening and are you up to the challenge of joining our entrepreneurial team? If so, please send your application (preferably by e-mail) to:

Computational Chemist (CRP-427) Saffron Walden, near Cambridge, UK

Computational Chemist (CRP-427) Saffron Walden, near Cambridge, UK

As part of continued expansion, BioFocus is increasing the size of its computational chemistry group, based at its Head Office near Cambridge, UK. You will be working alongside BioFocus’ Scientists in Biology and ADME/PK departments as well as Medicinal Chemistry with a diversity of global organizations in a variety of therapeutic areas and will be making a real impact on projects from the start.
As an enthusiastic individual with excellent problem solving abilities and a desire to succeed and learn, you will provide innovative solutions to continuingly evolving problems on both multidisciplinary and stand alone computational chemistry projects. You must have the ability to multitask and deliver to tight deadlines.
Clear and compelling communication skills, both written and oral, are vital and you must be a confident presenter and able to think on your feet.
Technical competences must include a strong scientific background with exposure to the pharmaceutical industry. A skill set including experience in structure-, ligand- or fragment-based methodologies is paramount. Familiarity with software such as Moe, Cresset, Discovery Studio, Pipeline Pilot and the Schrödinger suite is an advantage. You must have the right to work for any company in the UK.
Do you want to work in a challenging and rewarding culture that will offer the opportunity to develop and broaden your horizons? Would you like to work in a dynamic and entrepreneurial organization and join a successful and established computational chemistry group under pinned with an excellent hardware and software infrastructure where you will have the opportunity to have an impact? If so, we want to hear from you!
At Galapagos, BioFocus and Argenta, we aim to recruit the best people, who stand out among their peers, with integrity and excellent interpersonal and organizational skills. Our employees are the strength behind Galapagos, a highly motivated team, eager to maintain Galapagos’ leading position and achieve breakthroughs in pharmaceutical research. Galapagos offers a competitive remuneration package and a dynamic work environment.
To apply, please send your CV and a covering email to

Postdoc in Theory and Computation @ Alexandrova Lab, UCLA, USA

Position is open immediately.

Required qualifications
strong background in quantum chemistry, knowledge of statistical mechanics, programming and scripting skills;

Preferred qualifications
: experience in simulations of biological molecules, or materials.
Email your CV and cover letter indicating your interests and qualifications, and arrange for 2 letters of recommendation to be emailed directly to Prof. Alexandrova ( 

For more information of Alexandrova lab's research:


Ph.D. - Computational Chemistry

Ph.D. students and Postdoctoral researchers (three positions in total)

We are seeking Ph.D students and postdoctoral researchers for projects involving protein structure prediction and virtual screening. There has been a dramatic increase of structural information for GPCRs during the last five years. We are interested in how the recently published crystal structures of GPCRs can be used to generate accurate models for receptors of unknown structure. The project involves (1) Development of new approaches for homology modeling of GPCRs and (2) Structure-based discovery of ligands to GPCRs (both crystal structures and models) using molecular docking. All projects are carried out in close collaboration with experimental groups.

We are also seeking Ph.D. students and postdoctoral researchers for a project involving molecular dynamics (MD) simulations of membrane receptors. The recently published structures of GPCRs in different stages of activation have made it possible to use molecular simulations to study how these receptors work at atomic resolution. The project will also involve development and application of methods for predicting GPCR-ligand binding affinities from MD simulations.

The ideal background for the Ph.D positions is a M.Sc in chemistry or physics. Candidates for the postdoctoral researcher positions should have experience from molecular modeling techniques, e.g. molecular docking and molecular dynamics simulations.

Interested? Contact me!

Post-Doc Computational Chemistry

Three post-doctoral positions in my research group.
The research topics will include modeling and simulation of RNA molecules (riboswitches) and of RNA-protein complexes (RNA-helicases). The techniques used will range from atomistic molecular dynamics, combined with advanced accelerating techniques (replicaexchange, metadynamics, etc), to coarse-grain modeling using Gaussian network models, to secondary-structure prediction methods for RNA.The involved people up to now are: me as the principal investigator, Prof. Cristian Micheletti as an expert of coarse-grain models, Dr. Francesco Colizzi, a pharmaceutical chemist currently doing a post-doc in SISSA, and Francesco Di Palma, a PhD student. We also have collaborations with several experimental groups interested in these topics.

There will be space for both method-development and applicative research lines. Ideal candidates would be computational physicists or chemists, but we will be happy to consider also more biological-oriented profiles (e.g. bioinformatics or pharmaceutical chemistry) if they have a strong experience with simulations.

The post-doctoral positions will be paid by an Italian national grant (FIRB - Futuro in Ricerca 2010) and should start before end 2012. Their salary will be proportional to their experience and competitive with respect to European standards.

For more information, contact me as soon as possible.

Principal Investigator, Computational Chemistry

Principal Investigator, Computational Chemistry

Opportunity to join the drug discovery group of a rapidly growing pharmaceutical company in Cambridge, MA. Connect with me on Linkedin or for details.