PhD Studentship on Structural Informatic Analysis of the Protein/Ligand Interface

This 4 year studentship, due to start Jan-Mar 2013, is a collaboration
between the Department of Biochemistry, University of Cambridge, the
Cambridge Crystallographic Data Centre and UCB Pharma, a global 
pharmaceutical company. It is funded under the BBSRC Industrial CASE 
Award scheme and BBSRC UK Residency criteria apply.

Please see the link below for further details and how to apply:

http://beta-www.ccdc.cam.ac.uk/CCDC/Careers/pages/Careers.aspx

Two Ph.D. Studentship in Computational Chemistry

Two Ph.D. student positions are available in Prof. Qian's group in 
computational chemistry at the Department of Chemical Engineering, 
University of Arkansas starting immediately. The research topics in
Prof. Qian's group focus on biomass conversion to biofuels, responsive
polymers, salt effects on protein folding and unfolding. A variety of 
computational tools are used including quantum mechanical methods,
classical and ab initio molecular dynamics simulations and QM/MM.

  
Interested candidates please contact: 
Prof. Xianghong Qian
Department of Chemical Engineering
University of Arkansas
Tel: 479-575-8401
Email: xqian@uark.edu

Applications Scientist

Schrodinger, a technology leader specializing in software solutions for
life science research and development, is searching for an Applications
Scientist to be based in Cambridge, MA. Applications Scientists work on
the development of new computational methods for drug discovery,
scientific publications, and assist customers with using Schrodinger
software to solve challenging scientific problems.

Applications Scientists also work at the interface between customers and
Schrodinger software developers, sales, and marketing.  Responsibilities
include engaging in scientific discussions with customers, giving
presentations at conferences, demonstrating optimal use of the software,
and providing customer training. Collaborative projects with customers,
presentations at scientific meetings, and publication is encouraged.

Applications Scientists gain familiarity with our entire suite of
structure-based and ligand-based software, including packages for
docking, molecular simulations, homology modeling, pharmacophore
modeling, cheminformatics, and quantum mechanics. A strong background in
molecular modeling and computational chemistry with application to
biological problems is highly desired. Exceptional communication skills,
an outgoing personality, and a willingness to travel are required.

Requirements:
- Ph.D. in computational chemistry or biophysics plus experience with
  pharmaceutical applications of molecular modeling software tools

- Excellent interpersonal, communication, and organizational skills

- Strong problem-solving ability

- A broad knowledge of molecular modeling theory and applications

- Ability to conduct independent research

Preferred:
- Post-doctoral research and/or relevant experience in the commercial sector

- Python programming experience

Schrodinger is an equal opportunity employer.

Please visit our website at:  www.schrodinger.com/careers .

PFIZER - Systems Biologist/Toxicologist

We are looking to recruit a Senior Scientist/Principal Scientist for the 
Compound Safety Prediction group (CSP). The CSP group develops and applies 
computational modeling techniques (for physico chemical properties, 
structure activity relationships and biological pathways) in concert with 
mechanism-based screening tools (cell based, in vivo "biosensors" and high 
content biology platforms) to help select the safest chemical substrate. 
Underpinning all of this is a scientific focus on identifying and 
characterizing broad underlying biological mechanisms associated with 
undesired toxicity endpoints. This is an exciting new function for 
Worldwide Research & Development (WRD), with the opportunity to have a 
very positive and impactful contribution to the quality of our portfolio.

This position is for a systems biologist or systems toxicologist to work 
within the Chemical and Biological Mechanisms Group, where the candidate 
will help design and conduct research projects to improve our understanding 
of basic toxicity mechanisms. It will require someone who can put existing 
high-content results and data into biological context in terms of the 
molecular pathways and use this to design experiments that would add 
further understanding or value to the interpretation of the assay results. 
Such results and data may include high content biology/systems biology 
platforms and require knowledge and experience of computational approaches 
for data mining such or pathway mapping.  The position will also be 
expected to make recommendations for follow-on testing to confirm 
hypotheses or design and execute experimental confirmation of the 
mechanisms indicated from their analysis.


WORK EXPERIENCE: 
Experience in molecular biology or toxicology with experience in high 
content data mining / analysis (e.g., ~omics technologies) and multi-
parametric data modeling with a background in one or more of the following: 
 Transcriptomics / Gene Expression data sets
 Proteomics 
 Metabonomics 
 Signal transduction 
 Molecular toxicology


Please apply on-line at our website, www.pfizercareers.com and search for
Job ID 969499.

Postdoc, Compotational Chemistry/Biology

The Center for Integrative Chemical Biology and Drug Discovery (CICBDD) in 
the UNC Eshelman School of Pharmacy is engaged in the discovery of 
small-molecule therapeutics and chemical probes for biomedical research. 
At the CICBDD, chemists, biologists and computational scientists work 
closely together in multidisciplinary project teams. More information about 
the Center can be found at http://www.pharmacy.unc.edu/research/centers/center-for-integrative-chemical-biology-and-drug-discovery.

We are currently looking for a creative, independent and highly motivated 
individual to join our research effort in developing and applying 
computational approaches to chemical biology and drug discovery. The 
appointee is expected to perform large-scale data analyses on heterogeneous 
data sets, such as outputs from molecular dynamics, virtual and biochemical 
screening experiments. He will make use of state-of-the-art data processing 
tools (such as R, Matlab, Pipeline Pilot, etc) and develop new advanced 
methodologies. He will also run virtual screening experiments, contribute 
to structure-based drug design in close collaboration with medicinal 
chemists and biologists, and contribute to the development of informatics 
tools for the Center.

The successful candidate will have a Ph.D. degree in Computational 
Chemistry/ Biology or a related discipline, a demonstrable track record 
in computer-aided drug design and familiarity with major modeling/simulation 
software, data analysis and chemoinformatics tools. Computer programming and scientific writing skills will be an asset.

This position will report to Professor Dmitri Kireev, Director of 
Computational Drug Discovery. More information on his research interests, 
projects, publications and track record can be found at 
http://www.pharmacy.unc.edu/Directory/kireev.

The position is available immediately. Qualified applicants should send a CV 
by email to Dr. Kireev at dmitri.kireev@unc.edu and be ready to provide at 
least 2 reference letters. Applications will be considered until the 
position is filled.

PhD fellowships - Ecole Polytechnique Federal de Lausanne

Two computational/theoretical chemistry PhD positions are available in the Laboratory for 
Computational Molecular Design headed by Prof. Clemence Corminboeuf at the Swiss Federal 
Institute of Technology (EPFL, Lausanne). 

The PhD fellowships are available in the framework of the ERC-Starting Grant (project COMPOREL)awarded to C. Corminboeuf.

The objective of the COMPOREL project is to develop a computational screening approach for identifying promising molecular precursors to organic electronics.

The candidates should have a Master degree in Chemistry (Theoretical, Physical) or Physics and 
experience in computational/theoretical chemistry. Knowledge of Linux-/Unix-based computer 

systems and Fortran programming languages is desirable. 

The two fellowships are for 4 years. The annual salaries are roughly 50,000 CHF.

PhD positions at EPFL require acceptance in the doctoral program of Chemistry and 
Chemical Engineering. Interested candidates should fill an application at:

http://phd.epfl.ch/edch

For detailed information on the projects, interested candidates are encouraged to 
contact Clemence Corminboeuf by email at clemence.corminboeuf@epfl.ch and include a CV,
a brief description of research interests.

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).

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: argenta_jobs@glpg.com.

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 biofocus_jobs@glpg.com.

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

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 (ana@chem.ucla.edu). 

For more information of Alexandrova lab's research:  http://www.chem.ucla.edu/~ana/

Website:

http://www.chem.ucla.edu/~ana/join.html

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 tryan@istaffinc.com for details.