Wednesday, 27 July 2011

PhD position in molecular dynamics simulations of proteins

PhD position in molecular dynamics simulations of proteins

The Biomolecular Modelling Group at WABRI has an opening for a highly
qualified Ph.D. research student with interests in applying molecular
dynamics simulation techniques to investigate the structure and function of
proteins. A scholarship (worth AUD$25,000 per year) and a waiver of all
university fees will be offered to the successful applicant, who will join
a growing research group that currently comprises three postdoctoral
research fellows, two PhD students and two honours students. The group is
headed by Professor Ricardo L. Mancera.

The research project that the successful applicant will work on involves
the characterisation of the oxygen tunnel in the enzyme cholesterol
oxidase: the tunnelling mechanism of oxygen into the active site, the
conformational changes in the protein associated with this process, the
free energy pathways for the diffusion of oxygen into the active site and
the relationship between the tunnelling of oxygen into the active site and
the redox mechanism of action of the enzyme. This project will be carried
out in collaboration with Professor Alice Vrielink (University of Western
Australia), who was been determining very high resolution X-ray structures
of cholesterol oxidase for several years.

Applicants for this position must have completed by the time of enrolment
a first-class or upper-second class honours undergraduate degree and/or
master's degree in chemistry, physics, materials sciences, biochemistry,
chemical engineering or related field. Applicants MUST have demonstrable
research experience in molecular dynamics simulations of proteins.
International students will need to satisfy Curtin University's English
language proficiency requirements by achieving a minimum overall mark of
7.0 in the IELTS or 580 in the TOEFL paper test (237 in the computer
version or 100 in the internet version).

Curtin University ( is the largest university in
Western Australia and is ranked amongst the top universities in Australia.
The Biomolecular Modelling Group is setting up its own dedicated GPU
cluster and is also one of the major users of the Western Australian
high performance computing centre (iVEC) and the National Computational
Infrastructure facility. The group will also have access to the Pawsey
Centre, an $80 million Federal Government initiative to establish a
petaflop computing facility in Perth. In addition, living in the state
capital Perth offers a great lifestyle due to Western Australia's superb
weather, beaches and outdoors activities.

Only applicants that fulfil the above requirements need apply by submitting
a copy of their full CV to Prof. Ricardo L. Mancera
(, including full details of all academic degrees
obtained, research skills and experience, publications and conference
presentations, and the names of 2-3 referees.

PhD in computational and structural chemistry, University of Canterbury, Christchurch, New Zealand

One three-year PhD scholarship is available from January 1, 2012 
to work under the supervision of Dr Deborah Crittenden. This project 
involves the design and development of new ultra-light photo-
switchable hydrogen storage materials. The safe, efficient and portable 
storage of hydrogen gas produced during photolysis is one of the few 
remaining challenges to establishing the hydrogen economy and 
reducing world dependence on fossil fuels for energy production. 
Computational quantum chemical methods will be used to tune the 
hydrogen-adsorbing abilities of and transition energies between 
different quantum states of functionalized polymers and nanoporous 
lattice materials to produce a material that releases hydrogen gas 
upon irradiation with visible light, and readsorbs hydrogen in the dark.

Applicants for this scholarship should have a good knowledge of 
quantum mechanics. Experience using unix-based computer systems 
and quantum chemical programs would be advantageous but is not required.

A second three-year PhD scholarship is available in structural chemistry 
to work under the supervision of Dr Sarah Masters with the same start date. 
The group employs the technique of gas electron diffraction (GED) to study 
molecular structure in the gas phase, with current focus in the novel area of 
structure determination of short-lived species. Interpreting the diffraction 
patterns involves the use of computational quantum chemical methods as 
part of the structure refinement process. The GED apparatus has been modified 
to use, where appropriate, very high temperature inlet systems to generate 
transient species in situ. This project will continue the development of new 
methods for species generation, concentrating on photolysis methods. 

For this project, experience in the use of photolysis methods is desirable, 
along with the use of computational techniques for structure determination. 
A strong interest in the development of new experimental techniques is essential.

For both projects, candidates should have, or be about to receive, a first-class 
Honours degree (or equivalent) in chemistry or physics. 

Further details are available through the Department of Chemistry website at
the University of Canterbury ( or by visiting
Dr Crittenden's website (
or Dr Masters' website (
Applicants should send a full CV and the names and contact details of two 
referees to

Successful applicants must also apply for a University of Canterbury scholarship 
(closing date 15th October 2011). Two types of UC scholarship are available, 
Canterbury scholarships for NZ citizens or permanent residents and UC 
International Doctoral Scholarships for international students.

Applications will be assessed from 1st August 2011 - 15th October 2011.

Thursday, 21 July 2011

Principal Scientist - Computational Chemistry Scientific Programmer, Pfizer CT

The Computational Sciences Center of Emphasis (CS CoE) has an opening at its Groton, CT site for a Computational Chemistry Scientific Programmer. The successful candidate will work as part of a team responsible for developing tools and applications for use by project teams working to discover new medicines. S/he will work with other members of the CS CoE as well as directly interfacing with end users. Duties of the position will include (but are not limited to) design and implementation of new algorithms/features, interfacing with project teams to help them leverage tools, and development of innovative computational solutions. The incumbent will also frequently interact with other computational chemists and biologists that are technology- or TA-aligned at our sites, with our Partner Lines, and with Research Informatics. 

Qualifications Requirements: 
- PhD with 5 years experience or BS/MS with 10 years experience in the pharmaceutical industry. Degree should be in chemistry/computational chemistry or related field. 
- Expertise as a scientific programmer particularly in java both developing user interfaces and algorithms. 
- Proven track record of developing computational solutions to difficult problems. Team player able to work as part of a larger development team and/or directly with end users. To be successful, excellent communication skills are a must.
- Strong linux and windows skills. 

Other skills: 
- Experience working with compute clusters in particular LSF. 
- Knowledge/experience related to GPGPU programming. 
- Expertise in c/c++, python, objective c. 
- Experience as a system administrator for both windows and linux systems. 
- Web application development.
To apply please go to and search for job ID 953392.

Computation chemist position in Roche Shanghai, China

A highly creative and motivated computational chemist in the fields of computer-aided drug design. You will be able to execute structure-based drug design using crystal structure in lead generation and optimization. You will also be able to apply various computational approaches such as pharmacophore modeling, homology modeling, conformational analysis, etc, in day-to-day compound design with synthetic medicinal chemists. You will work closely and collaboratively with the project team to deliver milestones from lead generation to lead optimization.

Who you are:
* Ph.D. in computational chemistry, medicinal chemistry, or related fields.
* 0-3 years of post graduate experience.
* Experience and expertise in synthetic chemistry is highly desirable.
* Experience in cheminformatics and data mining is desirable.
* Strong knowledge in protein structure, protein modeling, and protein- ligand interactions.
* Solid knowledge in QSAR methodologies, visualization, library design, conformational analysis, and 2D and 3D similarity.
* Ability to be multitasking, work on multiple projects, and work on a timeline.
* Excellent oral and written communication skills as well as good presen- tation skills is a must.

You are also welcome to apply directly by submitting your cv to:

Computer-Aided Drug Discovery (CADD) Position in Roche Shanghai, China

An established computational chemist with experience in the fields of cheminformatics, computational chemistry, and bioinformatics. You will able to apply various in silico approaches in target evaluation, lead generation and HTS data analysis, as well as supporting compound design in lead optimization. You will be able to drive the drug discovery project from a molecular design aspect. You will also be able to represent Roche Shanghai in both internal and external meetings.

Who you are:
* Ph.D. in computational chemistry, cheminformatics, or related fields.
* At least 2-5 years of post graduate industry experience.
* Experience in informatics, cheminformatics, data mining, or bioinformatics is highly desirable.
* Experience with structure-based drug design, protein modeling, and protein-ligand interactions.
* Ability to be multitasking, manage multiple projects, and work on a timeline.
* Excellent oral and written communication skills as well as good presentation skills is a must.

You are also welcome to apply directly by submitting your cv to: