The Department of Chemistry has a vacancy for a research fellow in molecular computational chemistry and spectroscopy for three years within the project ”Nano-solvation in Hydrogen-Bonded Clusters”. A description of the position including details of the subject areas and areas of responsibility, special duties and other circumstances given special emphasis in connection with the position is available on the following web-address: http://folk.uib.no/nkjkb/PhDposition.html
Monday, 1 August 2011
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 (http://www.curtin.edu.au) 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
(r.mancera@curtin.edu.au), 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 (http://www.chem.canterbury.ac.nz) or by visiting
Dr Crittenden's website (http://www.chem.canterbury.ac.nz/people/crittenden.shtml)
or Dr Masters' website (http://www.chem.canterbury.ac.nz/people/masters.shtml). Applicants should send a full CV and the names and contact details of two
referees to diane.caddick@canterbury.ac.nz
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.Wednesday, 20 July 2011
Principal Scientist - Computational Chemistry Scientific Programmer, Pfizer CT
Responsibilities
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 www.pfizer.com/careers 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.
Qualification
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:
shanghai.rdcrecruit##roche.com
frank.yan##roche.com
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.
Qualification
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:
shanghai.rdcrecruit(_)roche.com
frank.yan(_)roche.com
Tuesday, 28 June 2011
Microscopic Simulation of Solvation, at TUM, Munich, Germany
Develop an accurate method for the atomistic simulation of complexes
in solution we are looking for a physicist or chemist with a solid background
in theory as well as programming experience. The project relies on a
statistical approach to the distribution of solvent molecules around the
solute. This classical approach to the structure of a molecular solvent will
be coupled with a quantum mechanical method for an accurate description of
the solute. Parallel algorithms for an efficient implementation of the method
will be developed together with the Department of Computer Science
(Scientific Computing) and a theory group at a leading university in the USA.
Applications aim at case studies in catalysis and environmental chemistry. The International Graduate School of Science and Engineering at TUM supports
this international cooperative project with a generous scholarship.
For further information or submission of your detailed application
please contact Prof. N. Roesch, Theoretical Chemistry and Catalysis Research Center,
TU Muenchen, Garching, Germany, Email roesch@mytum.de
Computational Chemistry and Biology Opportunities at D. E. Shaw Research
Extraordinarily gifted computational chemists, biologists, and other
computational scientists are sought to join a New York-based
interdisciplinary research group that is pursuing an ambitious,
long-term strategy aimed in part at fundamentally transforming the process
of drug discovery.
Candidates should have world-class credentials in computational chemistry,
biology, or physics, or in a relevant area of computer science or applied
mathematics, and must have unusually strong research skills. Relevant
areas of experience might include protein structure prediction, the
computation of protein-ligand binding affinities, the study of biologically
important systems using molecular dynamics and/or Monte Carlo simulation,
and the application of statistical mechanics to biomolecular systemsbut
specific knowledge of any of these areas is less critical than exceptional
intellectual ability and a demonstrated track record of achievement.
Current areas of interest within the group include molecular dynamics
simulation of functionally significant globular and membrane proteins,
the prediction of protein structures and binding free energies,
structure- and ligand-based drug design, characterization of
protein-protein, protein-nucleic acid and protein-lipid interactions,
and the development of algorithms for biomolecular simulations.
We are eager to add both senior- and junior-level members to our
world-class team, and we are prepared to offer above-market compensation
to candidates of truly exceptional ability.
To submit an application, please use the link provided below:
http://www.deshawresearch.com/recruit/jobs/Ads/CCL/Chem
D. E. Shaw Research does not discriminate in employment matters on the
basis of race, color, religion, gender, pregnancy, national origin, age,
military service eligibility, veteran status, sexual orientation, marital
status, disability, or any other protected class. To submit an application, please use the link provided below:
http://www.deshawresearch.com/recruit/jobs/Ads/CCL/Chem
Computational Chemistry PhD Scholarships - NTU, Singapore
A few PhD research scholarships (up to 4 years) are available in our group
at Division of Chemistry & Biological Chemistry (CBC), School of Mathematical
& Physical Sciences (SPMS), Nanyang Technological University (NTU).
The successful candidate will use DFT, QM/MM, docking simulation, or other
computational approaches (e.g. MD) to investigate the structure and
reactivity of metalloenzymes, catalysts, or drug targets. The applicant must
hold a bachelor's or master's degree, preferably in computational chemistry,
and have interest and motivation to work on computational chemistry projects.
Our university offers admission of graduate students twice a year (in August
and January) and the next round is January 2012. Interested candidates are
encouraged to apply online for admission at
http://www.spms.ntu.edu.sg/CBC/Graduates/GradProgramOverview.html. Please also send CV directly to me via e-mail before applying online.
The monthly stipend will be S$2000, which may be increased after passing
the PhD qualifying examination. Feel free to contact me with any queries.
Contact person:
Hajime Hirao (Assistant Professor)
Division of Chemistry & Biological Chemistry
School of Physical & Mathematical Sciences
Nanyang Technological University
SPMS-CBC-04-01, 21 Nanyang Link, Singapore 637371
Email: hirao@ntu.edu.sg
Thursday, 16 June 2011
Computational Chemistry / Biochemistry - Berkley
Post-doctoral and research assistant positions are available for recent PhD or Master's students interested in the areas of computational chemistry, computational biology, bioinformatics, genomics and proteomics. Please submit full details that include a detailed CV, phone number, email, etc. The position is open for both US and non-US citizens.
For more details on research description, see http://www.mcs.csueastbay.edu/~kbalasub/ send email with attachments to kris.bala@csueastbay.edu
Chemoinformatician - Cambridge, UK
Cellzome is a privately-owned company applying its world-class technology to the discovery and development of small molecule therapeutics targeted at inflammatory conditions. We are looking to recruit a Chemoinformatician to support our ongoing Drug Discovery efforts. The successful applicant will be responsible for: - Administration of our corporate database, ensuring data integrity and the application of business rules - Development and implementation of tools and interfaces to support our Drug Discovery project teams - Application of Chemoinformatic techniques to aid in the selection of screening compound libraries and guide decision making within projects The nature of the job requires working closely with other Chemoinformatic, Bioinformatic and Scientific colleagues, therefore good communication and organisational skills are essential. The ideal candidate will be educated to at least degree level in chemistry with experience working in a chemoinformatics role within a pharmaceutical or biotech environment.
Experience of working with Pipeline Pilot and relational databases / SQL would be highly desirable. Additional experience of JavaScript, PL-SQL or Cambridgesoft software would also be an advantage. Ideally, the role will be located at our Chesterford Park site, UK although consideration will also be given to candidates who may prefer to be located at our Heidelberg site, Germany. Cellzome offers an excellent compensation package including a competitive salary, health care scheme, bonus scheme and life insurance. Applicants should send their CV quoting TH110 together with salary expectations and earliest starting date to: Mr James Smith - james.smith@cellzome.com Cellzome Limited, Chesterford Research Park, Little Chesterford,Cambridge, CB10 1XL http://www.cellzome.com
Closing date for applications Friday 29th July 2011
Experience of working with Pipeline Pilot and relational databases / SQL would be highly desirable. Additional experience of JavaScript, PL-SQL or Cambridgesoft software would also be an advantage. Ideally, the role will be located at our Chesterford Park site, UK although consideration will also be given to candidates who may prefer to be located at our Heidelberg site, Germany. Cellzome offers an excellent compensation package including a competitive salary, health care scheme, bonus scheme and life insurance. Applicants should send their CV quoting TH110 together with salary expectations and earliest starting date to: Mr James Smith - james.smith@cellzome.com Cellzome Limited, Chesterford Research Park, Little Chesterford,Cambridge, CB10 1XL http://www.cellzome.com
Closing date for applications Friday 29th July 2011
Thursday, 9 June 2011
PhD fellowship in computational chemistry/chemoinformatics, Bergen, Norway
3-year position as research fellow (PhD student) is available at Department of Chemistry, University of Bergen, Norway, more specifically, in the research group of Prof. Vidar R. Jensen.
SOME BACKGROUND INFORMATION ON THE OVERALL PROJECT:
The available position is linked to the project A method for automated denovo optimisation of functional transition-metal complexes, funded by the Norwegian Research Council, and is devoted to development of a de novo system for automatic generation of new functional coordination compounds with optimal properties. The project involves a close collaboration between the research groups of Profs. Bjorn K. Alsberg, Department of Chemistry at the Norwegian University of Science and Technology (NTNU), and Vidar R. Jensen, Department of Chemistry at the University of Bergen (UiB), and also involves further collaborating groups, both nationally and internationally. Catalysts constitute an example of functional coordination compounds which in particular will be the subject of investigation. The kind of de novo software to be developed is already in widespread use in
optimization and development of pharmaceutical substances (i.e., in silico drug design), but has not yet been applied in coordination/organometallic chemistry and catalysis, mainly because the traditional methods of drug-design are not directly applicable to coordination compounds.
DESCRIPTION OF THE PHD PROJECT:
The PhD student will participate in the development of the software for de novo evolutionary development of coordination compounds together with the other project participants. The PhD student will in particular work to integrate molecular-level computational software packages (quantum chemical and molecular mechanical, stays in collaborating research groups in the UK and the US are planned in connection with this work), identification/development and implementation of molecular descriptors (for coordination compounds), development and implementation of algorithms for efficient optimization of transition states (based on an QSAR/QSPR extrapolation scheme), as well as testing and validation of
the software in general.
EXPECTED QUALIFICATIONS OF THE CANDIDATES:
Candidates should have a strong background in computational chemistry (molecular modeling and/or quantum chemistry), whereas some background
from chemoinformatics/chemometrics also is desirable. Experience from programming and knowledge of inorganic/organometallic chemistry is an advantage.
SALARY:
Starting salary on grade 48 (code 1017/pay framework 20.8) in the Civil Service pay grade table scale; currently NOK 383,900 gross p.a.(salary will be adjusted); following ordinary meriting regulations.
FURTHER INFORMATION:
A more detailed description of the position and how to apply is available on the following web-address http://jensen.uib.no/stillingsomtale_PhD_B.htm. For further information, please do not hesitate to contact Professor Vidar R. Jensen, Department
of Chemistry (tel: +47 55 58 34 89; e-mail Vidar.Jensen@kj.uib.no).
Monday, 6 June 2011
Remodelling/Redesigning of Proteins - Artificial Protiens
Proteins are the core molecules behind every life activities. They are the functional part of every organisms with life. The outcome of every protein in a living organism is controlled by the DNA/GENEs. Variant proteins are expressed in the body in different situations in different quantities. Unusual of the amount of different proteins are considered to be the main indication of most of the genetic diseases. In the case of cancer, it is very clear that, a number of unusual proteins are produced in the body or the amount of some proteins gets increased. Pirh2 is one of the main proteins expressed in most of the lung cancer.
Through these preliminary studies, we tried to implement a structural function modification in the protein from the sequence alteration. For this, the Zinc finger CHY-type (ZF_CHY) domain of Pirh2 is allowed to get substituted with Tip60 (an inhibitor) protein sequence. We expect a change in the protein function in such a way that, the same protein can inhibit other cancer proteins also. For this, the altered protein structure is modeled by the software MODELLER. The modeled structures are minimized using NAMD with VEGAZZ. The structures are verified for stereochemistry, 3D features and conformations by various validation tools.
It is expected that the structural modification of a protein is more stable if it is done in the sequence level. This may give more stability to the altered protein in the highly dynamic body system. But here the biggest challenge in the future studies lies on the synthesis of these protein.
Work carried out by Girinath G. Pillai and Raji Pillai.
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