Wednesday, 29 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

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:

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:

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
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

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

send email with attachments to

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 - Cellzome Limited, Chesterford Research Park, Little Chesterford,Cambridge, CB10 1XL 

Closing date for applications Friday 29th July 2011

Friday, 10 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.

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. 

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.

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.

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.

A more detailed description of the position and how to apply is available on the 
following web-address
For further information, please do not hesitate to contact Professor Vidar R. Jensen, Department 
of Chemistry (tel: +47 55 58 34 89; e-mail

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.