Tuesday, 6 December 2011

Postdoc position Scientific Programmer Cheminformatic in Berlin/Germany

The Leibniz-Institut fuer Molekulare Pharmakologie (FMP) seeks a Scientific Programmer
for the technology platform of chemical biology, funded by the Max-Delbrueck Centre fuer
Molekulare Medizin (MDC).

-  Development of problem-orientated algorithm in cooperation with 
   experimentally working groups;
-  implementation of the algorithms and design of data structures and 
-  Use of the new routines in connection with experimental work
-  maintenance and documentation of the object and data models.


The candidate should meet the following prerequites:
-  A degree in computer science or a related field or equivalent experience, 
   preferably completed PhD
-  Development and project experience with object-oriented programming
-  Sound knowledge in C + + / Java, including JDBC, Java Beans,
   Java Servlets (Apache Tomcat)
-  Knowledge in Cheminformatic API desirable (jchem, marvin, CDK etc)
-  Knowledge of scripting languages (Perl, PHP, Python, etc)
-  Database experience desirable, solid SQL skills (experience in installation 
   and maintenance of large databases (MySQL, Oracle, DB2 etc)
-  Knowledge of XML, XSLT / XPath, and related technologies
-  Willingness and ability to work in a Linux based environment, Windows (client platform)
-  Willingness to engage in interdisciplinary cooperation
-  Good knowledge of English and German

From a personal point of view we expect:
-  Principal interest in chemistry and bioinformatics
-  Strong analytical skills and structured work

To apply, e-mail your CV and list of publications to Dr. Bernd Rupp
(e-mail: rupp@fmp-berlin.de)along with the names of at least three 
references and in your cover letter highlight how you will fit into and 
complement the on-going research in our lab.

Postdoctoral Vacancy in Computational Biophysics / Biochemistry at Uppsala University

Postdoctoral vacancy in computational biochemistry/biophysics in the 
Kamerlin lab at Uppsala University. The focus of our research is on evolutionary based protein 
redesign, using in silico approaches to navigate sequence space. The position is available from 
early January (or as soon as possible thereafter), and we are looking for exceptionally driven and 
talented researchers to join us to work in this highly competitive research area.

Further information about the vacancy can be found here:


To apply, send a CV, publications list, brief overview of research interests and contact details to 
three people who can provide letters of recommendation to Lynn Kamerlin, kamerlin@icm.uu.se.

Postdoc in theoretical chemistry at Iowa State University

Prof. Xueyu Song is looking for a Postdoctoral
Fellow with strong theoretical and/or computational background in chemistry or physics, starting
from January 2012.  The position is initially for one year and
may be renewed for additional years depending upon the performance and
funding. Salary is commensurate with experience in the range of $35-40k/yr.

The candidate should have a Ph.D in chemistry or physics with a 
strong background in statistical mechanics or related
fields. Practical knowledge in simulations with experiences in FORTRAN or C programing
are required. 

Applicants should send their curriculum vitae and names of at least two reference persons to 
Dr. Song at xsong@iastate.edu.

Screening of applicants will begin as soon as possible. Applications will
be accepted until the position is filled. Iowa State University is an
equal opportunity educational institution/equal opportunity employer.

Scientist, Computational Chemistry

Dart NeuroScience LLC (DNS) is a privately held Delaware Limited Liability 
Company with facilities in San Diego CA.  DNS will discover new technologies 
and develop new therapies to help maintain cognitive vitality throughout 
life.  DNSs Scientific Computing Department focuses on (i) development of 
novel bioinformatic tools to facilitate gene discovery, (ii) development of 
novel software tools to facilitate drug discovery, (iii) computational 
chemistry project support, structure-based drug design, combinatorial 
chemistry and statistical modeling, (iii) information systems and 
automation and (iv) general IT infrastructure to support scientific 
research and company administration.

The successful candidate will have broad knowledge and experience applying 
computational chemistry to solve complex scientific problems.  S/he will 
support small-molecule design teams from early screening through lead 
optimization using computational chemistry. The candidate will work with 
the Methods (software), Information Management and Bioinformatics groups 
within the Scientific Computing Department to develop novel tools to 
facilitate small-molecule design.   A solid understanding of 
structure-based and ligand-based drug design is required.  The successful 
candidate will be expected to make individual contributions to drug 
discovery projects and enhance the composition of the DNS compound 
collection through computer-aided design.


- Ph.D. with 3+ years experience (or M.S with 8+) in computer-aided design, 
preferably in the pharmaceutical industry. CNS experience is preferred, 
but not required.

- Extensive experience with structure-based methods such as docking, 
molecular mechanics and homology modeling AND/OR ligand-based methods 
such as pharmacophores and QSAR are preferred.  Knowledge of statistical 
modeling methods and experience using the ChemAxon and OpenEye chemistry 
toolkits and Schrdinger Software would be a plus.  

- Good oral and written communication skills and the ability to communicate 
with medicinal chemistry, informatics, bioinformatics and software 
developers are a must.

- DNS offers competitive salaries and a great benefits package including 
incentive bonuses, healthcare, vision, dental, long-term disability, 
life insurance, flexible spending and a 401(k) retirement savings plan.

Interested individuals should submit a cover letter, curriculum vitae, 
a brief summary of research experience and accomplishments, 
research interests and goals and list of publications using our 
online application: http://jobsco.re/sQD82F.

PDF files are strongly encouraged.

For more information please visit our web site at www.dartneuroscience.com.

Scientist, Cheminformatics

Dart NeuroScience LLC (DNS) is a privately held Delaware Limited Liability 
Company with its principal place of business in San Diego CA.  DNS will 
discover new technologies and develop new therapies to help maintain 
cognitive vitality throughout life.  DNSs Scientific Computing department 
focuses on (i) development of novel bioinformatic tools to facilitate gene 
discovery, (ii) development of novel software tools to facilitate drug 
discovery, (iii) computational chemistry project support, structure-based 
drug design, combinatorial chemistry and statistical modeling, 
(iii) information systems and automation and (iv) general IT infrastructure 
to support scientific research and company administration. We are seeking 
a new employee to work in information systems and automation.

The successful candidate will have a solid foundation in 
synthetic/medicinal chemistry, and an interest in applying that 
knowledge to the construction and support of informatics systems that 
assist chemists in their work. S/he will provide direct support to 
chemists in using commercial or in-house tools for chemistry data 
deposition, retrieval, and knowledge extraction. S/he will also 
participate in the design and implementation of new and upgraded 
informatics systems, and be responsible for testing these systems and 
training scientists to use them. S/he will configure commercial 
systems to integrate into DNS workflow, and may extend these systems 
via macros or scripts.

- M.S. or B.S. with 3 years experience, preferably in the pharmaceutical 

- Solid understanding of synthetic/medicinal chemistry

- Experience with SQL and/or data pipelining tools (Pipeline Pilot or 
KNIME) is a plus, but not required

- Experience with ELNs, LIMS and/or content management systems is a plus

- Ability to learn new technologies and techniques quickly without 
formal training

- Good oral and written communication skills and the ability to 
communicate with and explain new concepts to bench scientists, 
other informatics scientists, and software developers

- Strong organizational skills and attention to detail are essential
DNS offers competitive salaries and a great benefits package including 
incentive bonuses, healthcare, vision, dental, long-term disability, 
life insurance and a 401(k) retirement savings plan.

Interested individuals should send a cover letter, curriculum vitae, 
a brief summary of research experience and accomplishments, 
research interests and goals and list of publications via our 
online application: http://jobsco.re/tXDrT5.

PDF files are strongly encouraged.
For more information please visit our web site at www.dartneuroscience.com.

Computational Chemist at AstraZeneca Molndal, Sweden

The Computational Chemistry section within the Medicinal Chemistry 
department in the Cardio-vascular and Gastro-intestinal Innovative 
Medicines  unit (CVGI iMed) at AstraZeneca in Molndal, Sweden, is 
currently recruiting a computational chemist for a temporary 
assignment via our staffing partner Proffice.

This position offers the opportunity to use your expertise in 
computational chemistry in all phases of drug discovery projects. 
It is a challenging position in the interplay of different disciplines 
in a fast developing field. The role requires enthusiasm, flexibility, 
and the ability to interact in a multi-disciplinary team and to 
communicate effectively. We are looking for a Ph.D in science with 
experience in cheminformatics, small molecule modeling, ligand- 
and structure-based design. Industrial experience from a similar role
and/or a background in, e.g., organic chemistry, physical chemistry, 
biochemistry, pharmacy or computer programming is advantageous.
Please apply in English at 
no later than 2011-12-12. We are continuously interviewing candidates 
since we are aiming at filling the position as soon as possible. 
For further information please contact Medina Sundstrom at Proffice, phone +46-733-434153 
or Jonas Bostrom (jonas.bostrom@astrazeneca.com).

Postdoc position Molecular Modeling/MD-Simulations in Berlin/Germany

Postdoctoral position in the field of  biomolecular simulations is available
at the Drug Design Group of the Leibniz-Institute of Molecular Pharmacology 
in Berlin, Germany.

The project objective is to understand basic mechanisms of antigen loading of
MHC class II molecules. Within this collaborative work the candidate is 
responsible for in silico simulations of antigen-MHC II interaction. 
The ideal candidate has relevant experience in Molecular Dynamics simulation 
of proteins using Gromacs and special applications like coarse grained and/or
replica exchange methods. The project is done in close cooperation with  
experimental partners. 

The two-years position is funded by the Deutsche Forschungsgemeinschaft (DFG). 
To apply, e-mail your CV and list of publications to Dr. Ronald Kuehne
(e-mail: kuehne@fmp-berlin.de)along with the names of at least three 
references and in your cover letter highlight how you will fit into and 
complement the on-going research in our lab.

To apply, e-mail your complete application to Dr. Ronald Kuehne 
e-mail: kuehne@fmp-berlin.de

PhD and Postdoc Positions in Computational Chemistry, NTU, Singapore

Graduate students:
A few PhD research scholarships (for Aug-2012 admission) are available in
our group at Nanyang Technological University (NTU). The successful
candidate will use DFT, QM/MM, MD, docking simulation, or other
computational approaches 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.
Interested candidates are encouraged to apply online at
Please also send CV directly to me via e-mail before applying online.
Having high TOEFL/GRE scores will be of great advantage to you in the

The prestigious Lee Kuan Yew Post Doctoral Fellowship 2012 is now open for

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
Tel: (65) 6592-2644 GMT+8h, Fax: (65) 6791-1961
Email: hirao@ntu.edu.sg
Webpage: https://sites.google.com/site/hiraoresearchgroup/

PhD/PostDoc/Assistant Professor positions in computational photochemistry/photophysics, Bologna University, Italy

"Structure and dynamics of biomolecules by two-dimensional ultraviolet

The work will be held at the Department of Chemistry "G. Ciamican" (www.ciam.unibo.it)
of Bologna University (www.unibo.it) in the group, and under the supervision,
of Prof. Marco Garavelli (www.unibo.it/docenti/marco.garavelli).

This is a 5 years project in computational photochemistry/photophysics/spectroscopy,
starting 1st March 2012, and involving the modeling of photoinduced events in DNA
and polipeptides/proteins (of biological/bio-medical interest) and the simulation of
the corresponding bi-dimensional UV spectroscopy for diagnostic purposes. Both
development and applications of computational tools/methods for delivering an
experimentally reliable analysis will be the target of these studies.

The project is part of a more general experimental/theoretical effort covered
by the ERC Adv Grant, involving a tight cooperation with the transient spectroscopy
group of Prof. Giulio Cerullo, at the Politecnico di Milano, that will perform
the experimental analysis. It will also involve collaborations with other theoretical
and experimental groups (e.g., Irvine University, California, USA).

PhD positions (3 years, 20 k/year gross salary) will formally start 1/1/2013,
but the selections will be finalized by September/October 2012. A background in
computational chemistry and/or photochemistry/photophysics and/or spectroscopy
is welcome. Interested candidates are already invited to send their CV and a
presentation letter to arrange an interview.

PostDoctoral positions (1 year renewable, with a negotiable salary proportional
to the experience, starting from ca. 25 k/year for a junior PostDoc) are now open,
first ones starting 1st March 2012. The ideal candidates are computational
photochemists/photophysicists, with a PhD (or equivalent experience) and a strong
background in excited state computations & related methods (applications and/or
method developments). However, candidates with a more biological-oriented profile
(preferentially in photoreceptors), and a strong experience with simulations, will
be also considered. Interested candidates are invited to send their CV, publications
list and a presentation letter to arrange an interview.

An Assistant Professor position (3+2 years position, from 50 k/year gross salary) is
now open up. The successful candidate will be an independent research team leader,
with at least 5 years research experience and a strong knowledge and background in
computational photochemistry/photophysics/spectroscopy, excited state computations,
(non-adiabatic) simulations and related methods. Autonomy and independence in decision
making and research is required. Interested candidates are invited to send their CV,
publications list and a presentation letter to arrange an interview.

Further inquires and application containing full CV and presentation letter can be
sent to: marco.garavelli@unibo.it

Prof. Marco Garavelli
Universita' degli Studi di Bologna
Dipartimento di Chimica "G. Ciamician"
Via Selmi, 2
I - 40126 Bologna, Italy
Phone (office): +39-051-2099476
Phone (lab): +39-051-2099495
Fax: +39-051-2099456
E-mail: marco.garavelli++unibo.it

Postdoctoral position in Computational Chemistry, LiU, Sweden

A postdoctoral position is available within the Division of Computational Physics at 
Linkoeping University, Sweden (http://www.ifm.liu.se/theomod/compphys).

The position involves research in the field of computational photochemistry, with particular focus
on quantum chemical and QM/MM studies of the mechanisms and ideal designs of synthetic
light-driven rotary molecular motors.

Candidates for the position should have a solid background in computational chemistry and 
experience of quantum chemical modeling of organic molecules in excited states, preferably
documented through relevant research articles in international journals. In addition, familiarity
with QM/MM methods would be advantageous. The appointee is expected to have the ability to
work both independently and in close collaboration with other researchers. A good command of
English is therefore essential.

The position, which carries a tax-free net salary of 20 000 SEK/month, is available immediately
and is initially for 1 year. Subject to satisfactory progress, prolongation of the position is both
desirable and possible.

The Division of Computational Physics at Linkoeping University offers a stimulating environment
for research, with scientists from all around the world working in a range of different areas, as 
described on the homepage cited above. The project in which the appointee will be working is
funded by a number of external sources and has ample access to high-performance computing
resources at the National Supercomputing Centre in Linkoeping (http://www.nsc.liu.se).  

Interested candidates are encouraged to contact Dr Bo Durbeej (bodur@ifm.liu.se) for further 
information. Please append your CV and list of publications to any inquiry.

Ph.D. Scholarship, Computational Biophysics, Australia

PhD Scholarship, $27,000 p.a. stipend.
Opportunity for an additional scholarship top-up Based in Melbourne, Australia

RMIT is a global university of technology and design, focused on creating
solutions that transform the future for the benefit of people and their
environments. The School of Applied Sciences is the top research school in
RMIT promoting a multidisciplinary approach that nurtures an innovative
research culture to deliver highly skilled and industry sought after

In this research project, computer simulations of membranes and ion channel
proteins will be carried out on local and supercomputing facilities to
elucidate their functional mechanisms. This includes the application of
statistical mechanical and electrostatic principles to understand the
permeation of ions, as well as the activation of channel proteins. The aim
is to work with experimental collaborators, both locally and overseas, to
extend to problems involving the interactions of membranes and channels
with a range of biomolecules and peptides, with therapeutic applications
for a range of neurological and cardiovascular diseases.

The successful applicant will have a first class honours Bachelor degree in
Research, Physics, Chemistry, Biology or Engineering and have carried out
an honours or master's research project in Biophysics, Physical Chemistry,
Chemical Physics, Condensed Matter Physics, Biology, Bioengineering,
Pharmacology or Nanotechnology. You will possess a strong desire to study
Biological problems using Physical and Chemical Methods and to make use of
extensive computer cluster and supercomputing facilities.

This scholarship is on offer for 3 years, with the proviso that the student
apply for an APA in 2012. The successful student will also be eligible to
apply for a top-up scholarship of up to $5,000/year through the Health
Innovations Research Institute, RMIT, in 2012.
For further information and to view a position description, please click on
Confidential enquiries can be made to Professor Toby W Allen on +613 9925 0439.

Chemoinformatic Scientist, Priaxon AG, Muenchen, Germany

Priaxon is an emerging pharmaceutical company building a pipeline of novel drug candidates in different therapeutic fields, but mainly focusing on protein-protein interactions in oncology and other diseases. The goal is to discover and develop candidates for validated but hard-to-drug targets using two orthogonal drug discovery platforms.
  • Ph.D. in Chemoinformatics, Computational Chemistry/Biology, Bioinformatics, or related field
  • skills and expertise in developing and applying molecular modelling and chemoinformatics methods (especially structure-based drug design, virtual screening, protein-ligand interactions, protein modelling, similarity searches, and chemical descriptors)
  • sound knowledge of (medicinal) chemistry and drug discovery
  • very good programming skills and experience in software development
  • you should be reliable, creative, highly motivated and enjoy working in an interdisciplinary team strongly preferred
  • good knowledge of protein-protein interactions and small-molecule protein-protein interaction modulators
  • basic knowledge of bioinformatics
  • experience in the pharmaceutical industry
  • experience in working with ChemAxon tools
  • German language skills
  • you will contribute to the drug discovery process by applying computational methods in close collaboration with medicinal chemists
  • you will develop new chemoinformatics tools and integrate them in the PriaXplore technology platform
  • you will work on the establishment of methods to address protein-protein interactions with small molecules on a rational way
Apply via email at:
contact@priaxon.com (Contact name: Dr. Juergen Kolb)
Please visit our Web site at: www.priaxon.com

Monday, 24 October 2011

2011 Erasmus Mundus Scholarships

In July 2011, the European Commission, through its Education, Audiovisual and Culture Executive Agency (EACEA) decided upon the 2011 Erasmus Mundus Action 2 - Strand 1 - Partnership programmes for its Asia Regional lots. They are one-way (Asia to Europe) scholarship programmes for students on undergraduate, master, doctoral and post-doctoral level as well as for university staff in academic or administrative positions, financed by the European Commission.

Swedish universities - Lund and Mälardalen - coordinate two of the five lots focusing on South Asia (Lot 12), and another two Swedish universities - Uppsala and KTH Royal Institute of Technology - are partners in Asia Regional lots (12 and 13).

The South Asian consortium members in the Lund University coordinated EMEA programme are: Delhi University; Jadavpur University, Kolkata; Indian Institute of Technology Kanpur (IITK); Tata Instititute of Social Sciences, Mumbai; Karachi University; Tribhuvan University, Kathmandu; and Jahangirnagar University, Savar, Bangladesh.

The South Asian consortium members in the Mälardalen coordiated IDEAS programme are: Indian Institute of Technology, Mumbai, India; Lahore University of Management (LUMS), Pakistan; Royal University of Bhutan; and Tribhuvan University, Nepal.

Applications for the lots coordinated by Lund and Mälardalen can be delivered from 15th October till 1 December 2011.

More information and on-line application for the EMEA programme. http://www.emeuropeasia.org/
More information and on-line application for the IDEAS programme. http://www.idt.mdh.se/ideas/
Three other Asia Regional lot 12 projects were selected on 15th July 2011. Two of them were re-selected from last year: The EXPERTS consortium coordinated by Karl August University, Göttingen, Germany, with nine South Asian partner universities in Pakistan, Bangladesh, Nepal, Sri Lanka and India (Uppsala University is a partner university in this lot); the EMMA West consortium coordinated by University of Nice Sophia Antipolis, France, with seven South Asian partner universities in Pakistan, Bangladesh, Nepal and India; and the STRONGTIES programme coordinated by City University London, UK, with eight South Asian partner universities in Bangladesh, Pakistan, Nepal, India, Bhutan and Afghanistan (University of Southern Denmark in Odense is a Nordic partner).
Besides, KTH Royal Institute of Technology is a Swedish partner in the Lot 13 AREAS (Academic Relations between Europe and Asia) consortium, coordinated  by Politecnico di Torino, Italy (with one South Asian partner university).

Read more about the South Asia oriented 2011 Erasmus Mundus Action 2 Asia Regional lots. http://www.sasnet.lu.se/node/59883

Sunday, 23 October 2011

Postdoc positions in Computational Catalysis at the KAUST, Saudi Arabia

Two postdoc positions in computational catalysis are available at the KAUST
Catalysis Center, King Abdullah University of Science and Technology,
Saudi Arabia (
http://www.kaust.edu.sa). The position is offered in the group
of Prof. Luigi Cavallo (
http://www.molnac.unisa.it/). The candidates should
be highly motivated, able to independently follow and develop a research
project, willing to work in team and to interact strongly with experimentalists.
Priority will be given to candidates with expertise in:

1) Biocatalysis (simulation of bimolecules by classical methods coupled with quantum mechanics expertise to model catalysis)
2) Water splitting by solid materials (modeling of solid state structure and properties)
3) Heterogeneous catalysis


PhD in computational chemistry or physics, or a related field
Expertise in static or dynamics simulation methods
Good programming skills
Good theoretical background
Good writing and communication skill in English

Appointment, salary and benefits:

The initial appointment is for one year renewable upon mutual agreement
up to three years. Salary is highly competitive, no tax paid to the
Kingdom of Saudi Arabia. Benefits include free fully furnished housing,
free high standard medical and dental insurance. Campus life at the KAUST
is vibrant, with impressive recreational facilities that include a private
beach, marina and golf course.

Applications should include a CV and contact information of at least
two references and should be submitted by email to Prof. Luigi Cavallo
at luigi.cavallo.@.kaust.edu.sa

Application Scientist, Tripos, Munich

In 2008, two companies, with nearly half a century of combined global
experience in their respective scientific domains, united to create a new
organization and a brand new approach to support productivity and decision
making across the spectrum of drug discovery through clinical drug
development. Formed from the blending of Tripos and Pharsight to bring
together world-class scientific consulting services and software, the new
company is Certara, a firm based directly on the vision and promise of
translational science, with the ultimate purpose of improving human health.

As part of the Certara group Tripos (
http://www.tripos.com) continues to
focus on innovation within its current technology portfolio, specifically
enhancing the core functionality and user experience of its computational
informatics product suite SYBYL-X, MUSE and a brand new technology focused
on off-target prediction.

For our Munich office we are looking for an Application Scientist for the
Tripos software portfolio.


* Provide technical and scientific support to customers and sales staff
  for the company's software portfolio before, during & after sales
* Clearly present technical concepts to customers through presentations,
  demonstrations and proposals highlighting all of the capabilities of
  the company's software.
* Answer customer questions and set appropriate technical expectations
  with customers.
* Prepare and present formal solutions to sample problem sets submitted
  by clients and prospects.
* May provide installation support, training, or post-sale consultation.
* Represent the company at scientific conferences and tradeshows.


* Ph.D. or equivalent in a scientific discipline like chemistry, biochemistry
  or pharmacy with demonstrated experience and capability in one or more
  areas of computational chemistry.
* Experience in ligand- and structure-based design, virtual screening,
  protein modeling, library design, or QSAR technologies are desirable.
* Knowledge of SYBYL, Linux, and scripting languages is a plus.
* This position requires good English communication skills, both written
  and oral, along with strong service and customer orientation.
* The candidate must be willing to travel.

In return we offer a competitive package, the opportunity for professional
and personal development and the great team spirit in our European team.

Please send a cover letter and resume in confidence for the attention of
Dr. Fabian Boes to:

Tripos International Spain S.L.
Zweigniederlassung Deutschland
Martin-Kollar-Strasse 17
D-81829 Munich

Or email to fabian.boes@certara.com

PhD Position in Theoretical/Computational Chemistry at the University of Southern Denmark Job ID 113022

A fully financed three-year PhD position in theoretical/computational chemistry is available for a highly motivated applicant at the Department of Physics and Chemistry at the University of Southern Denmark starting from 1 January 2012. The position is financed through the Sapere Aude programme under the Danish Council for Independent Research. The main focus will be on studying electronic processes in complex and biological environments and the developed methods will rely extensively on quantum mechanical formulations.
Application deadline is 2 November, 2011 at 12 o'clock noon.
Please see the full call, including how to apply, on www.sdu.dk/vacancies.

Post-doc/sabbatical Computational Pharmaceutics Scientist, AstraZeneca

AstraZeneca, our predictive science initiative is enabling us to build
up modelling capacity right across R&D. As part of this initiative,
we're now looking for Computational Pharmaceutics Scientists to enhance
our modelling capacity. Join us, and you'll have a key role to play in
increasing the quality and speed of our work whilst minimising the costs
of pharmaceutical development. It will be down to you to exploit
mechanistic-based modelling, optimising the physical and material
properties through the value chain and predicting the clinical
performance of new drug delivery opportunities. It's a chance to optimise
the chemical route and manufacturing process of active compounds and the
final formulated products - so you'll have a direct impact on our success.

We have number of post-doc opportunities at both a senior level and
entry level. The senior positions could also be in the form of
a sabbatical. Based at our Moelndal site in Sweden or at our Macclesfield
site in England, the positions are for one year with a possibility for
extension into a second year.

As one of the world's leading pharmaceutical companies, our business is
focused on providing innovative, effective medicines that make a real
difference in important areas of healthcare. At AstraZeneca, innovation
is about more than just research. We aim to stimulate continued
creativity throughout our organisation by maintaining a culture in
which our people feel valued, energised and rewarded for their ideas
and contribution to our success - ideas which can make a difference in
all aspects of our business. And we support and encourage our people in
discovering their own potential, through excellent learning and
development opportunities that are available to them throughout their

As a Post-doc Computational Pharmaceutics Scientist your main
responsibilities will involve:
Working in a global network of modellers, focusing on four key areas:
material and stability design; route and API process design;
formulation, package, device and product process design;
and clinical performance design
Realising the modelling science roadmap in collaboration with
relevant internal science networks, as part of the Predictive Science
Implementation team
Helping to deliver training on predictive science to the broader
pharmaceutical development organisation
Integrating modelling work into everyday work, including the delivery
of modelling results to drug development projects

As a Post-doc Computational Pharmaceutics Scientist, your skills and
qualifications will ideally include:
For senior post-doc positions, a PhD in a relevant modelling area in
chemistry, physics, material science or process engineering and either
experience from the pharmaceutical industry or post-doc experience from
For the entry level roles, a PhD in a relevant modelling area
Experience of using quantum chemistry, molecular dynamics/Monte-Carlo
simulations or fluid dynamics modelling, to investigate chemical
reactivity, phase transitions, dissolution and nucleation, mixing and
the processing of materials
What we will be looking for in you:
Excellent communication and influencing skills are essential,
as is a good team spirit.
For more information contact Anders Broo, PhD,
Predictive Pharmaceutics Implementation Leader
+46 31 776 28 42 or +46 722 108177.
e-mail: anders.broo@astrazeneca.com

Welcome with your application no later than November 7, 2011.
Use the following link to submit your application
Search for MOL000000PN as the job code.

AstraZeneca welcomes applications from all sections of the community

PhD Positions: Computational approaches to cancer biology, London Research Institute, UK

The Cancer Research UK London Research Institute (LRI) invites talented and
motivated final year undergraduates or recent graduates to apply for four
year PhD studentships to start in September 2012.

The London Research Institute has an international reputation for research
into the basic biology of cancer and is committed to training the next
generation of cancer research scientist. Our laboratories, based at
Lincoln's Inn Fields (Central London) and Clare Hall (just north of London),
are well-resourced with state-of-the-art core technology facilities.

PhD students are at the core of our scientific community.  To enable our
students to develop into independent research scientists with excellent
career prospects, we provide exciting and challenging research projects,
a supportive environment, and tailored transferable skills training. 

Our students are registered at University College London, which provides
additional academic and social facilities.

We are keen to attract outstanding applicants with backgrounds in
biological sciences, physics, chemistry, maths and computing who are
committed to doing a PhD. Applicants should hold or expect to gain a
first/upper second class honours degree or equivalent and have laboratory
or research experience (either as part of or outside of a university
degree course).

Shortlisted applicants will be invited to a three day interview programme,
which will be held at Clare Hall from 22nd to 24th January 2012 (inclusive)
and at Lincolns Inn Fields from 25th to 27th January 2012 (inclusive).

Successful applicants will be awarded a non-taxable annual stipend of
21,000. University tuition fees will also be paid by the LRI.

Applications must be made online via our website: 

This site also contains more detailed information about the LRI, its PhD
programme and the computational biology projects offered by Dr Paul Bates
and Dr Nick Luscombe. 

Closing date for applications: 17th November 2011

Postdoc in Theoretical/Computational Quantum Chemistry

Applications are invited for a postdoctoral research associate position in theoretical/ computational
chemistry in Prof. Hoffmann's research group at the University of North Dakota.  The successful
candidate will be involved with the development, implementation and application of multireference
methods for molecular electronic structure, with emphasis on Generalized Van Vleck Perturbation
Theory (GVVPT), to problems in nonadiabatic chemical dynamics. 

Specific chemical applications will include reactions of oxides. Significant software development is required and the successful candidate will have demonstrated proficiency with either the C or Fortran languages for large-scale scientific programming.  Initial appointment will be for one year and is renewable for additional years upon satisfactory performance and the availability of funding. 

Preference will be given to applicants who are available to start on or around 1 January 2012. 

Interested applicants should submit, via email (mhoffmann##chem.und.edu), a curriculum vita and statement of research interests, specifically as they relate to the advertised position, together with the names of three references to Prof. Mark R. Hoffmann, University of North Dakota, Chemistry Department, 151 Cornell St. Stop 9024, Grand Forks, ND  58202-9024. 
Completed applications must be received by November 12, 2011 for full consideration.

Applications will continue to be reviewed until the position is filled. The University of North Dakota is an Affirmative Action/Equal Employment Opportunity Employer and women and minorities are encouraged to apply.

PhD BASF, Ludwigshafen, Germany

We are the world's leading chemical company because we offer intelligent solutions for our customers and
for a sustainable future. We link and develop people with diverse talents all over the world. For you, this
means a variety of ways to advance. Not only your performance but also your personality matter to us. At
BASF, careers develop from opportunities.

A key success factor for our research is the tight collaboration with the InnovationLab GmbH (iL) located in
Heidelberg. iL is a combined, application-oriented platform for research and knowledge transfer in science
and business in the Rhine-Neckar metropolitan region. For this cooperation project we are looking for a

            PhD Student in Modelling Organic Electronics (m/f)

What you can expect:
The InnovationLab GmbH is working on the future technology of organic electronics, forming a central
component of the strategy for success of the BMBF Leading-Edge Cluster Forum Organic Electronics.
Your thesis aims at understanding and predicting properties of self-assembled monolayers on electrode
surfaces for use in organic electronics by means of quantum chemistry. In close collaboration with
synthetic chemists and device engineers, you will watch your predictions and proposals set into practice.
You are an integral part of a major research project that reaches from organic synthesis of surface active
molecules to manufacturing printed organic electronics.

What we expect:
You have a master in chemistry or physical chemistry with above average grades and a sound
knowledge in molecular simulations and quantum chemistry. Programming skills and experience with
unix systems is a must. Beyond these abilities in your field, you have a very good command of
German and English, and you are enthusiastic about working in a practical research environment
cooperating with potential customers, universities and research institutes. Along with these
credentials, you are an excellent team player as well as a creative self-starter.

We offer:
BASF in Ludwigshafen offers you a challenging work environment and a committed team to be
part of. With your doctoral advisor Dr. Marek Sierka and as a member of the innovationLab
you are in direct contact with the leading research groups in the field.
For further details please contact Mr. Robert Send,
Email: robert.send.@.basf.com

Expect to be surprised by the exciting range of career opportunities at BASF.
Reference code: EN51974245_ONLE_1

Please apply online at

or for more information please contact:
Tel.: 00800 33 0000 33
E-Mail: jobs@basf.com

Thursday, 29 September 2011

Phd: Development of a QM/MM Docking Code, Switzerland

Computational techniques including docking have become valuable tools for
drug design over the last decades. Main challenges for docking algorithms
include the accurate treatment of polarization and covalent interactions,
for example with transition metal ions, which need to be described on the
quantum chemical level. Goal of this project is the development of a fully
automated on-the-fly quantum mechanical/molecular mechanical (QM/MM) docking
approach and its application to the drug design for anti-cancer targets,
which will be evaluated in the translational research environment of the 
Medical Oncology Center in Lausanne.

We are seeking a highly motivated PhD student with a background in
(theoretical and organic) chemistry, (bio-) physics, or related disciplines
who is willing to work with a multi-disciplinary team. Basic programming
skills and proficiency in spoken and written English are prerequisites.
Starting date is negotiable.

The Swiss Institute of Bioinformatics in Lausanne provides a stimulating and
international environment as well as state-of-the-art computing facilities
and infrastructure. For more information see
Candidates should send a letter of motivation, a CV, contact details of two
referees, and a brief statement of research experience electronically to
Vincent Zoete (vincent.zoete@isb-sib.ch) and Ute Roehrig

Chemo-informatician Job

Drug Discovery Centre at the Paterson Institute is presently seeking an enthusiastic and proactive Informatician, on a 1-year fixed-term contract, to support, develop and expand the group's pre-existing capabilities in chemo- and bioinformatics.
The Drug Discovery Unit forms part of the Paterson Institute, one of Europe's premier cancer research centres. The Institute supports numerous basic and translational cancer research programmes facilitated by a comprehensive range of state-of-the-art research services (see: www.paterson.man.ac.uk) and is ideally sited next to The Christie, Europe's biggest specialist cancer hospital. The Institute lies at the heart of the Manchester Cancer Research Centre (MCRC), an exciting development that integrates cancer research within Manchester (www.mcrc.manchester.ac.uk). Details of the Unit itself can be found at http://www.paterson.man.ac.uk/drugdiscovery/
Qualified at least to BSc level in a chemical or biological discipline, or with appropriate equivalent experience, the successful candidate will have demonstrable experience in chemical and biological database administration, management and customisation within an Oracle environment. Experience in HTML and SQL would also be advantageous. Specific experience of informatics within a drug discovery environment and/or familiarity with the Dotmatics informatics platform is also highly desirable, perhaps gained through industrial experience. Additional familiarity with other chemo- and bioinformatics tools such as Pipeline Pilot, KNIME and Oncomine would also be desirable.
Informal enquiries should be addressed to Dr Allan Jordan, Head of Chemistry ( ajordan@picr.man.ac.uk )
To apply for this position please visit our website: www.paterson.man.ac.uk
For applicants who are unable to download this information from our website, please contact HR department on 0161 446 3231, email: jobs@atpicr.man.ac.uk to have this information sent by post.
The deadline for receipt of applications is 17th October 2011.

PhD positions at EPFL, Switzerland

Computational/theoretical chemistry PhD positions are available starting January 2012 
in the Laboratory for Computational Molecular Design at the Swiss Federal Institute of 
Technology (EPFL, Lausanne). The annual salaries are roughly 50,000 CHF. 

Our laboratory is interested in the development and application of accurate electronic 
structures approaches for rationally designing pi-conjugated molecules and materials. 

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, as well as 2 references. 
Prospective candidates should have finished their undergraduate studies and have some
background in theoretical/computational chemistry or physics. 
Knowledge of Linux-/Unix-based computer systems and Fortran programming languages 
would be an asset. 

These positions require acceptance in the doctoral program of Chemistry and Chemical 
Engineering, for which you may file an application at:

  contact Clemence Corminboeuf by email at clemence.corminboeuf@epfl.ch

Computational Science Ph.D. program

Applications are invited for a tenure-track assistant or associate 
professor in the new Computational Science Ph.D. program. Applicants 
should have a strong potential to obtain external funding and to become 
excellent researchers and teachers at MTSU. Successful candidate must be 
interested in working with students in the Computational Science Ph.D. 
program. Research in data intensive science (biological data, remote 
sensing, astro-informatics, scientific applications of computer vision, 
for example) is preferred, although areas of Computational Science will 
receive full consideration. 
Position starts August 1, 2012. 
Minimum Requirements: Ph.D. in Biology, Chemistry, Computer Science, Mathematics, 
Physics or Computational Science, research in an area of computational 
science with a strong potential for funding. 
Preferred Requirements: 
Experience mentoring Ph.D. students and teaching, strong publication 
record; proven record of obtaining research funding, experience working 
in an interdisciplinary environment. 
Apply at https://mtsujobs.mtsu.edu. 
If you have questions, please contact Dr. John Wallin, Director, at 
615-494-7735 or jwallin**mtsu.edu. EO/AA Employer.

Monday, 19 September 2011

QM/MM and QM Studies and Modeling of Heme and Nonheme Enzymatic Reactivity and Structure, and Brain Chemistry

Research Site:
The Institute of Chemistry and the Lise Meitner Minerva Center for 
Computational Quantum Chemistry, The Hebrew University of Jerusalem,
 Jerusalem, Israel

See for example the following papers:
(1) Shaik, S. Cohen, Y. Wang, H. Chen, D. Kumar, and W. Thiel
P450 Enzymes: Their Structure, Reactivity and Selectivity, Modeled by 
QM/MM Calculations
Chem. Rev. 110, 949-1017 (2010).
(2) S. Shaik, W.Z. Lai, H. Chen, Y. Wang
The Valence Bond Way: Reactivity Patterns of Cytochrome P450 Enzymes and
 Synthetic Analogs
Acc. Chem. Res. 43, 1154-1165 (2010).
(3) S. Shaik
Iron Opens to High Reactivity
Nature Chem. 2, 347-348 (2010).
(4) S. Shaik, H. Chen, D. Janardanan
Exchange-Enhanced Reactivity: A General Concept in Bond Activation by 
Metal-Oxo Enzymes and Synthetic Reagents
Nature Chem. 3, 19-27 (2011).
(5) H. Chen, W.Z. Lai, S.  Shaik
A Review on: Multireference and Multiconfiguration Ab Initio methods in
 Heme Related Systems: What Have We Learned So Far?.
J. Phys. Chem. B. 115, 1727-1742 (2011)

The candidate will participate in a project involving molecular dynamics
simulations, QM/MM and QM calculations of the highly active species of 
these enzymes. The applied techniques are described in the above papers
(see e.g., Ref. 1, above). In addition the candidate will participate in
 modeling and understanding the reactivity patterns (see Ref. 2 and 4
 above) Therefore, the candidate should have capabilities necessary to 
the computational methods and solid knowledge of quantum chemistry in
 order to do the modeling.

Candidate's profile:
The fellowship is designated for holders of Ph.D. in Chemistry 
(Theoretical Chemistry), Physics or a similar discipline, with curriculum
 adequate for the work described above. 

The candidate will be chosen based on the following criteria:
 The theoretical expertise gained during the Ph.D. or a previous postdoc 
research.  Important qualifications are: Expertise in applications of 
quantum chemical methods (DFT and Multireference or highly correlated ones)
, molecular dynamics methods, programming skills are good to have but not
 absolutely necessary.

 Indicators of scientific production, such as publications, conference
 presentations, books etc.
 Command of the English language

Extendible up to 4 years upon mutual consent.

The fellowship is paid according to the indices of the Hebrew University 
(5,600 IS/month + 150 USDA/month of housing support) and is tax free.

Required documents:
 Motivation letter, and a one-two page(s) research proposal.
 Curriculum vitae and list of publications
 3 letters of recommendation

a committee including the research Director, Prof. Sason Shaik, will 
evaluate the applications.

The applications should be submitted until October 7th, 2011. However, 
the deadline is extendable.
  Address for application submission:

Professor Sason Shaik, Director
The Lise Meitner-Minerva  Center for Computational Quantum Chemistry, 
Institute of Chemistry 
The Hebrew University of Jerusalem, Givat Ram Campus, 
Jerusalem 91904, ISRAEL
E-mail: sason.shaik@gmail.com
FAX: +972-2-6584680
Phone: +972-2-6585909

Computational protein engineering

Immediate openings of two postdoctoral research associates
interested in one or more of the following topics: 
1) drug resistance mutations in proteins;
2) computational engineering of protein stability;
3) protein unfolded states;
4) protein and RNA electrostatics 

- highly motivated individual holding a PhD in chemistry, chemical
  engineering, physics or a related field
- experience with one of molecular dynamics simulation packages such as
- programming and scripting skills
- good oral and written English language skills

We offer:
- training in the development and/or application of state-of-the-art
  molecular simulation techniques
- salary is commensurate with experience in the range of $34-40k/yr
- fun and flexible work environment
- one-year contract extendable up to three years upon mutual agreement

See http://ccb.ou.edu for details of the group research interests

Norman is a safe and low-cost college town close to Oklahoma City. In
2006, it was voted by CNN Money as one of the 50 best places in the US
to live. Contact Dr. Shen for more info on location.
Please email CV in PDF format and the names of two reference persons to
Dr. Jana Shen
Department of Chemistry and Biochemistry
University of Oklahoma
Norman, OK 73019
Web: http://ccb.ou.edu

Computation Studies of Aqueous and Ionic Liquids Interfaces

Postdoctoral Position: Molecular Theory Group at the Pacific Northwest 
National Laboratory has a postdoctoral position available immediately. 
Research interests will be focused on the development of classical and 
quantum statistical mechanical approaches to the study of bulk nanofluids 
and interfaces.
Interested applicants should send resume along with two 
letters of recommendation to Liem X. Dang (liem.dang@pnnl.gov), 
Chemical & Materials Sciences Division, Pacific Northwest National 
Laboratory, P.O. Box 999, Mail Stop K1-83, Richland, WA 99352

Postdoctoral position in biomolecular simulation at Temple University, Philadelphia, PA

Lab is developing new computational methods to design folding and binding properties of
proteins and peptide mimetics.  Projects include: (1) developing Markov State Model (MSM)
approaches for modeling the folding reaction and designing sequences for folding properties
(2) simulation-based prediction and design of non-biological (e.g. peptoid) foldamers
(3) multiscale fragment-based approaches for predicting binding affinities and specificities of
protein-peptide interactions.   

Our lab benefits greatly from high-performance computing resources and collaborations available
through the Institute for Computational Molecular Science  (http://www.temple.edu/cst/icms),
and inter-disciplinary collaborations through the new Moulder Center for Drug Discovery in the
School of Pharmacy.

More information at http://voelzlab.org

Applicant should have a Ph.D in computational/physical chemistry, biophysics, chemical
engineering, or related field, and a strong background in molecular simulation, physical
chemistry, statistical mechanics of biomolecular systems, and/or computational biophysics.
Relevant research experience may include:  conformational sampling using molecular dynamics
or Monte Carlo simulation, free energy estimation, methods for estimating protein-ligand
affinities, protein structure prediction, forcefield development, multiscale modeling.

Good programming skills are essential, as the applicant will be responsible for writing new
simulation algorithms and extending existing code bases.  Other relevant skills include:
familiarity with simulation/modeling packages such as AMBER, GROMACS, OpenMM; Python
scripting experience; familiarity with UNIX; experience with large-scale scientific computing.
Experience with parallel computing and/or GPUs a plus.

Start date: negotiable (early 2012)
Salary: Competitive and commensurate with experience.
One-year appointment, with the option to extend contingent on satisfactory progress.
To apply:  Email a cover letter and your full CV (details of all academic degrees obtained, research
skills and experience, publications, conference presentations) preferrably as a single PDF, along
with 2-3 letters of recommendation, to Prof. Vincent Voelz voelz@temple.edu.

MD free energy calculations, Univ. of New Orleans, LA

Seeking a postdoctoral candidate with experience in molecular simulations or molecular modeling 
to work on an exciting research project at the interface of chemistry, physics and biology. 
The research focuses on extending and applying molecular dynamics-based free energy methods 
for predicting binding between small molecules (such as potential pharmaceutical drugs) and 
protein receptors. For reference, see my published work in this area. An ideal candidate would have 
substantial background in molecular modeling, ideally including molecular dynamics simulations 
and/or Monte Carlo, including applications and methodology work. Experience with free energy 
techniques is also a plus. 

Interested applicants should send a cover letter plus a CV to dlmobley@uno.edu. Additionally, 
please have at least three letters of reference sent to the same address as well. All application 
materials should be received by Oct. 21, 2011. Prospective applicants are welcome to contact 
me for more information. The position will likely start in January, 2012. 

The University of New Orleans, and the New Orleans area, provide exciting opportunities for work 
in this area. In addition to the Mobley Lab at UNO, we maintain close contacts with Steve Rick's 
group, also in Chemistry at UNO, and Chris Summa's group in computer science. Both labs have
 interests in molecular simulations, free energy calculations, and statistical mechanics. We also
interact with the groups of Hank Ashbaugh and Lawrence Pratt at Tulane University, as well as 
various experimental and computational collaborators worldwide.

Thank you so much.
David Mobley
Department of Chemistry
University of New Orleans

Tuesday, 6 September 2011

Computational Chemistry, Rouen University, France

Our strategy: a quantum chemical approach in three major steps :

The analysis of the electronic properties of selected molecular systems requires a quantum
chemical approach. As a first step, we need to validate the method, comparing simulated fluorescence
spectra of already synthesized molecules with experimental ones. In order to avoid time-consuming
calculations, we decided to base all our calculations on density functional theory (DFT), a method of
choice for our problem. In particular, the time-dependent DFT (TDDFT) method produces an
accurate description of excited states, comparable to DFT for the ground state. On the other side,
Franck-Condon and Herzberg-Teller analyses can be used for computing the amplitudes for electronic
transitions from the ground and excited state frequency analyses. For instance, the combination of the
two have been recently employed with success to compute the Herzberg-Teller absorption and
fluorescence spectra of free-base porphyrins.8 It is interesting to mention that solvent effects can be
taken into account.

As a second step, we need to understand the reasons leading to the observed differences in
fluorescence activity between our selected analogues. Different approaches will be envisaged such as
orbital analyses or topological studies of the electron density, both in fundamental and excited states.
Concerning the topological approach, based on the quantum theory of atoms in Molecules (QTAIM),
excited state properties are yet completely unexplored, constituting a real challenge in this field of
quantum chemistry. This information could be of the prime importance to design the next generation
of epicocconone analogues.

In the final step, our validated approach will be used to predict fluorescence properties of the
newly designed series of analogues, guiding experimentalists for new syntheses.

Possible additional tasks:

1) Reactivity studies:
Mechanisms of some steps involved in the synthesis of these fluorophores, not only from a static 
viewpoint (transition states), but also dynamical. To this aim, the PW-GTO-mixed CP2K code could 
be used to carry out Born-Oppenheimer dynamical simulations. The exploration of these complex 
energy surfaces could be done through a metadynamics approach as pioneered by Laio and Parrinello. 
This method could also provide efficient way of evaluating entropy in solution (cf. Michel and Laio), 
and thus Gibbs energies, enabling a realistic description of the reactivity of such species. 

2)Theoretical developments: 
- new reactivity descriptors within the framework of conceptual DFT 
(from Morells dual descriptor) and QTAIM, applied to fluorescence problems. We are 
currently developping our own parallel code for topological analyses 
- new parameter to quantify the accuracy of TDDFT calculations (for instance, assesment 
and improvement of Tozers  parameter)
-  PCM solvent model and excited states
- implementation and design of fully non-local correlation functionals for van der Waals
interactions (such as Lundqvist, van Voorhis ones)

Additional information :

Salary : 1850 euros / month (contract for 12 months)

How to apply ? Please contact Prof. laurent Joubert: laurent.joubert@univ-rouen.fr
sending a detailed CV and explaining your motivation for this position.

Laboratory : IRCOF, University of Rouen, France. Group of theoretical chemistry

Wednesday, 24 August 2011

PhD Position in Computational Biophysics, Erlangen, Germany

Projects involve the investigation of 

- membrane-protein - lipid interaction using the method of 
  molecular dynamics simulations
- the design of proteins with modified pre-defined properties
- the development of novel methods for the prediction of 
  binding affinities of peptidic ligands and drugs to proteins, 
  including full flexibility for both the ligand and the receptor. 

The candidate for this position is expected to have completed a 
Master (PhD) in physics, chemistry, or bioinformatics, with a strong 
theoretical component, be strongly motivated and team-oriented.

The position is limited to three years and is funded according to 
the German E13 scale (50%/100%).

Work of the group for Computational Biology  is focused on the 
prediction of structure, function and (nano)dynamics of membranes and 


Erlangen is located next to Nuremberg, a lively city of about half 
a million inhabitants, with a visible history of almost one thousand 
years (< 2 hours to Munich, < 3 hours to Prague).  

Interested candidates should send their application by e-mail (*one* pdf 
document containing letter, cv, certificates, references) to


Prof. Dr. Rainer Boeckmann
Computational Biology
University of Erlangen-Nuremberg
D-91058 Erlangen, Germany

Saturday, 20 August 2011

PhD Position: Simulation Studies of DNA-Damage and Repair

PhD position on Molecular Simulation Studies of DNA-Damage and Repair
at Physics Department T38, Technical University Munich, Germany 
A PhD position (funded by DFG:SFB749) is available in the Theoretical 
Biophysics group (chair: Prof. Martin Zacharias) at Technical University 
Munich to start immediately. 
DNA molecules in cells are frequently damaged by radiation or chemical
modification. The recognition and repair of damaged DNA is of fundamental 
importance for the survival of cells and for preventing transformation into 
malignant (cancer) cells. Aim of the project is to elucidate the mechanism 
of specific recognition of damaged DNA by repair enzymes at atomic detail 
using molecular simulation techniques. The work involves molecular dynamics 
simulations and advanced sampling applications as well as ligand-receptor 
docking simulations. The computational work will be performed in close 
collaboration with experimental groups in the area of structural biopolgy 
and biophysics.

Successful candidates should have a diploma or master degree in either 
physics, biophysics or physical chemistry combined with a strong interest 
in (bio)molecular simulations. Experience with the Linux operating system 
and a programming language is a plus. 
The Technical University Munich belongs to the scientific top addresses
and is one of the nine Universities of Excellence in the Federal Republic 
of Germany. State-of-the-art computer equipment is available. Please 
contact Prof. Zacharias (martin.zacharias*o*ph.tum.de) or send your CV and 
cover letter describing your research interests including the addresses 
of two referees to:

Prof. Dr. Martin Zacharias
Chair of Theoretical Biophysics
Physics Department T38
Technical University Munich
James-Franck-Str. 1
D-85748 Garching, Germany
e-mail: Martin.Zacharias@ph.tum.de

Ph.D. Student in Computer-aided Drug Design

Laboratory of Dr Jian Hui Wu at the Lady Davis Institute, McGill
University Faculty of Medicine, Montreal, Canada, has an open position
for Ph.D. student in computer-aided drug design. 
(http://www.ladydavis.ca/ and http://www.medicine.mcgill.ca/oncology/). 
The admission time is Jan, 2012. This Ph.D. student will join Dr Wu's
team to work on projects aiming to discover novel anticancer agents by
integrating Structure-based Drug Design, Medicinal Chemistry  and
Molecular Biology. This student will spend most of the time on
theoretical study, including structure-based drug design and
development of methods for in silico target fishing. 

The student will have opportunity to learn 'wet' experimental
techniques in Molecular Biology or Medicinal Chemistry. For University
admission requirement, please check the following link:

The ideal candidate will possess a master degree in drug
design/molecular modeling, a strong background in Chemistry, a
scientific attitude, excellent programming skills, and the ability to
communicate written and orally in English.
Interested applicants should send a cover letter, CV, statement of
research interests, and contact information for three referees to Dr.
Jian Hui Wu at jian.h.wu|-|mcgill.ca. The admission time of this Ph.D.
student is Jan, 2012.

Scientist/Senior Scientist, Structural Biology: Macromolecular Modeler

Pacific Biosciences is seeking a highly motivated macromolecular modeler for a position at the Scientist/Senior Scientist level. The candidate will work within a dynamic interdisciplinary team to model enzyme variants and their interactions with nucleotide analogs. The candidate will be able to draw on data from a wide variety of sources including crystallography, kinetic characterization and single molecule studies. He or she will use these data to both help design experiments that test mechanistic hypotheses and to design variants with desirable sequencing properties. The individual will be working in a fast-paced environment interacting with scientists from a wide variety of backgrounds. The title will be based on the selected individuals experiences and determined at the offer stage.
Position Requirements:
  • Education Requirement: PhD with more than 3 years of experience. Experience within the biotechnology or pharmaceutical industries is a plus.
  • Experience with macromolecular modeling is required. Experience in modeling protein:nucleic acid complexes is desired.
  • Experience with analyzing information in databases, curating databases is desired.
  • Knowledge of protein design/folding principles would be beneficial.
  • Ability to work on several projects simultaneously.
  • Effective communication (written/verbal) and ability to work independently and collaboratively as part of a team are critical.
Application Instructions:
For immediate consideration, please follow this link to submit your resume:

Senior Developer, Scientific Libraries at Schrodinger

Schrodinger, a technology leader specializing in software solutions for
life science research and development, is seeking a senior developer to
extend and maintain the core libraries that power our software.
This position provides the chance to contribute to a unique and exciting
scientific field. Specific domain knowledge is not required, but the ability
to pick up chemical concepts is. The successful candidate will have good
software design skills, a sound computer science background, and in-depth
algorithm knowledge.
Required qualifications include:
- 5 or more years of C/C++ development experience
- computer science degree
- mastery of algorithms and data structures
- recent and relevant object-oriented software design/architecture experience
- physical science or engineering background, either a degree or work
  experience in a science or engineering development environment
- excellent written and verbal communication skills
- code refactoring proficiency
- experience profiling and optimizing code
Desirable qualifications include:
- Python development experience
- multi-platform development experience (Linux, Windows, Mac OS X)

Schrodinger is an equal opportunity employer.
To apply, please visit: www.schrodinger.com/careers

Monday, 8 August 2011

Postdoctoral Positions in Structural Bioinformatics

The Grant lab ( http://thegrantlab.org/ ) is pursuing an unprecedented understanding of the 
structure, dynamics and interactions of key biomolecules.  Current projects focus on molecular 
motor and molecular switch systems, and entail the development and application of 
state-of-the-art computational techniques to facilitate efficient inhibitor development and the 
engineering of novel biomachines.

Ideal candidates will have a strong quantitative background (Ph.D. in bioinformatics, computational 
biology or related field).  Extensive knowledge of molecular simulation protocols (molecular 
dynamics, Brownian dynamics), and computer programming (R, Python, C).  Excellent 
communication skills, and a high level of enthusiasm to engage with experimental scientists.  
Candidates with interdisciplinary training in biology and computing are especially encouraged to 
apply.  The starting date is negotiable.

Applicants should send a CV, contact information of three references and a one-page cover letter 
describing prior research experience and candidate suitability to Professor Grant 
(bgrant@mccammon.ucsd.edu).  Please combine all files into one PDF, and use the subject line 
Postdoc Application: (name of the applicant).

Computational Chemistry Scientific Programmer

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.

- 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 
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 from job ID 953392.

Scientific programmer for high performance molecular modeling

VeraChem LLC seeks a skilled, efficient scientific programmer with a 
background in the theory and application of molecular modeling and computer 
simulations to join our team developing advanced high-performance software 
for modeling protein-ligand binding. The successful candidate will have a 
Ph.D in computational chemistry/biology or a masters degree with 5 years 
experience. He/she must be capable in modern Fortran, MPI, OpenMP, and CUDA 
programming and have knowledge of force fields and various solvation 
models. We are looking for a team player who is professional and creative 
and has excellent communication skills and strong initiative. VeraChem is 
located in suburban Marylands vibrant biotechnology corridor, near the NIH 
and Washington DC, and offers competitive salary, excellent benefits, and 
opportunities to advance and expand, both technically and professionally. 
To apply, please email your cover letter, CV or resume, and contact 
information for at least two references to Michael J. Potter 
(potterm@verachem.com) VeraChem LLC is an equal opportunity employer.

Tuesday, 2 August 2011

Computational Organic Chemistry with the University of Oxford and AstraZeneca

Fully Funded PhD studentship in Computational Organic Chemistry with the
University of Oxford and AstraZeneca

Industrial Sponsor: AstraZeneca
Oxford Supervisor: Dr Robert Paton (http://paton.chem.ox.ac.uk)

A fully funded PhD studentship with AstraZeneca as the industrial
collaborator is available at the University of Oxford to begin in
October 2011. This research project will explore C-H functionalization
with predictive computational methods. The research will be carried out
under the supervision of Dr. Robert Paton and the work will be carried
out in the Chemistry Research Laboratory at Oxford. Find out more about
ongoing research at: http://paton.chem.ox.ac.uk

Direct functionalization of unactivated C-H bonds is a powerful way to
increase molecular complexity and is of great interest to academia and
the pharmaceutical industry. This PhD project will investigate C-H
functionalization reactions using computational modelling techniques to
establish a set of general principles that may be used to design and
predict the usefulness of C-H functionalization for a given substrate.
The PhD student will have the opportunity to collaborate with
world-class theoretical and experimental co-workers in Oxford and
AstraZeneca and will have access to the computational resources of the

Oxford Supercomputing Centre.
The prospective student should be committed to and motivated by
chemistry, with aspirations to pursue a career in academia or the UK
chemical industry. Applicants should have, or expect, a first or second
class honours degree, or equivalent, in a relevant discipline
(Chemistry, Biochemistry, Physics). The studentship will cover the fees
and maintenance for 3 years for UK and EU citizens.

The Chemistry Research Laboratory is a state of the art research
facility at the University of Oxford. Opened in 2004, it has five floors
covering ~17,000 sq.m of laboratory and office space and cost £60
million to construct.

AstraZeneca is a global research-based biopharmaceutical company,
focusing on discovering, developing and marketing medicines for some of
the world’s most serious illnesses, including cancer, heart disease,
neurological disorders such as schizophrenia, respiratory disease and

For enquiries regarding the research project please contact Dr Paton:
For further information please see:

To apply please see here:

For enquires relating to the application and admissions process please
Aga Borkowska, Graduate Studies Administrator:

+44 (0) 1865 272569

The University of Oxford is an Equal Opportunities Employer.

International PhD Program : Genova, Italy

The Nanochemistry Department at the Italian Institute of Technology (IIT), headed by professor Liberato Manna, aims to develop nanostructures with chemical approaches for applications in diverse sectors, such as optics, photonics, electronics, energy conversion and storage (photovoltaics, batteries), and biomedicine (multi-modal approaches to diagnosis and therapies for tumors). The present staff is composed of PhD students and postdocs with different backgrounds (chemistry, biology, physics, engineering) and the Facility has several joint projects with other groups, at IIT as well as at other research institutions in Italy and abroad. We are looking for highly motivated and talented students, with an exceptional academic record, for a three-year PhD scholarship position, in conjunction with the local University of Genoa (which includes tuition and a living stipend of 1300 Euros/month after tax).

Research topics covered:
1. Surface functionalization of inorganic nanoparticles and nanostructures based on inorganic nanoparticles
2. Synthesis of pH and thermo-responsive polymers and their combination with inorganic nanoparticles for controlled drug delivery
3. Analysis and modeling of the mechanical behavior of 3D nanoparticles superstructures
4. Synthesis and assembly of nanoparticles into superstructures for applications in photovoltaic devices
5. Novel catalytic materials based on nanocomposites for the water gas shift reaction and selective carbon monoxide oxidation
6. Synthesis and assembly of nanoparticles for applications in lithium ion batteries

For administrative aspects (i.e. how to apply, documentation requested) please contact Drs. Iulia Manolache (iulia.manolache@iit.it); For scientific aspects please contact Drs. Teresa Pellegrino (teresa.pellegrino@iit.it) for topics 1-2 and prof. Liberato Manna (liberato.manna@iit.it) for topics 3-6.