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* 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

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. 
( and 
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|-| 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:

Monday, 8 August 2011

Postdoctoral Positions in Structural Bioinformatics

The Grant lab ( ) 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 
(  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 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 
( 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 (

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:

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 (; For scientific aspects please contact Drs. Teresa Pellegrino ( for topics 1-2 and prof. Liberato Manna ( for topics 3-6.

(PhD candidate) in molecular computational chemistry: Bergen, NORWAY

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:


The research project is supported by the Research Council of Norway and is devoted to provide fundamental insight to how ions, molecules and acids/bases are solvated in nano-sized droplets of water, methanol and other hydrogen-bonded liquids, and involves a close collaboration between Department of Chemistry at the University of Oslo (UiO) and Department of Chemistry at the University of Bergen (UiB). One PhD student and one postdoctoral fellow will be recruited to the project during 2011. The PhD student recruited here will participate in electron-spectroscopy studies at the MAX-lab facility in Lund. The PhD student will have extended research stays at MAX-lab and at the University of Uppsala to develop experimental skills. Analysis of the spectra is a main activity and a main source to information about the solvation processes. The second and dominant component of the PhD project involves testing and validating computational methods, followed by large-scale production calculations to model the systems studied experimentally. Applicants must have achieved a master’s degree or equivalent in chemistry, physics or bordering fields, or have submitted their master thesis for assessment by the application deadline. It is a prerequisite, however, that the formal admission requirements for the PhD programme are met before appointment can be made. Candidates should have a strong background in computational chemistry (molecular modelling and/or quantum chemistry) and an interest for developing experimental skills in cluster-beam technology and electron spectroscopy, whereas some background from experimental physical chemistry is also desirable. Experience from programming or high-vacuum experiments is an advantage. The research fellow must take part in the University's approved PhD programme leading to the degree within a time limit of 3 years. Application for admission to the PhD programme, including a project plan outline for the training module, will be worked out in collaboration with a supervisor. The fellowship period may be reduced if the successful applicant has held previous employment as research fellow. More information about the position can be obtained by contacting professor Knut J. Børve, phone +47 55 58 33 65 / e-mail: The teaching language will normally be Norwegian. State employment shall reflect the multiplicity of the population at large to the highest possible degree. The University of Bergen has therefore adopted a personnel policy objective to ensure that we achieve a balanced age and sex composition and the recruitment of persons of various ethnic backgrounds. Persons of different ethnic backgrounds are therefore encouraged to apply for the position.


Starting salary on grade 48 (code 1017/pay framework 20.8) in the Civil Service pay grade table scale; currently NOK 391,300 gross p.a.; following ordinary meriting regulations.

Additional Job Details

Send electronic application, CV, certificates, diplomas, and any scholarly works by clicking on the button marked "APPLY FOR THIS JOB" on this page. The application should include a brief statement of the applicant's motivation for applying. Applications sent by e-mail to random individuals at the department will not be considered. Closing date for applications: 12 August 2011 Quote reference number: 2011/7582