Jul
14
2010

Molecular Modeling Jobs

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  • Date Added: 25/01/16
  • Job Title: Post-doctoral position in development of Computational Protein Design methods
  • Company / Institution: LISBP
  • Website: http://www.lisbp.fr
  • Description:The Biosystems and Process Engineering Laboratory (LISBP), located on the grounds of the INSA-Toulouse (France) is seeking for a postdoctoral researcher to work at the intersection of Computational Structural Biology and Discrete Optimization, on models and algorithms for Computational Protein Design. The laboratory is affiliated to the French National Centre for Scientific Research (CNRS, UMR INSA-CNRS 5504) and the French National Institute for Agricultural Research (INRA, UMR INSA-INRA 792).

    The work will take place in an interdisciplinary project, funded by the ‘Initiative d’excellence de l’Université de Toulouse’ and associating computational structural biologists of LISBP with computer scientists specialized in discrete optimization from the INRA MIAT lab, in Toulouse. Together, they have recently shown that cutting-edge combinatorial optimization techniques from Artificial Intelligence, namely “Cost Function Network” (CFN) could push Computational Protein Design well beyond the limits of usual methods [1-6]. Capitalizing on prior work with the aim of further exploring the potential of CFN-based approaches to meet the Computational Protein Design challenges, the work will mainly involve the development of novel computational enzyme design methods capable of handling more complex protein design models, incorporating local and global backbone flexibility with positive and negative design targets.

    We are looking for a highly motivated scientist who has an excellent research background and expertise in computational structural biology (especially in 3D protein structure modeling and simulation) and excellent programming skills in efficient compiled languages (ideally C++). Background in search algorithms and combinatorial optimizations methods would be extremely beneficial.

    The perspective researcher will have the opportunity to work in a diverse and rich multidisciplinary environment, surrounded by both computational and experimental experts in the field of enzyme engineering. Applicants should enjoy teamwork and have very good communication skills. Good English skills are required and notions of French would be a plus.

    The position is available from March 14, 2016 and for duration of one year (from six to nine additional months could be possible upon funding).

    Applicants should send as soon as possible CV, summary of previous research and contact addresses of references to: Sophie Barbe, Research Scientist INRA: sophie.barbe@insa-toulouse.fr

    1. Traoré S, Roberts K, Allouche D, Donald B-R, André I, Schiex T, Barbe S. (2015) Fast search algorithms for Computational Protein Design. Journal of Computational Chemistry (in press).
    2. Traoré S, Allouche D, André I, de Givry S, Katsirelos G, Schiex T, Barbe S. (2013) A new framework for computational protein design through Cost function optimization. Bioinformatics. 29:2129-36.
    3. Simoncini D, Allouche D., de Givry S, Delmas C, Barbe S, Schiex T. (2015) Guaranteed Discrete Energy Optimization on Large Protein Design Problems. Journal of Chemical Theory and Computation. 11 (12), 5980-5989.
    4. Traoré S, Allouche D, André I, de Givry S, Katsirelos G, Barbe S, Schiex T. (2012) Computational Protein Design as a Cost Function NetworkOptimization Problem. CP2012 Proceedings. 18th International Conference on Principles and Practice of Constraint Programming, Québec, Canada, Oct, 8-12, 2012– Proceeding.
    5. Allouche D, Davies J, de Givry S, Katsirelos G, Schiex T, Traoré S, André I, Barbe S, Prestwich S, O’Sullivan B. (2014) Computational Protein Design as an Optimization Problem. Artificial Intelligence Journal 2014. 212:59-79.
    6. Viricel C, Simoncini D, Allouche D, de Givry S, Barbe S, Schiex T. (2015). Approximate Counting with Deterministic guarantees for Affinity Computation. In, proceedings of the international conference on Modelling, Computation and Optimization in Information Systems and Management Sciences, MCO 2015, Metz, France: Advances in Intelligent Systems and Computing – Springer.

    Laboratory address : Laboratoire d’Ingénierie des Systèmes Biologiques et des Procédés (LISBP) – Equipe de Catalyse & Ingénierie Moléculaire EnzymatiqueS / UMR INSA – CNRS 5504 – INRA 792 Institut National des Sciences Appliquées 135 Avenue de Rangueil F-31077 Toulouse Cedex 04 – France http://www.lisbp.fr

  • Contact Sophie Barbe
  • E-mail sophie.barbe@insa-toulouse.fr


  • Date Added: 17/09/13
  • Job Title Postdoctoral Position in Computational Bioengineering
  • Company / Institution Rice University
  • Website http://www.kavrakilab.org
  • Description The Kavraki group at Rice University is looking to hire an enthusiastic postdoctoral researcher to enhance their research efforts in computational structural biology, drug design, and computational bioengineering. The group has significant expertise in the development of methods for motion planning for complex systems in robotics. Their Open Motion Planning Library is now used both in academia and industry and is part of ROS. Inspired by its successes in motion planning, the group is developing modeling frameworks and algorithms for analyzing large-scale conformational changes in molecules and molecular assemblies. Applications range from drug design to the decipherment of the inner mechanisms of viruses. The postdoctoral research associate will assist in these efforts. The position becomes available in January of 2014. The duration of the position is one year and can be renewed for a second year. Compensation is commensurate with experience. Qualifications and Application The ideal candidate will have a strong enthusiasm for interdisciplinary work. Required skills include excellent analytical skills, excellent software engineering skills, experience with programming in C++, and extensive exposure to biochemistry and biophysics. A Ph.D. in a related field is required for the position. Experience with Rosetta is highly desirable. In the past successful candidates have had degrees in Computer Science, Bioengineering, Biophysics, Physics, and Chemistry. Excellent communication and collaboration skills are required as the selected candidate will be expected to work closely with current lab members and with collaborators. To indicate interest please send a CV to Lydia Kavraki. Applications will be accepted until the position is filled. Environment The Kavraki Group is a small but vibrant group and provides a stimulating working environment. Most of its alumni are now in academic or upper-level research positions. For more information about the group check http://www.kavrakilab.org. The Computer Science and Bioengineering Departments at Rice are part of the Gulf Coast Consortia for for Quantitative Biomedical Sciences and offer an unparalleled training environment. Rice University is a leading research university in the vibrant urban setting of Houston, TX, the fourth largest city in the U.S. Rice is a small, private university with exceptional strengths in engineering, biomedicine, and nanotechnology. The Computer Science Department is among the top 20 in United States, while the Bioengineering Department is ranked among the top 10 departments in United States by US News & World Report.
  • Contact Lydia Kavraki
  • E-mail kavraki@rice.edu

  • Date Added: 19/04/13
  • Job Title: Protein Design Scientist-04293
  • Company: Johns Hopkins Applied Physics Laboratory
  • Website: http://www.jhuapl.edu/employment/
  • Introduction: The Johns Hopkins University Applied Physics Laboratory (APL), a national leader in scientific research and development, located midway between Baltimore and Washington, DC is seeking a Protein Design Scientist.
  • Job Summary: This scientist will lead and contribute to the efforts of a multidisciplinary team of scientists and engineers by designing, purifying, and characterizing novel proteins. Applicants should have extensive experience with the Rosetta modeling suite, as well as complementary skills in protein expression, purification, assay development and data analysis. The ideal candidate will have a demonstrated record of success in computational protein design, excellent communication skills, and a desire to work on challenging national security problems.
  • Duties:
  1. Plan and execute cutting edge research in protein design to support the development of new reagents, sensors, and technologies.
  2. Manage resources, including staff, budgets, and infrastructure to achieve research goals.
  3. Function as a subject matter expert on a broad variety of biological and chemical topics.
  4. Communicate ideas, approaches, and results to internal management, external sponsors, and key collaborators.
  5. Motivate and mentor others: teach new approaches, provide and receive constructive criticism, recognize opportunities to contribute.
  6. Engage funding agencies, and write research proposals aligned with organizational goals and strategy
  • Required Qualifications:
  • PhD in an appropriate field (e.g. biochemistry), and at least 3 years of experience in computational design and modeling with Rosetta.
  • Demonstrated proficiency with biochemical tools for purification and evaluation of designed proteins, e.g. recombinant expression systems, column chromatography, CD spectroscopy, mass spectrometry, assay development, enzymology.
  • Ability to work in teams of scientists and engineers with diverse backgrounds and levels of experience, in both leadership and contributor roles, including the ability to train and mentor others.
  • Excellent oral and written communications skills.
  • Security: Applicant selected will be subject to a government security clearance investigation and must meet the requirements for access to classified information. Eligibility requirements include U.S. citizenship.
  • Benefits: APL offers a comprehensive benefits package including a liberal vacation plan, a matching retirement program, significant educational assistance, a scholarship tuition program for staff with dependents, and competitive salaries commensurate with skills and experience. For more information about our organization, please visit our web site at www.jhuapl.edu.
  • Equal Employment Opportunity: Johns Hopkins University Applied Physics Laboratory is an equal opportunity/affirmative action employer that complies with Title IX of the Education Amendments Acts of 1972, as well as other applicable laws, and values diversity in its workforce.
  • Location: Laurel, Maryland, USA

  • Date Added: 27/03/13
  • Job Title: Scientist in Protein Engineering and Antibody Technologies
  • Company: EMD Serono
  • Link: http://www.emdserono.com/en/careers/job_center/job_center/jobsearch/job-1301057/Scientist_in_Protein_Engineering_and_Antibody_Technologies.html?mode=detail&page=&jobLanguage=en&jobField1=Research+-+Pharmaceuticals&job1Location1=United+States&sortBy=date
  • Description: EMD Serono is the biopharmaceutical division of Merck KGaA, Darmstadt, Germany, a global pharmaceutical and chemical group. We strive to create value and benefit patients by transforming medical science into breakthrough solutions in our core therapeutic areas of neurodegenerative diseases, fertility and metabolic endocrinology, as well as oncology and autoimmune/inflammatory diseases as emerging areas of expertise.
  • PURPOSE OF THE ROLE: Contribute to the Discovery projects portfolio by planning, executing and drawing conclusions from experiments to evaluate the clinical potential of engineered biotherapeutic candidates. Actively contribute new ideas for evolving our antibody discovery and engineering programs to the next level, and execute plans to realize these ideas. Propose new approaches to developing biotherapeutics against therapeutic targets, especially “hard” targets such as membrane proteins. Prior experience working with membrane proteins (e.g. GPCRs,ion channels) and a track record of publication of structure-function studies of membrane proteins is highly desired.
  • MAIN INTERFACES:
    • INTERNAL WITHIN EMD SERONO:• Scientific staff within own department, across sites

      • Customers/downstream scientists in other functions and across projects

    • EXTERNAL TO EMD SERONO:• Academic collaborations, CROs, external consultants or scientists

      • Identify and implement new technologies and equipment

  • KEY TASKS & RESPONSIBILITIES: (In order of importance and time spent; should include 80% of responsibilities)• Demonstrated experience using in vitro biochemistry assays such as: cell binding via FACS, Kinexa or other; affinity determination via label-free methods (SPR, Interferometry) or fluorescence based methods (fluorescent probes, anisotropy, FRET); ELISA or chemiluminescence (MSD).

    • Experience in expression, mutagenesis and characterization of membrane proteins as evidenced by publication in this field highly desired. Stable cell line generation and/or Flp-In or Jump-In desired.  Experience with liposomal or VLP preparations an asset.

    • Proven ability to implement in vitro assays in medium to high throughput mode.

    • Molecular biology (PCR,  subcloning) and protein expression/purification experience in different hosts an asset.

    • Proven track record of independently designing, executing and troubleshooting experiments based on protocols provided by the literature, seminars, or other scientists.

    • Good publication record required.

    • Present experimental results, conclusions, and future plans clearly and in context of larger organizational goals to own department, project team members and project team.

    • Ability to work with and pro-actively engage with a multi-disciplinary team of diverse scientists.

    • Autonomously write study reports and scientific papers that require minimal revisions

    • Read and critically evaluate the literature in specialized scientific field, and share relevant topics with team.

    • Some knowledge of bioinformatics and/or molecular modeling an asset, as main interfaces will be to computational scientists.

    • May supervise and guide daily activities of junior lab staff or students. Train staff from other groups or projects in own area of expertise from.

    • Search for expertise relevant to scientific area available both inside and outside the company

    • Effectively operate a range of laboratory instrumentation and recommend modifications/upgrades.

    • Work effectively with people in other laboratories and across projects as required.

  • Qualifications:
    • CANDIDATE’S PROFILE
    • EDUCATION & LANGUAGES• PhD in Life Sciences.

      • Fluency in English is required

    • PROFESSIONAL SKILLS & EXPERIENCE• 1 to 3 years postdoctoral experience

      • Good knowledge of protein biochemistry (structure, stability, and protein-protein interactions)

      • Specific experience in antibody structure/function studies or other biotherapeutic types an asset

      • Experience working with membrane proteins an asset

    • PERSONAL SKILLS & COMPETENCIES• Ability to work in intense, fast paced, matrixed, multinational work environment

      • Excellent oral and written communication skills required to work with a diverse team

      • Good interpersonal skills essential to effective collaborations and ability to work simultaneously in different teams

    • ADA REQUIREMENTS: Normal and routine office duties

  • Date Added: 09/01/13
  • Job Title: Postdoctoral Fellow
  • Company / Institution:Eli Lilly
  • Responsibilities: This postdoctoral fellow position is an opportunity for a recent Ph.D. graduate to gain training in molecular evolution and structure-based protein design, while additionally obtaining exposure to the drug discovery process and the transformation of basic research into clinically viable molecular entities. The responsibilities of the research fellow will be to independently lead and perform protein and antibody engineering projects to enable targeting of novel biological pathways or modes of disease intervention.The researcher will collaborate within a multidisciplinary team of both internal researchers and external academic researchers with diverse backgrounds including molecular biology, biochemistry, biophysics, biology, immunology, oncology, and pharmacology.An expectation will be to publish research findings in high-impact journals and protect ideas that lead to valuable intellectual property through patenting. The researcher is expected to communicate results through both oral presentations and writing.Ultimately, the skills (technical, written, and oral) that are developed within this position should enable the researcher to run their own laboratory in either an industrial or academic setting.The research interests of the mentor (Stephen Demarest) are reflected in his publication history in PubMed.
  • Basic Qualifications: A recent Ph.D. in Chemistry, Biophysics, Biochemistry, or Biology. Detailed knowledge of proteins—Protein Design, Protein Biochemistry, or Protein Biophysics—is required. The applicant should have a growing body of published work that illustrates their productivity and scientific background.
  • Additional Skills/Preferences: A background in structure-based protein design or molecular evolution techniques (high-throughput screening, error-prone PCR, phage or yeast display) would be advantageous. Some experience in basic molecular biology techniques is preferred.
  • Additional Information: The candidate would be part of a growing community of post-doctoral fellows at Eli Lilly in various US and global sites.Lilly credits its exceptional employees for its successes, and knows the key to ongoing achievement lies in attracting top-notch individuals. A company rich in heritage, Lilly conducts research and markets products worldwide. The strategy Lilly has taken to succeed in the challenging pharmaceutical environment is to invest in discovery research (and innovation) both internally and externally. Through this philosophy, Lilly continues to provide for the unmet needs of patients.Lilly earns consistent and wide recognition for creating an exceptional work environment while maintaining our highly regarded reputation in the Pharmaceutical Industry and Community.ELI LILLY AND COMPANY IS AN EQUAL OPPORTUNITY EMPLOYER.
  • Contact: CV and cover letters can be sent directly to Stephen Demarest (demarestsj@lilly.com)

      • Date Added: 21/10/12
      • Job Title: Protein Design Scientist
      • Company / Institution: JHU Applied Physics Laboratory
      • Description: The Johns Hopkins University Applied Physics Laboratory (JHUAPL) is recruiting a protein design scientist. This scientist will lead and contribute to the efforts of a multidisciplinary team of scientists and engineers by designing, purifying, and characterizing novel proteins. Applicants should have extensive experience with the Rosetta modeling suite, as well as complementary skills in protein expression, purification, assay development and data analysis. The ideal candidate will have a demonstrated record of success in computational protein design, excellent communication skills, and a desire to work on challenging national security problems. Job Duties: Plan and execute cutting edge research in protein design to support the development of new reagents, sensors, and technologies Manage resources, including staff, budgets, and infrastructure to achieve research goals Communicate ideas, approaches, and results to internal management, external sponsors, and key collaborators Motivate and mentor others: teach new approaches, provide and receive constructive criticism, recognize opportunities to contribute. Engage funding agencies, and write research proposals aligned with organizational goals and strategy. Function as a subject matter expert on a broad variety of biological and chemical topics Qualify for access, handle, and safeguard classified information. Qualifications: PhD in an appropriate field (e.g. biochemistry), and at least 3 years of experience in computational design and modeling with Rosetta. Demonstrated proficiency with biochemical tools for purification and evaluation of designed proteins, e.g. recombinant expression systems, column chromatography, CD spectroscopy, mass spectrometry, assay development, enzymology. Ability to work in teams of scientists and engineers with diverse backgrounds and levels of experience, in both leadership and contributor roles, including the ability to train and mentor others Excellent oral and written communications skills
      • Contact: joshua dot wolfe at jhuapl dot edu

      • Date Added: 06/10/12
      • Job Title: PhD and Postdoc openings for the computational and experimental characterization of peptide-mediated interactions and their context
      • Company / Institution: The Furman Lab, Hebrew University of Jerusalem, Israel
      • Website: The Furman Lab
      • Description: The Furman lab is expanding and looking for talented and motivated PhD students and Postdocs! We are interested in improving our understanding and ability to manipulate protein interactions at the molecular level. We focus on interactions that involve short peptides, linear motifs within proteins, and study how these are integrated into functional signals within the cellular context. To do so, we combine computational tools for modeling of the structure and binding of peptide-protein interactions with bioinformatic approaches. We have recently obtained funding by the ERC to open a wet lab that will complement our computational studies. Ideal candidates should have a strong background in Structural Biology and Biophysics, experimental characterization of proteins and their interactions, Bioinformatics, and Computer Sciences. Strong motivation to combine computational and experimental work is encouraged.
      • Contact: For more information, please contact Ora Schueler-Furman oraf@ekmd.huji.ac.il

      • Date Added: 23/09/12
      • Job Title: Postdoc position on Computational Protein Design
      • Company / Institution: LAAS-CNRS
      • Description: The Robotics and Interactions group at LAAS-CNRS (Toulouse, France) is seeking for a postdoctoral researcher to work in an interdisciplinary project on Computational Protein Design. The project, ProtiCAD, is funded by the French National Research Agency (ANR). It involves three research groups with expertise in computer science / robotics, computational biology and enzyme engineering, and a start-up company. The work will mainly involve the development of algorithms to efficiently explore very large state-spaces, which correspond to different sequences and conformations of a protein. Candidates should have strong background in search algorithms and combinatorial optimization methods, as well as excellent programming skills. Research will be carried ou in close collaboration with people in the other laboratories; therefore, applicants should enjoy teamwork and have very good communication skills. Good English level is mandatory and notions of French would be a plus. Toulouse is a beautiful, dynamic and safe city situated in the South West of France, within only 1.5 hour drive from the Pyrenees and the Mediterranean Sea. Toulouse offers outstanding opportunities for culture, entertainment and outdoor activities. The position is available from December 2012, for a duration of up to two years.
      • Contact: Applications, including a CV, a cover letter and contact information of at least two references, should be sent by email to Juan Cortés (juan.cortes@laas.fr) with subject: “ProtiCAD postdoc application”.

      • Date Added: 23/09/12
      • Job Title: Post-doctoral Position in Structural Biology
      • Company / Institution: Purdue University
      • Description: A post-doctoral position is available for a person with experience in protein or virus crystallography. Some experience in electron microscopy would be desirable but not essential. The work of the laboratory centers on the structure and function of viruses. Salary will depend on experience. A starting post-doc salary is around $39,000/year.
      • Contact: Applications should be send by e-mail to Michael Rossmann mr@purdue.edu

      • Date Added: 29/08/12
      • Job Title: Principal Scientist, Informatics
      • Job Role: Computational Structural Biology – Informatics
      • Company: UCB
      • Contact: Dr. Jiye Shi by email at Jiye.Shi@ucb.com
      • Job reference: INF_CSB_2012_01
      • Location: Slough, Thames Valley, UK
      • Notice:

The following position is planned to be open for application in the coming months. At this time we would like to share this information with interested parties in order to speed up the recruitment process once the position is open.

      • Description:

At UCB our sense of purpose is to help people suffering from severe central nervous system or immunological disorders lead normal, everyday lives. Our ambition is to offer them innovative new medicines and groundbreaking solutions that go beyond the drug. We are committed to enabling cutting-edge scientific research that is driven by the patients’ needs.

This is an exciting opportunity to join a dynamic and forward-looking Informatics team working with Research colleagues to deliver medicines to patients.

The successful candidate will contribute to the development and implementation of innovative Computational Structural Biology technologies with an emphasis on delivering novel scientific insights and technologies to therapeutic projects. The candidate will be expected to develop and maintain strong links with therapeutic project teams, influencing the design of experiments, interpreting experimental results and contributing to the data-driven decision-making process.

        • Responsibilities:
          • Establishing, maintaining and expanding internal collaborations within and across UCB’s research centers in Braine and Slough.
          • Gathering requirements of New Medicines (drug discovery) for novel methods in Computational Structural Biology.
          • Carrying out independent and collaborative scientific research, developing computational methods that can make tangible contributions to therapeutic projects.
          • Supporting New Medicines (drug discovery) functions broadly through meeting their bioinformatics needs.
        • Experience:

Candidates must be of Ph.D. level (or equivalent) with proven experience in the following areas:

        • A deep understanding of Computational Structural Biology principles and practice is a necessity for the role. The successful candidate will have a solid educational background in Computational Structural Biology or a similar field.
        • The successful candidate will have proven and relevant experience in delivering support/solutions within a working environment.
        • The ideal candidate will have direct and extensive experience of working in a scientific discipline, as well as demonstrable experience in the application of current Computational Structural Biology techniques within the pharmaceutical/biotechnology industry.
        • Excellent verbal and written communication skills are essential. The ideal candidate will be a confident and influential proponent of informatics principles and solutions and their role and value in the scientific workflow. The candidate will be a strong communicator with the ability to transform complex theories/methodologies into messages suitable for a broad audience.
        • This individual must be self-driven to maintain a competitive expertise in the Computational Structural Biology field, and must work well within a team-orientated, highly flexible and dynamic group.
      • Technical Skills:
        • Strong expertise in Computational Structural Biology and Bioinformatics.
        • Solid skills in relevant techniques used within pharmaceutical research would be very valuable. The skills include, but not be limited to, homology modeling, ab initio modeling, protein-protein docking, antibody modeling, membrane-protein modeling, molecular dynamics simulation, quantum mechanics, etc.
        • Proficient coding skills using the C/C++, Java and/or Python programming languages.
        • Familiar with grid, distributed and/or cloud computing platforms for scientific computing under a Linux operation system.
        • Skills in parallel programming and large-scale parallel computing is a big plus.

      • Date Added: 29/08/12
      • Job Title: Principal Scientist, Informatics
      • Job Role: Computational Structural Biology – Informatics
      • Company: UCB
      • Contact: Dr. Jiye Shi by email at Jiye.Shi@ucb.com
      • Job reference: INF_CSB_2012_02
      • Location: Slough, Thames Valley, UK
      • Notice:

The following position is planned to be open for application in the coming months. At this time we would like to share this information with interested parties in order to speed up the recruitment process once the position is open.

      • Description:

At UCB our sense of purpose is to help people suffering from severe central nervous system or immunological disorders lead normal, everyday lives. Our ambition is to offer them innovative new medicines and groundbreaking solutions that go beyond the drug. We are committed to enabling cutting-edge scientific research that is driven by the patients’ needs.

This is an exciting opportunity to join a dynamic and forward-looking Informatics team working with Research colleagues to deliver medicines to patients.

The successful candidate will contribute to the development of innovative Computational Structural Biology technologies through external collaborations. The candidate is expected to develop and maintain strong links with academic institutes and researchers, especially those within Europe, contribute intellectually to the collaborations and deliver the resulting technologies to UCB’s research scientists.

        • Responsibilities:
          • Establishing and maintaining close relationships with prominent researchers and research institutes in Computational Structural Biology worldwide, especially within Europe.
          • Liaising with Research Business Development, Intellectual Property Department and Legal Department to manage collaboration contracts and intellectual property rights.
          • Managing external computing resources (e.g. Amazon cloud computing platform)
          • Gathering requirements of New Medicines (drug discovery) for novel methods in Computational Structural Biology.
          • Evaluating new technologies on a regular basis, bringing in those of significant value to New Medicines (drug discovery).
          • Carrying out independent and collaborative scientific research, developing computational methods that can make tangible contributions to therapeutic projects.
          • Supporting New Medicines (drug discovery) functions broadly through meeting their bioinformatics needs.
        • Experience:

Candidates must be of Ph.D. level (or equivalent) with proven experience in the following areas:

        • A deep understanding of Computational Structural Biology principles and practice is a necessity for the role. The successful candidate will have a solid educational background in Computational Structural Biology or a similar field.
        • The ideal candidate will have proven and relevant experience in contract negotiation, working together with Business Development, Intellectual Property Department and Legal Department.
        • The ideal candidate will have direct and extensive experience of working in a scientific discipline, as well as demonstrable experience of the application of current Computational Structural Biology techniques within the pharmaceutical/biotechnology industry.
        • Excellent verbal and written communication skills are essential. The ideal candidate will be a confident and influential proponent of informatics principles and solutions and their role and value in the scientific workflow. The candidate will be a strong communicator with the ability to transform complex theories/methodologies into messages suitable for a broad audience.
        • This individual must be self-driven to maintain a competitive expertise in the Computational Structural Biology field, and must work well within a team-orientated, highly flexible and dynamic group.
      • Technical Skills:
        • Strong expertise in Computational Structural Biology and Bioinformatics.
        • Good understanding of Intellectual Property Rights in the context of collaborating with academics.
        • Knowledge and skills in contract negotiation is a big plus.
        • Solid skills in relevant techniques used within pharmaceutical research would be very valuable. The skills include, but not be limited to, homology modeling, ab initio modeling, protein-protein docking, antibody modeling, membrane-protein modeling, molecular dynamics simulation, quantum mechanics, etc.

      • Date Added: 14/12/11
      • Job Title: 485 – Protein Designer, Rosetta
      • Company: Intrexon
      • Description: A position is available in the Applied Research Unit (ARU) for a protein engineer or computational biologist with experience in the Rosetta Software Suite for protein design. The Protein Designer will be part of a cross-disciplinary team of biologists and bioinformaticians generating novel proteins for both therapeutic and industrial applications. The ideal candidate will have considerable experience in utilizing in silico protein models to answer questions related to protein folding and stability, protein-protein interactions as well as enzymatic activity, and will also have the experience to play a large part in the development of assays and screens to measure and quantify the completed designs.
      • Essential Duties and Responsibilities:
        • Play a leading role in researching and developing proteins with predicted novel functionality.
        • Assist in developing assay methods to best screen novel designed proteins, and provide ongoing support to such efforts as they are transferred to the respective corporate divisions.
        • Request and manage bioassays, and analyze data from multiple platform technology projects both independently and as part of a team.
        • Work with a diverse group of biologists and software developers to improve existing database functionality and enhance the available database analysis features and toolsets.
        • Work as a subject matter expert with individuals and groups throughout the company to apply knowledge of protein structure to current tasks and projects as requested.
      • Job Requirements:
        • Ph.D. with 0-3 years experience in computational biology, structural biology, computational chemistry, biophysics, structural bioinformatics or a related field.
        • Experience with the Rosetta Software Suite is essential. Additional experience in other software packages such as Discovery Studio, MOE, or YASARA is highly desirable.
        • Experience with molecular modeling and structural analysis of macromolecules is required.
        • Understanding of standard molecular biology techniques, basic enzymology (steady state and transient analysis), and medium/high throughput biological assay design/screening/analysis is required.
        • Programming experience in common scripting languages for operating Rosetta and data analyses is required.
        • Knowledge of enzyme kinetics or protein-protein interaction assays such as SPR, ForteBio, FRET, or similar methodologies is advantageous.
        • Experience in application of directed evolution methods and mutant library design for protein function is a plus.
        • Possess a high degree of personal responsibility.
        • Ability to achieve in a milestone-driven, rapidly changing research environment.
        • Ability to work collaboratively in a team environment with scientists of different backgrounds and experience levels.
        • Excellent interpersonal and communication skills.
        • Skills in work and time management under project multitasking conditions.
        • Ability to provide and apply creative solutions to maintain work flow.
        • Planning, organization and execution skills.
        • Ability to solve practical problems and deal with a variety of concrete variables in various situations.
        • Ability to interpret a variety of instructions furnished in written, oral, diagram or schedule form.
      • Contact: jobs@intrexon.com

      • Job Title: Postdoctoral Positions
      • Company / Institution: Los Alamos National Lab
      • Description: Postdoctoral Positions in computational and experimental molecular biology: protein biosensor structure designLos Alamos National Lab Bioscience (B) Division is currently seeking two postdoctoral candidates in structural and molecular biology.
        • Project: Design and fabrication of protein-based biosensors and affinity reagents. Principle work involves the creation of computer algorithms for protein structure design and the supervision of the fabrication and testing of constructs. One project involves modeling and design of symmetric protein interactions and unstructured proteins. This will require formulating and programming new algorithms for computational optimization on novel protein potential energy surfaces. Constructs will be fabricated and evaluated in the laboratory either by the applicant or with collaborators. The ideal candidate will have strong structural modeling experience but also have worked on or closely with laboratory projects, and have a strong curricular foundation in protein molecular biology.
        • Desired skills: Accomplishments in areas related to protein interactions or determinants of binding or computational macromolecular design or structural modeling. Ability to use sophisticated structure prediction software and to develop algorithms. Specific experience with the Rosetta Structure modeling algorithm is very highly sought. Ability to read and modify object oriented C++ helpful and python is helpful. All applicants should have strong computational modeling interest and aptitude, but degrees in either computational or laboratory molecular biological studies are welcome.
      • Contact: Charlie Strauss, cems@lanl.gov, Tel: 505 665 4838

      • Date added: 08/06/11
      • Job Title: PhD. Structure Mining
      • Company / Institution: EMBL-Hamburg
      • Website: http://www.embl-hamburg.de/
      • Description: A PhD-fellowship is available in the group of Thomas Schneider at EMBL-Hamburg to develop methods for mining structural data in terms of fragments and ensembles to be used in the interpretation of electron density maps in low-resolution crystallography and high-resolution electron microscopy. EMBL Hamburg is located on the DESY campus where a lot of exciting facilities for structural biology are in operation or being set up including the PETRA III synchrotron, the FLASH laser facility, and the future European X FEL. With groups active in methods development and in challenging structural biology projects, the EMBL Outstation in Hamburg offers a stimulating multi-disciplinary environment.
      • Contact: Dr. Thomas R. Schneider, email: thomas.schneider@embl-hamburg.de
      • Code / Promotion / ID:

      • Date added: 08/06/11
      • Job Title: Scientist (Enzyme Design)
      • Company / Institution: Arzeda
      • Website: http://www.arzeda.com/
      • Description: Arzeda is seeking a creative and motivated protein engineer who likes to work in a small and extensively multi-disciplinary team environment to join our efforts. Arzeda is a young and dynamic biotech start?up at the forefront of the “green” chemistry revolution. Leveraging our core expertise in computational protein design and experimental biochemistry, we identify and engineer novel enzymes and metabolic pathways for a sustainable future. To date, Arzeda has successfully designed novel enzymes for its partners using its computational enzyme design technology.The successful candidate will play a major role in Arzeda’s enzyme design programs with opportunities to grow with the company. At the scientist level, she/he will be responsible for: * Carrying out literature analyses for key chemical reactions * Analyze and develop mechanistic models of enzyme active sites * Computationally design new enzymes * Perform enzyme assays (includes enzyme expression, purification and subsequent data analysis and technical report preparation). Job Requirements A Ph.D. in life sciences with 1+ years of relevant experience or a M.S./ B.S. in biological sciences with a minimum of 3 years experience in an industrial setting and the ability to work independently are required for this job. Recent Ph.D. graduates who wish to apply for a similar position at the postdoctoral level will also be considered. Prior research experience in protein engineering and protein structural biology is required. A working knowledge of enzymology and protein engineering software, such as Rosetta, as well as the ability to understand and code in C++ and/or common scripting languages (Python, Perl…) is highly desirable. Additional experimental experience in genetics, such as knowledge of yeast expression systems and genetics, would also be beneficial. The successful candidate is expected to have strong written and oral communications skills, and finally the candidate must be willing to learn, as we are a growing company that will always keep you intellectually stimulated and scientifically challenged! For further information about this position and to apply please send your CV and a cover letter.
      • Contact: jobs@arzeda.com
      • Code / Promotion / ID:

      • Date added: 15/02/11
      • Job Title: Senior Scientist Level Protein Design Engineer
      • Company / Institution: Permeon Biologics
      • Website: http://www.flagshipventures.com/
      • Description: Senior Scientist level Protein Design Engineer to be part of initial team at a venture-backed start-up company based on technology from Harvard University. Doctorate in Bioengineering, Chemical Engineering, Chemical Biology, Biochemistry or similar required. Candidates need proven abilities in the design and testing of proteins such as antibodies, enzymes, or proteins demanding modification of surface properties. Knowledge of moieties that facilitate penetration/escape of cellular compartments is beneficial. Candidates must have strong technical communication skills to communicate with the management team and with external parties. Candidates need an entrepreneurial mindset and be fully capable of self-direction including setting up computational software platform. Also must be able to translate findings from lab of academic collaborators. Knowledge and lab abilities in molecular cloning, cell biology and in vitro assays desired. Position may initially be as a consultant.
      • Contact: Ann Dewitt at Flagship Ventures, email: adewitt@flagshipventures.com
      • Code / Promotion / ID:

      • Date added: 29/09/10
      • Job Title: Postdoctoral Position in Structural Bioinformatics
      • Company / Institution: Indiana University
      • Website: http://sparks.informatics.iupui.edu/
      • Description: Do you have the ambition and motivation to take on the challenge of employing your knowledge of mathematics, statistics, and/or physics to make innovative discovery in structural bioinformatics — a field where physical interactions rule biology and to produce a significant impact in future medicine through genome-scale data mining and inhibitor design? The main area of our interest is bioinformatics and theoretical study of proteins and protein-ligand, protein-DNA/RNA interactions.
      • Contact: Please send your CV with cover letter, and the names, addresses, and phone numbers of two referees who are familiar with your work. Email to yqzhou@iupui.edu
      • Code / Promotion / ID:

      • Date added: 29/09/10
      • Job Title: Assistant Member – The Structural Biology Program
      • Company / Institution: Sloan-Kettering Institute
      • Website: www.ski.edu
      • Description: The Structural Biology Program of the Sloan-Kettering Institute invites applications for a tenure-track faculty position at the Assistant Member level (equivalent to Assistant Professor). We are interested in outstanding individuals who have demonstrated records of significant accomplishment. Areas of interest include x-ray crystallography, NMR spectroscopy, EM and optical imaging, as well as the interface of structural, chemical and computational biology. Faculty will be eligible to hold graduate school appointments in the Gerstner Sloan-Kettering Graduate School of Biomedical Sciences, the Weill Cornell Graduate School of Medical Sciences, as well as the Tri-Institutional MD/PhD Training Program.
      • Contact: Julie Kwan at kwanj@mskcc.org or Dr. Nikola Pavletich, Chair, Structural Biology Program at palvletin@mskcc.org
      • Code / Promotion / ID: The deadline for applications is November 1, 2010

      • Date added: 29/09/10
      • Job Title: Postdoctoral Researcher in Structural Biology
      • Company / Institution: Institute of Bioinformatics and Structural Biology, National Tsing Hua University
      • Website: http://sites.google.com/site/hsushangte
      • Description: A postdoctoral research position supported by the International Human Frontier Science Program (www.hfsp.org) is immediately available to pursue studies on knotted protein folding. The project aims to devise an experimental strategy based on solution state NMR spectroscopy to probe the structures and dynamics of a variety of knotted proteins along their folding pathways in order to monitor knot formation and to identify potentially common key elements that are responsible for promoting the knotting events. An integrated approach combining biophysical, biochemical and computational methods will be employed to generate structural models of protein folding intermediates in order to address the question of how and when these knotted structural elements are attained during folding and what their biological significance may be.
      • Contact: stdhsu@life.nthu.edu.tw
      • Code / Promotion / ID:

      • Date added: 29/09/10
      • Job Title: Postdoctoral position – Membrane Protein Structural Biology
      • Company / Institution: University of Virginia
      • Website:
      • Description: Postdoctoral level preferred, but more senior (or more junior) positions are possible. Relevant experience is certainly desirable. Current areas of research include bacterial outer membrane active transport, eukaryotic/mammalian membrane protein structural genomics, and methods development (for membrane protein structural biology). The scientific and intellectual environment for membrane research is very good. Eight labs working in membrane protein biochemistry, biophysics and structural biology are sited in a modern research building. The Center for Membrane Biology includes additional investigators, holds a regular seminar series, and maintains a cohesive, lively and collegial environment. Applicants, please send me a cover letter, cv, and names of three references. Also, any other queries can be directed to me, as well.
      • Contact: Michael Wiener
      • Code / Promotion / ID:

      • Date added: 29/09/10
      • Job Title: Senior Director, Structural Biology
      • Company / Institution: Takeda Pharmaceuticals North America, Inc.
      • Website: www.takedasd.com
      • Description: Directs, develops and integrates the Company’s Structural Biology resources to ensure timely achievement of major goals. Oversees and provides direction for the Molecular Biology, Crystallography, and Protein Chemistry sub-groups. Provides deep expertise and strategic leadership in X-ray crystallography, and across structure based drug design programs in oncology, inflammation and metabolic diseases. Invents and advances drug candidate compounds towards preclinical and clinical development.
      • Contact:
      • Code / Promotion / ID:

      • Date added: 29/09/10
      • Job Title: Researcher
      • Company / Institution: Rosetta Labs around the world
      • Website: http://www.rosettacommons.org/positions/index.html
      • Description: The Rosetta Commons is seeking for talented and highly motivated applicants. If you are interested in computational biology and looking at protein structures on the screen makes you happy, please contact us.
      • Contact:
      • Code / Promotion / ID:

      • Date added: 22/09/10
      • Job Title: Senior Scientist, Informatics – Computational Chemistry
      • Company / Institution: EMD Serono
      • Website: http://www.emdserono.com/en/careers/job_center/job_center.html
      • Description: Work in interdisciplinary teams and actively contribute to drug discovery projects at all stages. Perform structure and ligand-based design of biologically-active compounds, data analysis and HTS hit triage, in-silico screening, ADMET and property prediction. Actively design new molecules with improved potency, physical properties and safety profiles. Evaluate, implement and apply new computational methodologies and strategies. Establish and maintain excellent collaborative efforts within the research organization.
      • Contact:
      • Code / Promotion / ID: Requisition ID: 1001107

      • Date added: 28/08/10
      • Job Title: Post Doc Research Fellow – Daniel Kirchhofer Lab
      • Company / Institution: Genentech, Inc.
      • Website: http://www.gene.com/gene/research/postdoctoral/mentors/strchembio/kirchhofer/
      • Description: Responsibilities: We are looking for a Postdoctoral Fellow to study the structural and functional basis of how antibodies regulate catalysis of proteases. Another aspect of the project is the biochemical and biological characterization of a novel trypsin-like serine protease involved in inflammatory disease. Requirements: The candidate should have a Ph.D. in biochemistry or biophysics or related field with a strong background in protein chemistry. Candidates with expertise in protein purification/characterization and knowledge of protein structures (incl. Pymol) are preferred. The individual should be highly motivated, demonstrate creative thinking, able to work independently and interact well with other members of the lab.
      • Contact:
      • Code / Promotion / ID: REQUISITION NUMBER: 10-1000034532

      • Date added: 14/08/10
      • Job Title: Staff Scientist
      • Company / Institution: SAIC-Frederick, Inc
      • Website: www.saic-frederick.com
      • Description: Responsibilities will be to conduct a range of activities such as structure and ligand based design, homology modeling, ADME/tox modeling, QSAR and chemoinformatics. The position will use the appropriate blend of chemical and biological knowledge with state-of-the-art computational software technology to understand molecular data through visualization, prediction and analysis of trends in the ‘drug-hunting’ process and, in collaboration with a wide variety of multi-disciplinary scientists, devise creative solutions, perform structure- and ligand-based molecular design, HTS data analysis, virtual screening, ADMET and physicochemical property prediction. Will evaluate, implement and apply new computational methodologies and strategies. Will also be responsible for the operation and maintenance of computational workflows supporting multi-investigator small molecule drug discovery. Also entails interaction, oversight and management of chemical biology projects conducted by external collaborators/contractors and facilitate the achievement of key goals on time and on budget. Oversees daily operation of cheminformatics tasks and workflows in support of a multiple-investigator hit-to-lead/hit-to-probe drug discovery center. Operates, maintains, and develops PC- and server-based computational capabilities related to the hit-to-lead stage, as well as general lead and probe discovery efforts. Integrates data input/output between workflow components and between workflows and users. Participates in developing cheminformatics operations in response to changing needs, including development of the informatics associated with a first-stage compound storage plan. This position is subject to obtaining a Public Trust Clearance.
      • Contact:
      • Code / Promotion / ID: position #179679

      • Date added: 14/08/10
      • Job Title: Postdoctoral fellow – Protein degradation
      • Company / Institution: Roche
      • Website: http://www.gene.com/gene/research/sci-profiles/proteng/fairbrother/profile.html
      • Description: The department belongs to the Biologics Research unit which has its focus on identification, characterization and development of novel therapeutic proteins for different medical indications such as oncology and inflammation. The work will focus on the following aspects: • Discovery of the structural features that govern protein stability and avoid chemical degradation such as asparagine deamidation or methionine oxidation. • Generation of high-quality three-dimensional protein structures via homology modeling to define structural prerequisites for “degradation hotspots” • Generation and characterization of a collection of “stressed” protein samples using established methods such as CE-IEF and LC-MS • Generation of protein variants aiming at improved stability, and crystal structure determination to verify your hypotheses • Planning, performing and interpretation of experiments in an independent manner • Shared mentorship between the Protein Analytics department and an academic partner will ensure high scientific standards and provide fundamental input from both biopharmaceutical industry and academic research • Beeing a part of a highly motivated team using state of the art equipment and software
      • Contact:
      • Code / Promotion / ID: 00021722

      • Date added: 14/08/10
      • Job Title: Postdoctoral fellow – Protein NMR
      • Company / Institution: Genentech
      • Website: http://www.gene.com/gene/research/sci-profiles/proteng/fairbrother/profile.html
      • Description: The main focus of the protein NMR group is to apply and develop techniques for studying the solution structures of proteins and protein/protein or protein/ligand complexes of therapeutic interest. In addition, the group undertakes studies of biologically active peptides and small molecules with particular emphasis on determining their conformations. The protein NMR facilities include dedicated 800, 600, and 500 MHz spectrometers, Linux workstations, and a fully equipped protein expression and purification lab. The NMR facility complements protein engineering, protein crystallography and modeling efforts within the Protein Engineering and Structural Biology Departments. Highly motivated researchers, capable of independent work in a collaborative environment are sought for this position. A postdoctoral researcher is sought to conduct fundamental computational research to understand molecular origins of aggregation in protein therapeutics, especially monoclonal antibodies and antibody based therapeutics. The research shall involve an inter-disciplinary mix of statistical analyses, bioinformatics, high performance grid computing, molecular biophysics, molecular modeling, and simulation techniques to advance our understanding of protein structure-function-aggregation relationships and mechanism(s) of aggregation. The researcher shall be expected to develop novel approaches to detect aggregation prone regions and three dimensional aggregation prone motifs and suggest ways to improve manufacturability of biotherapeutics via rational design.
      • Contact:
      • Code / Promotion / ID: 09-1000028004 PD PE

      • Date added: 15/07/10
      • Job Title: Postdoctoral Position – Free Energy Calculation Techniques Applied to Membrane Protein Complexes – New York, NY USA
      • Company / Institution: Mount Sinai School of Medicine
      • Website: http://www.mssm.edu
      • Description: The Filizola Lab at Mount Sinai School of Medicine in New York, NY (URL: http://atlas.physbio.mssm.edu/filizola/) is seeking a talented and highly motivated post-doctoral fellow with outstanding skills in developing and/or applying free energy calculation techniques such as umbrella sampling, metadynamics, free energy perturbation theory, etc. The selected candidate will use these techniques to investigate protein-ligand binding, ligand-induced conformational specificity, and/or allostery in membrane protein complexes such as G-protein coupled receptor oligomers. He/She will work as part of a multidisciplinary research team on NIH-funded projects focused on understanding structural, dynamic and electronic determinants of biological mechanisms underlying physiological functions. A Ph.D. degree in Physics, Chemistry, Biophysics, Theoretical/Computational Chemistry, or related discipline is required. Extensive training in statistical mechanics and thermodynamics is a major plus. Qualified applicants should send a CV and at least 2 reference names by email to Dr. Marta Filizola. Applications will be considered until the position is filled.
      • Contact: Marta Filizola
      • Code / Promotion / ID: mafjul15

      • Date added: 15/07/10
      • Job Title: PhD position – Interfering with Protein-Protein Interactions
      • Company / Institution: Pharmaceutical Bioinformatics University Freiburg
      • Website: http://www.pharmaceutical-bioinformatics.org
      • Description: Duration: 3 years Abstract: Disease-relevant intracellular protein-protein interactions occurring at defined cellular sites have great potential as drug targets. They allow for highly-specific pharmacological interference with defined cellular functions. Drugs targeting such interactions are likely to act with fewer side effects than conventional medication influencing whole cell functions. The successful candidate will work on a structural drug design process to identify new agents suitable for interfering with protein-protein interactions. Requirements: Master’s degree or comparable in bioinformatics or one of the life science subjects with computational background good command of English Desirable Skills: programming skills (Python) experiences in the use of protein-analyzing software (e.g. PyMol, Schroedinger platform) experiences in the use of databases (SQL) Salary is paid according to the TVoeD (50% position). In keeping with the University of Freiburg policy regarding gender equity, female applicants are particularly encouraged. Disabled people with identical qualifications will be favored. Please send your applications/further inquiries to Dr. Stefan Günther (e-mail preferred: stefan.guenther[at]pharmazie.uni-freiburg.de until July 30, 2010. Applicants should submit CV, cover letter indicating research interests and experience, and the name and contact details of two referees.
      • Contact: Björn Grüning
      • Code / Promotion / ID: phabi201023

      • Date added:    12/07/10
      • Job Title:    Postdoctoral fellow – Biotherapeutics
      • Company / Institution:    Pfizer
      • Website:    http://www.pfizer.com/careers
      • Description:    A postdoctoral researcher is sought to conduct fundamental computational research to understand molecular origins of aggregation in protein therapeutics, especially monoclonal antibodies and antibody based therapeutics. The research shall involve an inter-disciplinary mix of statistical analyses, bioinformatics, high performance grid computing, molecular biophysics, molecular modeling, and simulation techniques to advance our understanding of protein structure-function-aggregation relationships and mechanism(s) of aggregation. The researcher shall be expected to develop novel approaches to detect aggregation prone regions and three dimensional aggregation prone motifs and suggest ways to improve manufacturability of biotherapeutics via rational design.
      • Contact:
      • Code / Promotion / ID:    941315

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