Jul
14
2010

Molecular Modeling Jobs

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  • 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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