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    Opportunity: Molcular Modeler / Computational Chemist / Bioinforatician @ Protagonist Therapeutics -- Menlo Park, CA (US)
    Submitted by Kathy Neill; posted on Tuesday, August 13, 2013


    Protagonist Therapeutics ( is a US biotechnology company dedicated to the discovery of disulfide-rich peptides as well differentiated orally active peptides against those targets/diseases for which suitable small molecule or biologic options are not available.


    Protagonist Therapeutics is seeking a talented and highly motivated scientist to join the drug design group. The candidate will use proprietary molecular modeling tools in combination with existing commercial software packages to design new compounds and optimize existing compounds. Protagonist is pursing the development of orally stable peptide derivatives for gastrointestinal diseases.

    Duties and responsibilities include, but are not to:
    • To be responsible for the structure-based drug design of one or more targets
    • To optimize affinity of peptide-derivatives whilst maintaining and optimizing oral stability features
    • To have up to date knowledge of the literature of one or more target
    • The use of drug-design tools such as database searching, docking, scoring etc for the structure-based design of biologically active molecules
    • To interpret and to use structural data, biological assay data, stability data, mutagenesis data, sequencing data, pharmacological data etc in the design of biological active molecules.


    The successful candidate will have a PhD in computational chemistry, bioinformatics or related discipline. The candidate will have previous involvement in all elements of molecular design impacting on IND candidate generation and proven ability to enhance peptide stability and permeability. In addition, the candidate will be familiar with molecular recognition and improving potency, be familiar with accessing public domain sequence, function, and structural information, has knowledge of disulfide rich peptides, macrocyles, clustering algorithm, molecular modeling packages, scripting/programming languages, with a preference for C++ and has worked in a Linux environment. The candidate well versed of the relevant literature, and have demonstrated hands on experience in structure based design. At least three years of industry experience is desirable.

    Knowledge and Skills/Experience:
    • PhD in computational chemistry, bioinformatics or related discipline is required
    • Proven translational experience towards IND candidates
    • Knowledge of disulfide rich peptides and macrocycles
    • Knowledge and practical experience in improving stability of peptides and macrocyles
    • Previous experience in clustering
    • Ability to program, preferably in C/C++
    • Working experience with pharmacophores
    • Previous experience in structure-based drug design
    • Thorough understanding of molecular recognition
    • Thorough understanding of the drug design literature
    • To have experience in scaffold hopping and peptide/protein engineering
    • Develop and maintain integrated chemoinformatic database/registry
    • Previous experience in database searching and docking
    • Understanding of scoring functions
    • Understanding of sequence search/alignment (Blast)
    • Knowledge of SQL and Oracle Database
    Personal Qualities:
    • Ability to work in an efficient and well organized manner
    • Ability to work collaboratively with internal and external team colleagues
    • Ability to work with minimal supervision
    • Ability to adhere to specific work schedules and meet deadlines
    • Methodical approach to problem solving
    • Excellent written and verbal communication skills
    • Excellent interpersonal skills
    • Sound problem-solving skills


    Protagonist Therapeutics provides competitive salary packages commensurate to experience to ensure that we are able to hire the best people from around the world.


    Email: hr[at]


    28th August, 2013

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