Computational Chemist - Newark, CA | Biospace
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Computational Chemist

Protagonist Therapeutics, Inc.

Newark, CA
Posted Date:
Position Type:
Full time
Job Code:
Required Education:
Areas of Expertise Desired:
Computational Chemistry,

Job Description

Position Description:

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 or peptidomimetics for gastrointestinal diseases.

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 selection. In addition, the candidate will be familiar with molecular recognition and improving potency, developing Structure Activity Relationships, be familiar with accessing public domain sequence, function, and structural information and extensive scripting/programming expertise, with a preference for C++. The ideal candidate will have significant knowledge of constrained peptides, macrocyles, peptide engineering, design of libraries of molecules, in the context of in vitro display techniques (eg phage display). The candidate will be well versed of the relevant literature, and have demonstrated hands on experience in structure based design in an industrial setting.



The candidate will hold a Ph.D. in computational chemistry or molecular modelling or related discipline, with significant industrial research experience. Experiences in drug design, molecular recognition, structure activity relationships and enhancing peptide affinity, stability are essential.  Project planning and meeting deadlines is an absolute advantage. Moreover, proven capacity in scripting and coding is highly desirable.


To be responsible for the structure-based or ligand-based drug design of one or more targets
To optimize affinity of peptide-derivatives whilst 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

Professional Experience / Skills:

PhD in computational chemistry or related discipline is required
Proven translational experience towards IND candidates
Knowledge of constrained peptides, peptidomimetics and macrocycles
Knowledge and practical experience in improving stability of peptides and/or macrocyles
Knowledge and experience in design of libraries as related to in vitro display techniques
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