Associate Director, Computational Chemistry
Protagonist Therapeutics, Newark, CA, United States
Location:
Newark, CA
Job Id:
401
# of Openings:
0
Job Description:
Protagonist Therapeutics is seeking a talented and highly motivated computational chemist to join our Drug Design group. The successful candidate will leverage proprietary molecular modeling tools, commercial software packages, and AI algorithms to design novel compounds and optimize existing leads. Protagonist is advancing the development of orally stable peptides, peptidomimetics, and small molecules. The ideal candidate will hold a PhD in computational chemistry, bioinformatics, artificial intelligence, or a related discipline and will have broad hands‑on experience across all aspects of molecular design that directly impact IND candidate selection. In addition, the candidate must be well versed in molecular recognition, structure‑activity relationship (SAR) development, and potency optimization. Strong familiarity with public‑domain sequence, functional, and structural databases, along with extensive scripting and programming expertise, is required. Knowledge of AI‑driven drug design is highly desirable. The ideal candidate will also possess significant expertise in constrained peptides, macrocycles, peptide engineering, and small‑molecule design. The candidate must be well versed in the relevant scientific literature and demonstrate proven hands‑on experience in structure‑based drug design within an industrial setting.
Duties and Responsibilities include:
Leading structure-based and/or ligand-based drug design for one or more targets
Maintaining up-to-date knowledge of the scientific literature relevant to assigned targets
Optimizing the binding affinity of peptide derivatives while simultaneously enhancing their oral stability and pharmacokinetic properties
Utilizing computational drug-design tools (such as database searching, molecular docking, molecular dynamics (MD) simulations, and scoring functions) to design biologically active molecules
Interpreting and integrating structural, biological assay, stability, mutagenesis, sequencing, and pharmacological data to guide the design of biologically active compounds
Requirements:
PhD in computational chemistry or a closely related discipline
Proven translational experience advancing projects toward IND candidates
In-depth knowledge of constrained peptides, peptidomimetics, and macrocycles
Practical experience optimizing the stability of peptides and/or macrocycles
Proficiency in writing scripts and programs
Hands‑on experience with pharmacophores
Proven expertise in applying molecular modeling methods to structure-based and/or ligand-based drug discovery
Thorough understanding of molecular recognition principles
Thorough understanding of the drug design literature
Hands‑on experience with a broad range of computational methods, including virtual screening, programming, statistical analysis, data analysis, molecular docking, molecular dynamics, and ADME modeling
Deep knowledge of advanced computational chemistry techniques, including FEP, ML, and QSAR
The base pay range for this position at commencement of employment is expected to be between $180K and $220K a year; however, base pay offered may vary depending on multiple individualized factors, including market location, job-related knowledge, skills, and experience.
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Newark, CA
Job Id:
401
# of Openings:
0
Job Description:
Protagonist Therapeutics is seeking a talented and highly motivated computational chemist to join our Drug Design group. The successful candidate will leverage proprietary molecular modeling tools, commercial software packages, and AI algorithms to design novel compounds and optimize existing leads. Protagonist is advancing the development of orally stable peptides, peptidomimetics, and small molecules. The ideal candidate will hold a PhD in computational chemistry, bioinformatics, artificial intelligence, or a related discipline and will have broad hands‑on experience across all aspects of molecular design that directly impact IND candidate selection. In addition, the candidate must be well versed in molecular recognition, structure‑activity relationship (SAR) development, and potency optimization. Strong familiarity with public‑domain sequence, functional, and structural databases, along with extensive scripting and programming expertise, is required. Knowledge of AI‑driven drug design is highly desirable. The ideal candidate will also possess significant expertise in constrained peptides, macrocycles, peptide engineering, and small‑molecule design. The candidate must be well versed in the relevant scientific literature and demonstrate proven hands‑on experience in structure‑based drug design within an industrial setting.
Duties and Responsibilities include:
Leading structure-based and/or ligand-based drug design for one or more targets
Maintaining up-to-date knowledge of the scientific literature relevant to assigned targets
Optimizing the binding affinity of peptide derivatives while simultaneously enhancing their oral stability and pharmacokinetic properties
Utilizing computational drug-design tools (such as database searching, molecular docking, molecular dynamics (MD) simulations, and scoring functions) to design biologically active molecules
Interpreting and integrating structural, biological assay, stability, mutagenesis, sequencing, and pharmacological data to guide the design of biologically active compounds
Requirements:
PhD in computational chemistry or a closely related discipline
Proven translational experience advancing projects toward IND candidates
In-depth knowledge of constrained peptides, peptidomimetics, and macrocycles
Practical experience optimizing the stability of peptides and/or macrocycles
Proficiency in writing scripts and programs
Hands‑on experience with pharmacophores
Proven expertise in applying molecular modeling methods to structure-based and/or ligand-based drug discovery
Thorough understanding of molecular recognition principles
Thorough understanding of the drug design literature
Hands‑on experience with a broad range of computational methods, including virtual screening, programming, statistical analysis, data analysis, molecular docking, molecular dynamics, and ADME modeling
Deep knowledge of advanced computational chemistry techniques, including FEP, ML, and QSAR
The base pay range for this position at commencement of employment is expected to be between $180K and $220K a year; however, base pay offered may vary depending on multiple individualized factors, including market location, job-related knowledge, skills, and experience.
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