Associate Scientist II, Molecular & Computational Biology

Job Description

Job Description

About Tonix*

Tonix is a fully integrated biotechnology company, publicly traded on NASDAQ (ticker: TNXP), with marketed products and a pipeline of development candidates The Company is focused on commercializing, developing, discovering, and licensing therapeutics to treat and prevent human disease. In August 2025, Tonix received FDA approval for Tonmya™ (cyclobenzaprine HCl sublingual tablets), a first-in-class, once-daily, non-opioid treatment for fibromyalgia. Tonmya is the first new fibromyalgia therapy approved in over 15 years, following successful Phase 3 trials demonstrating significant symptom improvement. Commercial launch is expected in the fourth quarter of 2025. Tonix also markets Zembrace® SymTouch® (sumatriptan injection) 3 mg and Tosymra® (sumatriptan nasal spray) 10 mg, both indicated for the treatment of acute migraine with or without aura in adults.

Tonix’s development portfolio includes product candidates in central nervous system (CNS), immunology, immuno-oncology infectious disease and rare disease. The CNS pipeline features both small molecules and biologics to treat pain, neurologic, psychiatric, and addiction conditions. The immunology portfolio includes biologics to address organ transplant rejection, autoimmunity, and cancer. The infectious disease pipeline includes a vaccine in development to prevent smallpox and monkeypox, which also serves as a live virus vaccine platform for other infectious diseases. Finally, the rare disease portfolio includes a product in development for Prader-Willi syndrome, which has both orphan drug designation and rare pediatric disease designation grants from the FDA.

Tonix owns and operates a state-of-the art infectious disease research facility in Frederick, Md.

Please visit for specifics on the pipeline.

*All of Tonix’s product candidates are investigational new drugs or biologics and have not been approved for any indication.

Position Overview

Tonix Pharmaceuticals is seeking a highly motivated Associate Scientist to join our multidisciplinary R&D team at the Frederick Research & Development Center. This role integrates computational protein structure analysis with hands-on molecular biology and protein biochemistry. The successful candidate will contribute to host-directed therapeutic discovery, antiviral platforms, and vaccine design by combining AI/ML-based protein modeling with molecular biology and protein science to generate, express, and analyze protein targets.

Key Responsibilities

• Perform protein structure modeling and design using platforms such as AlphaFold2/3, ESM, RFdiffusion, ProteinMPNN, and NetMHC.
• Build and refine bioinformatics workflows for large-scale sequence and structural analysis of host and viral proteins
• Perform molecular cloning, PCR, DNA and RNA isolation, bacterial transformation, and mutagenesis to generate expression constructs.
• Carry out protein expression and purification followed by protein characterization
• Collaborate with Tonix’s imaging and cell biology teams to translate computational predictions into testable hypotheses in assays and animal models.
• Contribute to the development of user-friendly computational pipelines and visualization tools for internal scientists.
• Document and communicate results in reports, regulatory filings, and presentations to internal teams, collaborators, and external partners.
• Maintain awareness of emerging computational biology technologies to enhance Tonix’s drug discovery capabilities.

Required Qualifications

• B.S. or M.S. in Microbiology, Biochemistry, Bioinformatics, Computational Biology, or related field.
• Hands-on experience with protein structure prediction and computational protein design tools.
• Familiarity with core molecular biology and protein biochemistry methods (PCR, cloning, bacterial expression, Western blotting).
• Strong communication skills and ability to work in cross-functional teams within Tonix’s integrated discovery pipeline.

Preferred:

• Experience with cloud computing platforms (Google Cloud, AWS) for large-scale protein modeling.
• Exposure to machine learning approaches in protein design and immunology.
• Prior experience with protein engineering for therapeutic applications.
• Track record of contributions to publications, posters, or conference presentations.
• Proficiency in Python, especially ML/AI packages. Experience in Linux operating systems and shell programming is desirable.

Recruitment & Staffing Agencies

Tonix does not accept agency resumes unless contacted directly by internal Tonix Talent Acquisition. Please do not forward resumes to Tonix employees or any other company location; Tonix is not responsible for any fees related to unsolicited resumes.

Compensation & Benefits

Annualized base salary ranges from $60,000 to $90,000 plus target incentive; actual salaries will vary and may be above or below this range commensurate with several factors including experience, education, training, location, and merit.

Tonix provides a comprehensive compensation and benefits package which includes:

• Medical, Dental & Vision Insurance, Basic and Voluntary Life and AD&D Insurance, Short- and Long-Term Disability Insurance, Flexible Spending Accounts, Health Savings Account, and Employee Assistance Programs
• Pet Insurance
• Retirement Savings 401k with company match and annual discretionary stock options
• Generous Paid Time Off, Sick Time, & Paid Holidays
• Career Development and Training

Tonix provides equal employment opportunities (EEO) to all employees and applicants for employment without regard to race, color, religion, sex, national origin, age, genetics, or any other characteristic protected by law.  In addition to federal law requirements, Tonix complies with applicable state and local laws governing nondiscrimination in employment.  This policy applies to all terms and conditions of employment, including recruiting, hiring, placement, promotion, termination, layoff, recall, transfers, leaves of absence, compensation, and training.  Tonix expressly prohibits any form of workplace harassment based on race, color, religion, gender, sexual orientation, gender identity or expression, national origin, age, genetic, information, disability, veteran status, or any other characteristic protected by law.