Scientist II Biomolecular Simulations Comp Chemistry

About this position: We are seeking a highly talented and motivated Scientist with expertise in Biomolecular Simulations to join our team in San Diego to advance Neomorph’s small-molecule drug discovery programs. As part of a multi-disciplinary team comprising of leaders in the field of targeted protein degradation, the suitable candidate will develop, implement and apply advanced physics-based and AI/ML computational methods to establish novel approaches for Drug Discovery and selection of therapeutic targets. This is a highly collaborative position that will focus on understanding the mechanistic details of small molecule mediated protein-protein interactions to enable the discovery of novel, more efficient, and selective degraders. Job responsibilities: Develop computational tools to predict small-molecule changes in protein-protein interactions and apply it to prioritize targets of interest. Identify and apply novel methods to predict dynamic ligandable sites. Use internal data such as affinity and protein degradation to develop, validate, and deploy high-accuracy scoring functions of ligand-PPI using Binding Free Energy and AI/ML methods. Implement and integrate high-throughput physics-based methods such as docking, molecular dynamics, free energy as well as AI/ML approaches to enable an efficient structure-based drug design environment. Collaborate with medicinal chemists to translate computational predictions into ligand designs and compound prioritization. Collaborate effectively within cross-functional teams, providing computational insights and expertise to support project goals and timelines. Stay up-to-date with the latest advancements in molecular dynamics, protein degradation, and drug discovery fields, and proactively apply new techniques and methodologies to improve project outcomes. Contribute to scientific publications, patents, and presentations to communicate research findings and contribute to the intellectual property portfolio of the company. Required Qualifications: Ph.D. in Computational Chemistry, Computational Biology, Computational Biophysics or related field with 2+ years of relevant industry experience. Knowledge and expertise in the use of molecular dynamics, enhanced sampling methods and free energy approaches applied to drug design. Background in the computational prediction of protein-protein interaction. Experience with molecular dynamics software such as AMBER, GROMACS, OpenMM and NAMD. Robust coding experience using modern scientific languages (Python/C++/etc.). Experience with Python API to analyze protein dynamics and protein-ligand interaction, i.e., (MDTraj, MDAnalysis, and Schrodinger Python API). Mastery of Linux OS and command-lines. Experience in distributed computing using HPC clusters or cloud platforms. Preferred Qualifications: Ability to communicate, collaborate, and deliver results as a member of multi-disciplinary teams. Basic knowledge of medicinal chemistry principles. Experience with commercial computational chemistry packages such as Schrodinger, Openeye or others is a plus. Experience with LLM protein structure prediction methods. Physical chemistry background and knowledge of organic chemistry. Experience with computational approaches to fragment-based ligand design or DNA-encoded libraries. What we offer: Industry competitive compensation Annual target bonus Stock options 401K plan Career advancement opportunities Monthly town halls to share business and scientific updates Work Hard, Stay Well Comprehensive medical, dental, and vision plans for employees and their dependents Health and Dependent Care FSA and HSA Plan with monthly Neomorph contribution Employee Assistance Program 10 holidays + Winter Shutdown + 3 weeks of vacation time with additional accruals after 2nd year of employment, separate sick leave. Supplemental pay for Pregnancy Disability Leave Paid Parental Leave for employees with a newborn child or a child placed with them for adoption or foster care Lifestyle Casual work environment Volunteer days off each year to spend time contributing to causes you care about Flexible work schedule Access to an onsite gym Onsite space to store your bicycle (or surfboard) Have Fun! We believe in work/life balance, and Fun is at the core of our Core Values. In addition to department and company happy hours, we have regular company-wide and department lunches and social events (e.g., Padres games, summer picnic, holiday party, bring your kids to work day). About Us: Neomorph is a venture-backed biotechnology company solving critical problems in human health through the discovery and development of innovative new medicines against ‘undruggable targets’. Our team is comprised of industry-leading experts in protein degradation and molecular glues who have a track record of ground-breaking discoveries in the field. We are committed to leadership in advancing the science and technology of molecular glue drug discovery, while prosecuting a pipeline of projects through clinical development. Our patient-first, science-driven approach is complemented by our dedication to a supportive and collaborative work environment. Neomorph is headquartered in San Diego, California, and has a key collaboration with the Center for Protein Degradation at the Dana-Farber Cancer Institute. Neomorph is committed to pursuing and hiring a diverse workforce and is proud to be an equal-opportunity employer. All qualified applicants will receive consideration for employment and will not be discriminated against on the basis of any characteristic protected by applicable federal, state, or local law.

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