Structural Engineer Jobs in Portland, IN (NOW HIRING)

At Apheris, we are building the future of how AI is applied in pharmaceutical R&D. We enable leading pharmaceutical teams to discover and develop drugs faster by hosting the industry's largest federated data networks for drug discovery AI, spanning co-folding, ADMET, and antibody developability. Across these networks, models are trained on proprietary industry datasets to achieve higher performance and broader applicability while keeping data control and IP protected.

We deliver these superior models through drug discovery applications that enable teams to run them at scale, further customize them, and integrate them into existing R&D workflows. AI Structural Biology (AISB) Network: Eight top-20 pharma companies collaborate in the field of co-folding, structure-based binding affinity predictions and antibody design. ADMET Network: Five top-50 pharma and biotechs collaborate to improve small-molecule property prediction and expand to further drug modalities (e.g., PROTACs).

Antibody Developability Network: Pharma partners collaborate to federate historical and purpose-built antibody developability datasets for secure ML training, without data leaving each partner's environment. About the role We are looking for a hands‐on Senior Software Engineer to build and evolve the backend systems that power Apheris' federated computing platform. In this IC3 role, you will be a strong individual contributor with end‐to‐end ownership of meaningful technical scope.

You will design, implement, deploy, and operate backend services used in production by leading pharmaceutical companies. While this role does not include people management, it requires technical leadership through example, strong ownership, and active collaboration across teams. You will work closely with other software engineers, ML engineers, quality engineers, and product to deliver reliable, secure, and scalable systems.

This role is ideal for someone who enjoys shipping high‐quality software in a fast‐moving startup environment, takes pride in execution, and is motivated to continuously improve both the product and the way we build it. What you will do Design, build, and maintain backend services and APIs, primarily in Golang, with Python used where it best fits the problem domain. Develop, deploy, and operate software across both cloud and on‐premise environments, leveraging Docker and Kubernetes as core platform technologies.

Collaborate closely with cross‐functional teams across engineering, quality, and product to deliver cohesive, end‐to‐end product functionality. Take end‐to‐end ownership of features, from technical design and implementation through deployment, monitoring, and ongoing operation in production. Contribute to system design and architectural discussions, helping evolve backend and platform components as the product and customer base scale.

Write high‐quality, maintainable, and well‐tested code, and actively participate in code reviews to uphold strong engineering standards. Improve reliability, performance, security, and observability of services running in distributed and resource‐intensive environments. Debug and resolve issues across application code, containerized workloads, and infrastructure layers in both customer and internal environments.

Continuously look for ways to improve development efficiency and software quality by adopting better tooling, workflows, and emerging technologies - including experimenting with modern developer tools and AI‐assisted workflows where they add real value. Stay curious and proactive about learning new approaches, technologies, and best practices, and apply them pragmatically in a fast‐moving startup environment. What we expect from you A degree in computer science, engineering, or equivalent hands‐on experience in professional software engineering roles.

4+ years of professional experience as a software engineer, with a strong focus on backend systems. Strong programming skills in Golang, with practical experience using Python where it is the best fit for the problem domain. Hands‐on experience designing, building, and operating production‐grade backend services and APIs.

Solid experience working with Docker and containerized applications in production environments. Practical experience with Kubernetes, including deploying, operating, and debugging cloud‐native workloads. Experience working with AWS or another major cloud provider, ideally in hybrid environments that include on‐premise deployments.

Strong understanding of software engineering best practices, including testing strategies, code quality, and secure API design, with knowledge of common application security risks and how to mitigate them. A strong sense of ownership and accountability for technical outcomes, including reliability and long‐term maintainability. Comfortable working in a fast‐paced, iterative startup environment where priorities evolve and trade‐offs are part of daily decision‐making.

Curiosity and willingness to continuously learn and adopt new tools, workflows, and technologies to improve development efficiency and software quality. Excellent communication skills and fluency in English (verbal and written). Nice to have Experience building or operating distributed systems.

Experience working on systems with elevated security and privacy requirements. Experience supporting customers in production environments, including debugging issues and communicating technical context clearly and pragmatically. Experience with CI/CD pipelines and infrastructure‐as‐code.

Prior exposure to life sciences, machine learning platforms, or data‐intensive products (not required). Interest in federated systems, privacy‐preserving computation, or secure data collaboration. What we offer you Industry‐competitive compensation, including early‐stage virtual share options.

Remote‐first working – work where you work best, whether from home or a co‐working space near you. Great suite of benefits, including a wellbeing budget, mental health benefits, a work‐from‐home budget, a co‐working stipend, and a learning and development budget. Generous holiday allowance.

Office Days at our Berlin HQ or a different European location (3x a year). A fun, diverse team of mission‐driven individuals with a drive to see AI and ML used for good. Plenty of room to grow personally and professionally.

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