Computational Chemistry Software Developer Jobs (NOW HIRING)

General Proximity is a seed-stage startup developing the next generation of induced proximity medicines (IPMs). Our OmniTAC drug discovery engine furnishes molecules that co-opt existing cellular machinery to overcome therapeutic challenges, which have remained unapproachable to other modalities for decades.

We are seeking a first-rate computational chemist to help us pioneer this uncharted frontier of drug discovery.

A long-standing challenge in drug discovery is the development of molecules capable of modulating difficult or "undruggable" targets. Disease-causing proteins can be dysfunctional in many different ways, but our armamentarium for fixing them is quite limited. The most common mechanism of action for FDA-approved drugs is inhibition[1], but there are many other possible perturbation types whose potential remains unrealized.

General Proximity is a seed-stage drug discovery company developing a novel platform technology to solve this problem. We make bifunctional drugs that induce the modification of drug targets by existing cellular machinery (rather than through direct modulation by the drug, the classical approach).

Historically, the development of technologies that allow one to push new buttons in biology has been an incredibly fertile field for the discovery of new medicines[2, 3, 4], and our technology holds the same promise.

We are seeking an experienced Head of Computational Chemistry to build and lead our computational chemistry, cheminformatics, and molecular design capabilities. This role will drive small-molecule drug discovery programs by providing strategic and practical modeling support, implementing modern computational workflows, and building the cheminformatics and AI-enabled infrastructure needed to empower medicinal chemists and project teams. 

The successful candidate will be both a scientific leader and a hands-on drug designer: someone who can partner closely with medicinal chemists, structural biologists, biologists, and DMPK scientists to guide compound design from hit identification through lead optimization and candidate selection. They will also deploy practical tools that improve decision-making, accelerate design-make-test-analyze cycles, and make computational and AI-driven methods accessible to bench chemists. 

The ideal candidate is a computational drug hunter who combines deep technical expertise with practical medicinal chemistry judgment. This person should not be an isolated modeler, but a true project partner who sits with chemistry teams, understands the design problem, proposes molecules, helps interpret data, and builds tools that make the broader organization faster and smarter. 

This role is ideal for someone who has worked in a pharma or biotech computational chemistry group and wants to build a modern, AI-enabled computational platform from the ground up while remaining directly involved in molecule design. 

This is an on-site position with flexible working hours.

What You'll Do 

Computational Chemistry and Molecular Design 

• Provide hands-on computational chemistry support to small-molecule discovery programs from target evaluation, hit identification, hit-to-lead, and lead optimization through candidate nomination. 
• Apply structure-based and ligand-based design approaches to guide compound design, including docking, molecular dynamics, pharmacophore modeling, QSAR, scaffold hopping, virtual screening, FEP/free-energy methods, and multi-parameter optimization. 
• Use structural biology data, including X-ray structures, cryo-EM structures, homology models, and AlphaFold-derived models, to generate actionable design hypotheses. 
• Partner with the medicinal chemistry team to interpret SAR, optimize potency, selectivity, physicochemical properties, ADME/PK, developability, and synthetic feasibility. 
• Lead computational design discussions with project teams and translate complex modeling results into clear, practical medicinal chemistry recommendations. 
• Support portfolio prioritization by evaluating target tractability, ligandability, binding-site quality, chemical matter, and developability risks. 

Cheminformatics and Data Infrastructure 

• Build and maintain a scalable chem and bioinformatics infrastructure to support compound registration, structure-searching, SAR analysis, property visualization, compound triage, library design, and project decision-making. 
• Implement tools for chemical data handling, including similarity and substructure searching, R-group analysis, matched molecular pairs, reaction enumeration, compound clustering, property prediction, and visualization. 
• Work with internal or external engineering and data science teams to integrate chemical, biological, DMPK, structural, and assay data into usable project dashboards and design tools. 
• Establish best practices for chemical data quality, assay-data curation, compound annotation, metadata standards, and reproducible computational workflows. 
• Evaluate, implement, and maintain commercial and open-source computational tools, including platforms such as Schrodinger, MOE, CCDC tools, ChemAxon, KNIME, Pipeline Pilot, RDKit, DataWarrior, Spotfire, and related systems. 

AI/ML and Digital Chemistry Tools 

• Lead the practical implementation of user-friendly AI/ML-enabled molecular design tools, including generative chemistry, predictive ADME/Tox models, property prediction, active learning, virtual screening, and decision-support systems. 
• Identify opportunities to incorporate AI tools into the DMTA cycle, including compound prioritization, library design, synthetic route ideation, molecular-property prediction, and design hypothesis generation. 
• Promote AI literacy across chemistry and project teams by training scientists on appropriate use, limitations, and interpretation of predictive models. 
• Build workflows that allow medicinal chemists to use modeling and AI tools without requiring deep computational expertise. 

Leadership and Strategy 

• Define the computational chemistry strategy for the company and align it with discovery portfolio needs. 
• Serve as the internal subject-matter expert for computational chemistry, cheminformatics, AI-enabled design, and molecular modeling. 
• Establish external collaborations with CROs, software vendors, academic groups, AI drug discovery companies, and computational chemistry consultants where appropriate. 
• Represent computational chemistry in portfolio reviews, program strategy discussions, investor diligence, scientific advisory board meetings, and external collaborations. 
• Maintain awareness of emerging computational, AI, and cheminformatics technologies and recommend adoption where scientifically and operationally justified. 

High Agency. Initiative, independence, and self-accountability are some of our most valued traits.

Enthusiastic. We love people who are excited about what they are doing and are generally attempting to build a high-energy team.

Intensity and Grit. Early-stage startups are hard. Drug discovery is doubly so. We are looking for candidates who have a demonstrated ability to stick with complex problems for the long haul, with a team that has your back along the way.

Prosocial. We are here to create life-saving medicines for the patients who need it most. You should be, too.

• PhD in Computational Chemistry, Medicinal Chemistry, Chemical Physics, Biophysics, Cheminformatics, Physical Organic Chemistry, or a related discipline
• A minimum of 15 years of relevant experience in pharma, biotech, or a drug discovery-focused research environment
• Demonstrated track record of using computational chemistry to impact small-molecule drug discovery programs, ideally through lead optimization, candidate selection, IND-enabling studies, or clinical development
• Deep expertise in structure-based drug design, ligand-based design, docking, molecular dynamics, virtual screening, QSAR, FEP/free-energy methods, pharmacophore modeling, and multi-parameter optimization
• Strong working knowledge of medicinal chemistry principles, SAR interpretation, physicochemical property optimization, ADME/PK concepts, and developability considerations
• Practical experience with cheminformatics platforms, chemical databases, chemical data curation, compound registration systems, and project-facing visualization tools
• Experience with AI/ML applications in molecular design, including predictive modeling, generative chemistry, active learning, or AI-enabled compound prioritization
• Strong programming or scripting ability, preferably Python, with experience using cheminformatics toolkits such as RDKit and modern data science workflows
• Ability to communicate complex computational concepts clearly to medicinal chemists, biologists, executives, and non-specialist stakeholders
• Demonstrated ability to lead cross-functional teams, mentor scientists, and influence project strategy without relying solely on formal authority
  
• Nice to have:
  • Experience building computational chemistry or cheminformatics capabilities in a biotech or fast-moving discovery organization
  • Experience implementing user-friendly modeling tools for medicinal chemists
  • Familiarity with cloud-based or high-performance computing environments
  • Experience with automated DMTA workflows, electronic lab notebooks, compound management systems, assay-data systems, and integrated discovery platforms 
  • Experience supporting discovery across multiple modalities, such as covalent inhibitors, molecular glues, degraders, etc. 
  • Familiarity with synthetic accessibility prediction, retrosynthesis tools, reaction enumeration, and library design
  • Strong external scientific reputation through publications, presentations, patents, open-source contributions, or demonstrated project impact

• Strong equity incentives. We are looking for candidates who will bring a strong sense of ownership to drive their project areas forward, and we believe that you deserve to be compensated accordingly.
• Top tier medical, dental, and vision coverage + One Medical membership.
• 401(k) retirement plans.
• Education and health/fitness incentive programs.
• Meditation retreats-do a ten-day Vipassana retreat without counting towards vacation days. 
• Reading budget! We will buy you books.
• Located in the MBC BioLabs at 135 Mississippi Street, an entrepreneurial hub full of the best scientists and operators the Bay Area has to offer. Our lab is a very short walk from the 22nd St Caltrain Station and a number of wonderful restaurants and cafes.

Work Hard/Play Hard. We believe time is our most valuable commodity, so we strive to create a culture that reflects this. We won't drag you through unnecessary meetings or email you at 7 PM on a Saturday. When we're at work, we're there to get things done, and when we're off, we're really off.

Strong Communication. We like well-written documents over PowerPoints, OKRs over vague mission statements, and weekly one-on-ones over yearly reviews.

Writing First. We have a "writing-first" culture. We believe that clarity of writing reflects clarity of thinking and that the benefits of well-written documentation in a scientific environment are innumerable: democratization of ideation and decision-making, increased reproducibility, quicker scaling and onboarding, and better company-wide alignment, to name a few.

Growth. As an early-stage startup, we value scientists with an independent, can-do attitude. The more hats you can wear, the better. Our job as employers is to put you in positive feedback loops so you can grow in the direction of your choosing.

Title and compensation commensurate with experience. Applications from candidates of diverse backgrounds, women, and members of underrepresented minority groups are particularly welcomed. We look forward to hearing from you. :)

More info at jobs.generalproximity.bio