Role overview

Qualifications

BSc, MSc, PhD or equivalent in cheminformatics, computational chemistry, or a related field
3+ years preparing biological assay data in a discovery setting
Fluency in Python and RDKit
Good engineering code writing skills including version control and modular scripting

Responsibilities

Define and own the binding-data preparation protocol
Build tooling for data preparation with modular scripts and validators
Work forward-deployed with pharma representatives to walk them through protocols
Curate the public binding-data foundation to standard for model training

Key facts

Remote from: Europe
Full time
Mid-level (2-5 years)
English

Hard skills

Python (Programming Language) Data Binding Custom Scripting Version Control Federated Database Systems

Other skills

Collaboration
Problem Solving
Communication

About the company

Apheris

Artificial Intelligence & Machine Learning Services

Apheris is on a mission to collaboratively solve the largest problems our planet is facing by enabling organizations to securely build and deploy data applications and AI across boundaries. Our product enables governed, private, secure data access for ML and analytics. As model architectures become increasingly commoditized, data becomes an organization’s key differentiator. However, businesses need to safeguard their data assets and IP while leveraging it for ML. The Apheris Compute Gateway ensures only approved computations can be launched on that data and enables federation across organizational boundaries, allowing ML-powered insights with no need to centralize data, while ensuring compliance with data privacy, security, and governance obligations. Founded in 2019, Apheris is backed by top investors and tech industry innovators, including Octopus Ventures, Heal Capital, LocalGlobe, another.vc, MuleSoft founder Ross Mason (Dig Ventures), and Twitter board chairman and former CFO of Google, Patrick Pichette.

Company details

Company typeStartup

IndustryArtificial Intelligence & Machine Learning Services

Company size11 - 50

Links

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Job description

About Apheris

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. We host 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:Pharmaceutical companies collaborate in the field of co-folding, structure-based binding affinitypredictionsand antibody design.
ADMET Network:Pharmaceutical and biotech companies collaborate to improve small-molecule property prediction and expandinto further drug modalities.
Antibody Developability Network:Pharma partners collaborate to federate historical and purpose-built antibodydevelopabilitydatasets for secure ML training, without data leaving each partner’s environment.

About the role

We are looking for a Forward-Deployed Cheminformatician to own how binding data is prepared across our co-folding focused networks and initiatives. Binding data is the input that decides whether our co-folding and binding-affinity models perform in real drug programs. It arrives from pharma partners in heterogeneous shapes — different assay registries, different metadata, different chemical-representation standards, different choices on qualifiers, replicates and censoring. We need someone who turns this into a repeatable, well-documented preparation pipeline that pharma representatives can run alongside us, and that scales to the public-data corpus we build for our own model training.
This is half engineering, half forward-deployed work. You will define the protocol, harden it with validators and scripts, integrate it into the Apheris products, run it with each new partner, and own the equivalent pipeline for the public binding-data corpus.

What you will do

Define and own the binding-data preparation protocol — data schema, small-molecule standardization, assay metadata model, value handling (KD, Ki, IC50, pIC50), qualifier and censored-value handling,duplicateand replicate aggregation.
Build the tooling that runs it — modular scripts, validators with actionable errors, and reusable pipelines that survive different pharma upstream systems (Dotmatics, Spotfire, in-house registries).
Workforward-deployedwith pharma. Sit with their biologists and medicinal chemists, walk them through the protocol, sense-check what an assay columnactually measures, and unblock retrieval.
Maintain the small-molecule representation pipeline —RDKitstandardization, tautomer and ionization handling, stereochemistry preservation,andPAINS / frequent-hitter filtering.
Curate the public binding-data foundation —ChEMBL,BindingDB, PubChemBioAssay— prepared to the same standard, so our models train on the strongest public baseline anyone can assemble.
Hand the productized pipeline cleanly toengineering for scaling, and partner with ML to keep the data contractvalid asmodels and networks evolve.

What we expect from you

You should apply if:

You have a BSc, MSc, PhD or equivalent in cheminformatics, computational chemistry, or a related field, plus 3+ years preparing biological assay data in a discovery setting.
You are fluent in Python andRDKit. SMILES normalization, tautomer / ionization / stereochemistry handling, and scaffold extraction are second nature, and you understand why eachmattersfor activity cliffs and model training.
You have hands-on experience curating quantitative binding assay data (KD, Ki, IC50, pIC50) and HTS data — censored values, qualifiers, duplicates, replicate aggregation, and assay metadata interpretation.
You write good engineering code — version control, tested modular scripts, validators that return useful errors.
You are comfortable forward-deployed with pharma medicinal chemists and biologists. You can sit in a sense-check meeting, pull out what isactually meantby a column label, and encode that back into the protocol.
You enjoy turning a messy ad-hoc cleaning job into a repeatable protocol others can run.

Bonus points if:

You have practical familiarity with publicbinding-datasources (ChEMBL,BindingDB, PubChemBioAssay) and the gotchas in each.
You have applied LLM tooling (Claude, Codex, Cursor) to accelerate data cleaning or metadata harmonization.
You have worked across institutional data boundaries — federated, multi-party, or otherwise — where the data-preparation contracthas toholdunder partial visibility.
You have a publication record or open-source contributions in cheminformatics or quantitative pharmacology.

What we offer you

Industry-competitive compensation, including early-stage virtual share options
Remote-first work — work where you work best
Wellbeing budget, mental health support, work-from-home budget, co-working stipend, and learning budget
Generous holiday allowance
Office Days at our Berlin HQ or a different European location (3x per year)
A high-calibre, execution-focused team with experience from leading organizations