Freddie Martin

Ph.D. in Protein Design · Senior Scientist @ Schrödinger

Stroud, England, United Kingdom · GMT

Freddie Martin

About

My passion is to use advances in AI and a rational understanding of atomic interactions to develop new knowledge, tools, and therapies. I started out interested in small-molecule drug discovery, which led me to research the sequence-to-structure relationships dictating a protein's final fold, and how to design new protein–protein interactions and novel protein architectures to deliver new technologies and treatments for disease.

Experience

Senior Scientist I

2025 – Present
Computational biology and biologics modelling at Schrödinger. Working with internal and external partners to apply physics-based and AI methods across drug discovery campaigns, with a focus on protein design and engineering.

Postdoctoral Research Associate

2022 – 2025
Established a protein design pipeline in a new laboratory, leveraging AI and molecular biology for de novo protein design with a focus on therapeutic applications. Implemented and integrated state-of-the-art models (RFdiffusion, ProteinMPNN, AlphaFold, ESMFold, BindCraft) onto a local GPU cluster via Slurm for high-throughput in silico pipelines. Ran molecular dynamics simulations to evaluate designs and probe membrane-protein and ion-channel mechanisms. Mentored students and postdocs in protein design, organised group retreats and the NNF CPR Symposium, and contributed to grant writing and a review article.

Postdoctoral Research Associate

2022
Short post-PhD position writing up manuscripts from PhD projects, including internal and international collaborations.

PhD Candidate · Woolfson Lab

2017 – 2022
Thesis: Exploring the Dynamic and Conformational Landscape of α-Helical Peptide Assemblies. Combined rational design with computational tools (ISAMBARD, AMBER, AutoDock, Rosetta, AlphaFold2/RoseTTAFold) and biophysics (CD, AUC, SEC, fluorescence, X-ray crystallography, TEM, SAXS) to understand sequence-to-structure relationships in coiled coils and design improved assemblies. Secured beamtime at Diamond and ESRF and supervised MSc students.

GSK

Industrial Placement Student · DMPK / BST

2015 – 2016
Bioanalytical Sciences and Toxicokinetics group within DMPK. Developed and validated analytical methods for measuring drugs and metabolites in biological matrices to GLP standards.

Education

University of Bristol

2017 – 2022
Ph.D., Chemical Synthesis CDT — Protein Design (Woolfson Lab)

University of Bath

2013 – 2017
MChem, Chemistry for Drug Discovery with Industrial Training

Selected Publications

Validation and analysis of 12,000 AI-driven CAR-T designs in the Bits to Binders competition

2026

bioRxiv · de novo binders · CAR-T · benchmarking

A global competition benchmarking de novo binder design as CAR-T binding domains against human CD20. 12,000 designs from 42 countries were screened by pooled CAR-T proliferation, with retrospective filters nearly doubling success rates.

Structure of a contractile injection system in Salmonella enterica subsp. salamae

2025

bioRxiv · cryo-EM · bioinformatics

High-resolution cryo-EM structure of an extracellular contractile injection system, revealing a unique sheath architecture and a previously unannotated cluster of CISs. Contributed bioinformatic analysis and wet-lab support.

Full publication list on Google Scholar and ORCID.

Projects

protein design · machine learning · team leadership

Designed binders against a cancer antigen target as part of the AmigoAcids team in the UT Austin BioML Society challenge. Combined a wide variety of AI design tools with a uniform validation pipeline, achieving a 6 % (11/187) hit rate in the proliferation screen and placing 2nd overall. Helped lead a remote, international team and mentored newer members on protein design fundamentals.

Science Illustration

2023 – Present

Blender · ChimeraX · scientific communication

Renders and graphical abstracts that aim to capture the function and beauty of biological macromolecules — from membrane transporters to contractile injection systems. Get in touch if you'd like to commission or collaborate on a piece.

Skills

Protein Design
Structural Biology
Bioinformatics
Molecular Dynamics
Cryo-EM & SAXS
X-ray Crystallography
Biophysics (CD / AUC / SEC)
Peptide Synthesis
Drug Discovery
Scientific Communication
Mentoring & Leadership

Tech Stack

Python
PyTorch
RFdiffusion
ProteinMPNN
AlphaFold / ESMFold
BindCraft
Rosetta
ISAMBARD
AMBER
AutoDock
Schrödinger Suite
Slurm / Bash
R
Blender
ChimeraX / PyMOL

Certifications & Awards

Demo2Win! 2026 Masterclass

2026

2Win! Global

Introduction to Computational Antibody Engineering

2025

Schrödinger

EMBO Laboratory Leadership Course

EMBO

Volunteering

Student Mentor

2025 – Present

The Social Mobility Foundation

Mentoring aspiring students from diverse socioeconomic backgrounds who are pursuing higher education and careers in biology and chemistry — providing personalised advice on university applications, career pathways and professional skills.

Event Coordinator

2023

Pint of Science Denmark

Coordinated logistics and hosted Pint of Science Copenhagen at the Dispensary.