AtomicLevel Cryo-EM

AtomicLevel Cryo-EM

Structure Tells You What Sequence Cannot

Knowing that an antibody binds is not enough. Knowing exactly where it binds, which residues drive affinity and selectivity, and how the antibody physically engages its target — that is the information that separates a good lead from a clinical candidate. FairJourney Bio's AtomicLevel Cryo-EM platform delivers that information, at atomic resolution, in under four weeks.

Discuss Your Structural Biology Requirements

Structure Tells You What Sequence Cannot

Knowing that an antibody binds is not enough. Knowing exactly where it binds, which residues drive affinity and selectivity, and how the antibody physically engages its target — that is the information that separates a good lead from a clinical candidate. FairJourney Bio's AtomicLevel Cryo-EM platform delivers that information, at atomic resolution, in under four weeks.

Discuss Your Structural Biology Requirements

Structure Tells You What Sequence Cannot

Knowing that an antibody binds is not enough. Knowing exactly where it binds, which residues drive affinity and selectivity, and how the antibody physically engages its target — that is the information that separates a good lead from a clinical candidate. FairJourney Bio's AtomicLevel Cryo-EM platform delivers that information, at atomic resolution, in under four weeks.

Discuss Your Structural Biology Requirements

<5 weeks

high-resolution structure delivered

<3.5 Å

density map resolution

<12 weeks

epitope-based hit discovery post terminal bleed

300 kV

5th generation Titan Krios microscopes, San Diego

What AtomicLevel Cryo-EM Solves Across the Value Chain

Structural data is not a late-stage validation tool. At every stage of antibody discovery and development, the right structural question, answered at the right time, accelerates decisions and reduces risk. AtomicLevel Cryo-EM is built to answer those questions at the speed your programme demands.

Target Validation

What epitope do we need to target?

Structure Validation service: determine the 3D structure of your target protein to guide immunisation strategy and confirm the target is druggable at the intended site.

Hit Discovery

Fastest way to find an epitope-specific antibody?

Epitope-Based Hit Discovery service: a structure-first discovery workflow that uses cryo-EM to select epitope-specific, high-affinity antibodies directly from the NGS dataset of sorted B cells — delivering hits in under 12 weeks post terminal bleed.

Lead Selection

Which residues in the paratope make contact with the target?

Epitope Mapping service: atomic-level characterisation of the antibody-antigen interface, identifying the binding epitope, key interacting residues, and the molecular basis of affinity and selectivity.

Lead Improvement

How to improve the lead candidate?

Structure-based DeepDesign Engineering: structural output from Epitope Mapping feeds directly into DeepDesign Engineering, guiding targeted library design or in silico variant generation to achieve specific engineering objectives.

Development Candidate Selection

Which candidate has the best chance of becoming a product?

Structure Validation service: determine the 3D structure of your target protein to guide immunisation strategy and confirm the target is druggable at the intended site.

The Infrastructure Behind AtomicLevel

FairJourney Bio's cryo-EM facility is located in San Diego and operates 5th generation ThermoFisher Titan Krios electron microscopes — the current benchmark for throughput and image quality in protein structure determination. The facility is paired with on-premises computational infrastructure, enabling short sample-to-result turnaround times that are not possible when data collection and processing are decoupled.


  • 5th generation ThermoFisher Titan Krios — 300 kV, automated data collection

  • On-premises computational infrastructure — no data transfer bottleneck

  • High-resolution map and model in under 5 weeks

  • Deposition-ready structural models produced as standard

The Infrastructure Behind AtomicLevel

FairJourney Bio's cryo-EM facility is located in San Diego and operates 5th generation ThermoFisher Titan Krios electron microscopes — the current benchmark for throughput and image quality in protein structure determination. The facility is paired with on-premises computational infrastructure, enabling short sample-to-result turnaround times that are not possible when data collection and processing are decoupled.


  • 5th generation ThermoFisher Titan Krios — 300 kV, automated data collection

  • On-premises computational infrastructure — no data transfer bottleneck

  • High-resolution map and model in under 5 weeks

  • Deposition-ready structural models produced as standard

The Infrastructure Behind AtomicLevel

FairJourney Bio's cryo-EM facility is located in San Diego and operates 5th generation ThermoFisher Titan Krios electron microscopes — the current benchmark for throughput and image quality in protein structure determination. The facility is paired with on-premises computational infrastructure, enabling short sample-to-result turnaround times that are not possible when data collection and processing are decoupled.


  • 5th generation ThermoFisher Titan Krios — 300 kV, automated data collection

  • On-premises computational infrastructure — no data transfer bottleneck

  • High-resolution map and model in under 5 weeks

  • Deposition-ready structural models produced as standard

AtomicLevel Cryo-EM in the FairJourney Bio Value Chain

AtomicLevel Cryo-EM is active from Target Validation through to Development Candidate Selection — and is tightly integrated with DeepDesign Engineering so that structural insight becomes engineering action without delay.

Explore discovery-to-IND

Explore discovery-to-IND

One Platform. Structural Answers at Every Stage

Services

AtomicLevel Cryo-EM offers four integrated services covering the full antibody discovery and engineering pipeline: from the first structural question at target validation through to development candidate confirmation. Each service is designed to generate decision-enabling data, not just structural data.

One Platform. Structural Answers at Every Stage

Services

AtomicLevel Cryo-EM offers four integrated services covering the full antibody discovery and engineering pipeline: from the first structural question at target validation through to development candidate confirmation. Each service is designed to generate decision-enabling data, not just structural data.

One Platform. Structural Answers at Every Stage

AtomicLevel Cryo-EM offers four integrated services covering the full antibody discovery and engineering pipeline: from the first structural question at target validation through to development candidate confirmation. Each service is designed to generate decision-enabling data, not just structural data.

Service 1

Epitope Mapping

In-depth atomic-level understanding of your candidate molecule

Epitope Mapping by cryo-EM determines the structure of the antibody-antigen complex at atomic resolution: identifying the binding epitope, the key interacting residues in the paratope, and the molecular basis of affinity and specificity. This is the structural foundation for all downstream engineering decisions.

What FairJourney Bio requires


  • Purified target protein: generated by FairJourney Bio or provided by the partner

  • Purified Fab, VHH, or scFv: generated by FairJourney Bio or provided by the partner

FairJourney Bio generates purified complexes and performs imaging by cryo-EM.

What the data delivers


  • Density map at <3.5 Å resolution

  • Validated atomic model, deposition-ready

What the insights enable


  • Clear identification of the binding epitope and interaction mode

  • Mechanistic insight into how the antibody drives biological activity

  • Molecular understanding of the drivers of potency and selectivity

  • Actionable guidance for rational and AI-based engineering

Timeline

Approximately 5 weeks from complex preparation to validated structural model.

Service 1

Epitope Mapping

In-depth atomic-level understanding of your candidate molecule

Epitope Mapping by cryo-EM determines the structure of the antibody-antigen complex at atomic resolution: identifying the binding epitope, the key interacting residues in the paratope, and the molecular basis of affinity and specificity. This is the structural foundation for all downstream engineering decisions.

What FairJourney Bio requires


  • Purified target protein: generated by FairJourney Bio or provided by the partner

  • Purified Fab, VHH, or scFv: generated by FairJourney Bio or provided by the partner

FairJourney Bio generates purified complexes and performs imaging by cryo-EM.

What the data delivers


  • Density map at <3.5 Å resolution

  • Validated atomic model, deposition-ready

What the insights enable


  • Clear identification of the binding epitope and interaction mode

  • Mechanistic insight into how the antibody drives biological activity

  • Molecular understanding of the drivers of potency and selectivity

  • Actionable guidance for rational and AI-based engineering

Timeline

Approximately 5 weeks from complex preparation to validated structural model.

Service 1

Epitope Mapping

In-depth atomic-level understanding of your candidate molecule

Epitope Mapping by cryo-EM determines the structure of the antibody-antigen complex at atomic resolution: identifying the binding epitope, the key interacting residues in the paratope, and the molecular basis of affinity and specificity. This is the structural foundation for all downstream engineering decisions.

What FairJourney Bio requires


  • Purified target protein: generated by FairJourney Bio or provided by the partner

  • Purified Fab, VHH, or scFv: generated by FairJourney Bio or provided by the partner

FairJourney Bio generates purified complexes and performs imaging by cryo-EM.

What the data delivers


  • Density map at <3.5 Å resolution

  • Validated atomic model, deposition-ready

What the insights enable


  • Clear identification of the binding epitope and interaction mode

  • Mechanistic insight into how the antibody drives biological activity

  • Molecular understanding of the drivers of potency and selectivity

  • Actionable guidance for rational and AI-based engineering

Timeline

Approximately 5 weeks from complex preparation to validated structural model.

Service 2

Structure Validation

3D structural confirmation of your target protein

Structure Validation determines the 3D structure of the target protein in isolation or in complex — confirming the structural integrity of the target, identifying relevant conformations, and providing the structural context needed to design immunisation strategies and interpret binding data. Deployed at Target Validation and Development Candidate Selection.

Applications


  • Target protein structure determination to guide discovery strategy

  • Confirmation of protein conformation relevant to therapeutic mechanism

  • Structural context for interpreting functional and binding data

Service 2

Structure Validation

3D structural confirmation of your target protein

Structure Validation determines the 3D structure of the target protein in isolation or in complex — confirming the structural integrity of the target, identifying relevant conformations, and providing the structural context needed to design immunisation strategies and interpret binding data. Deployed at Target Validation and Development Candidate Selection.

Applications


  • Target protein structure determination to guide discovery strategy

  • Confirmation of protein conformation relevant to therapeutic mechanism

  • Structural context for interpreting functional and binding data

Service 2

Structure Validation

3D structural confirmation of your target protein

Structure Validation determines the 3D structure of the target protein in isolation or in complex — confirming the structural integrity of the target, identifying relevant conformations, and providing the structural context needed to design immunisation strategies and interpret binding data. Deployed at Target Validation and Development Candidate Selection.

Applications


  • Target protein structure determination to guide discovery strategy

  • Confirmation of protein conformation relevant to therapeutic mechanism

  • Structural context for interpreting functional and binding data

Service 3

Epitope-Based Hit Discovery

Structure-first discovery of epitope-specific, high-affinity antibodies

Conventional antibody discovery offers limited control over which epitope is targeted. Epitope-Based Hit Discovery uses cryo-EM to reverse this, identifying epitope-specific antibodies directly from the immune repertoire by structure, then recovering their sequences from the NGS dataset. The result is informed, accelerated discovery of antibodies with the epitope specificity required by the Target Product Profile.

Why this matters

Traditional discovery is time-intensive and offers limited control over epitope selection. AI-driven, sequence-from-structure workflows now enable a structure-first approach, delivering informed and accelerated discovery of desired antibodies by selecting for epitope specificity before a single expression experiment is committed.

Timeline

Under 12 weeks after terminal bleed.

Service 3

Epitope-Based Hit Discovery

Structure-first discovery of epitope-specific, high-affinity antibodies

Conventional antibody discovery offers limited control over which epitope is targeted. Epitope-Based Hit Discovery uses cryo-EM to reverse this, identifying epitope-specific antibodies directly from the immune repertoire by structure, then recovering their sequences from the NGS dataset. The result is informed, accelerated discovery of antibodies with the epitope specificity required by the Target Product Profile.

Why this matters

Traditional discovery is time-intensive and offers limited control over epitope selection. AI-driven, sequence-from-structure workflows now enable a structure-first approach, delivering informed and accelerated discovery of desired antibodies by selecting for epitope specificity before a single expression experiment is committed.

Timeline

Under 12 weeks after terminal bleed.

Service 3

Epitope-Based Hit Discovery

Structure-first discovery of epitope-specific, high-affinity antibodies

Conventional antibody discovery offers limited control over which epitope is targeted. Epitope-Based Hit Discovery uses cryo-EM to reverse this, identifying epitope-specific antibodies directly from the immune repertoire by structure, then recovering their sequences from the NGS dataset. The result is informed, accelerated discovery of antibodies with the epitope specificity required by the Target Product Profile.

Why this matters

Traditional discovery is time-intensive and offers limited control over epitope selection. AI-driven, sequence-from-structure workflows now enable a structure-first approach, delivering informed and accelerated discovery of desired antibodies by selecting for epitope specificity before a single expression experiment is committed.

Timeline

Under 12 weeks after terminal bleed.

Service 4

Structure-Based Design and Engineering

Cryo-EM structural insight feeding directly into DeepDesign Engineering

The structural data generated by Epitope Mapping becomes the design template for structure-guided engineering. Key interacting residues and the molecular basis of affinity and specificity are used to guide focused library design or in silico variant generation — significantly reducing experimental sequence space and increasing the probability of identifying improved variants.

Library approaches enabled by structural data


  • Structure-guided design of highly focused libraries in diverse formats

  • Significant reduction of experimental sequence space — enabling complete coverage in downstream screening

  • Applicable to phage, yeast, and mammalian display platforms

In silico approaches enabled by structural data


  • Design and modelling of a large number of variants using physics- and AI-based tools

  • Down-selection of promising variants before any experimental work begins

Engineering objectives supported


  • Affinity maturation

  • Humanisation

  • Developability improvement

Service 4

Structure-Based Design and Engineering

Cryo-EM structural insight feeding directly into DeepDesign Engineering

The structural data generated by Epitope Mapping becomes the design template for structure-guided engineering. Key interacting residues and the molecular basis of affinity and specificity are used to guide focused library design or in silico variant generation — significantly reducing experimental sequence space and increasing the probability of identifying improved variants.

Library approaches enabled by structural data


  • Structure-guided design of highly focused libraries in diverse formats

  • Significant reduction of experimental sequence space — enabling complete coverage in downstream screening

  • Applicable to phage, yeast, and mammalian display platforms

In silico approaches enabled by structural data


  • Design and modelling of a large number of variants using physics- and AI-based tools

  • Down-selection of promising variants before any experimental work begins

Engineering objectives supported


  • Affinity maturation

  • Humanisation

  • Developability improvement

Service 4

Structure-Based Design and Engineering

Cryo-EM structural insight feeding directly into DeepDesign Engineering

The structural data generated by Epitope Mapping becomes the design template for structure-guided engineering. Key interacting residues and the molecular basis of affinity and specificity are used to guide focused library design or in silico variant generation — significantly reducing experimental sequence space and increasing the probability of identifying improved variants.

Library approaches enabled by structural data


  • Structure-guided design of highly focused libraries in diverse formats

  • Significant reduction of experimental sequence space — enabling complete coverage in downstream screening

  • Applicable to phage, yeast, and mammalian display platforms

In silico approaches enabled by structural data


  • Design and modelling of a large number of variants using physics- and AI-based tools

  • Down-selection of promising variants before any experimental work begins

Engineering objectives supported


  • Affinity maturation

  • Humanisation

  • Developability improvement

Platform Capabilities

Platform Capabilities

Platform Capabilities

Broad application coverage

In-depth expertise in structure determination of antibody-antigen complexes, including membrane protein complexes and protein-small molecule complexes.

Proprietary workflows and integrated computation

Advanced data processing techniques for heterogeneous biological systems, high-performance atomic modelling, and rapid structure-guided computational protein design.

End-to-end, discovery-integrated workflow

Seamlessly connected from sample preparation through atomic models — tightly integrated with DeepDesign Engineering and structure-based drug design workflows.

Infrastructure

5th generation ThermoFisher Titan Krios microscopes at the FairJourney Bio San Diego facility. 300 kV, automated data collection, on-premises computational infrastructure for short sample-to-result turnaround.

Speed, Quality, and Decision-Ready Data

Process & Deliverables

Every AtomicLevel Cryo-EM project delivers a complete structural dataset, density map, validated atomic model, residue-level interaction analysis, at the turnaround times your programme requires, with direct handoff into DeepDesign Engineering for immediate engineering action.

Speed, Quality, and Decision-Ready Data

Process & Deliverables

Every AtomicLevel Cryo-EM project delivers a complete structural dataset, density map, validated atomic model, residue-level interaction analysis, at the turnaround times your programme requires, with direct handoff into DeepDesign Engineering for immediate engineering action.

Speed, Quality, and Decision-Ready Data

Every AtomicLevel Cryo-EM project delivers a complete structural dataset, density map, validated atomic model, residue-level interaction analysis, at the turnaround times your programme requires, with direct handoff into DeepDesign Engineering for immediate engineering action.

What FairJourney Bio Delivers

  • High-resolution density map at <3.5 Å

  • Validated, deposition-ready atomic model of the protein, protein-protein, or protein-ligand complex

  • In-depth analysis of protein structure, key residue interactions, and molecular dynamics

  • Identification of the binding epitope and paratope contact residues

  • Mechanistic interpretation: how the antibody drives biological activity

  • Actionable engineering guidance: targeted library design inputs or in silico variant design parameters

  • Seamless structural data handoff for DeepDesign Engineering campaigns

Integration with DeepDesign Engineering

AtomicLevel Cryo-EM and DeepDesign Engineering are designed to operate as an integrated unit. Structural output from cryo-EM is not delivered as a report and filed — it is used immediately to design the next engineering iteration. The same scientific project lead manages both the structural work and the engineering campaign, ensuring that structural insight translates into experimental design without any translation loss or delay.

Cryo-EM structure determination (5 weeks) feeds into library-based engineering (12–14 weeks) or in silico approaches (5–6 weeks) — with the structural data reducing the experimental sequence space significantly and increasing the probability of identifying improved variants in every campaign.

Integration Across the Value Chain

AtomicLevel Cryo-EM connects forward and backward within the FairJourney Bio platform. Structural data from early-stage Epitope Mapping feeds into DeepDesign Engineering for lead improvement. Later-stage structure determination supports the development candidate decision and contributes to the regulatory package through FastTrack IND.

  • FullSpectrum Characterization — structural context for binding and selectivity data

  • DeepDesign Engineering — structure-guided library and in silico design

  • FastTrack IND — structural data for the regulatory submission package

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