CrisPRO.ai: In-Silico Research Framework
Accelerating drug discovery through AI fusion
An in-silico research-use-only (RUO) framework designed to accelerate drug discovery by fusing the capabilities of discriminative and generative Artificial Intelligence. Our platform orchestrates a generalist genome foundation model with a suite of specialist predictors and structural oracles to achieve state-of-the-art performance across multiple benchmarks.
SAE Biological Mastery
Virus Hunter
Identifies viral sequences and prophage regions
3D Folding Master
Predicts protein structure from 1D sequences
Genetic Surgery
Precise CRISPR guide RNA design and optimization
Universal Knowledge
Cross-species biological understanding
Complete AI Platform Integration
From Genetic Chaos to Therapeutic Clarity
The promise of precision medicine is fundamentally limited by our ability to interpret the functional consequences of genetic variation. CrisPRO.ai was conceived to address this challenge by creating an orchestration layer that combines a genome-scale foundation model with specialist predictors (e.g., AlphaMissense) and structure/epigenome oracles (e.g., AlphaFold 3, Enformer). The result is a system that can not only interpret the full spectrum of genetic variation but can also generatively design novel therapeutic constructs.
Key Points
Traditional drug development is a $2.6 billion, 15-year gamble with 90% failure rates
Biotech companies spend months analyzing genetic data, only to discover their targets are invalid
Clinical trials fail because we can't predict which patients will respond to which treatments
We transform this chaos into clarity with definitive answers where others offer question marks
Business Impact
Transform genetic uncertainty into actionable intelligence and therapeutic blueprints
Evidence Backbone
Benchmarked performance across discriminative and generative AI tasks, grounded in peer-reviewed validation and transparent methodology.
All performance metrics are for research purposes. Not intended for diagnostic or therapeutic decision-making without independent validation and regulatory review.
Discriminative AI: The Intelligence Analyst
Validated performance that delivers real business impact
Our system's ability to interpret genetic variants is validated against multiple gold-standard datasets, delivering real business impact.
Performance Metrics
ClinVar (14,319 samples)
ClinVar (34,761 samples)
ClinVar (1,236 samples)
AUROC with lightweight classifier on CrisPRO.ai 40B embeddings
AUROC on all SNVs with AUPRC of 86.0%
SpliceVarDB (1,181 samples)
Business Impact
Comprehensive variant coverage enables reliable interpretation across all genomic regions
Generative AI: The Weapons Factory
Unprecedented R&D acceleration through novel biological design
Our platform's ability to design novel biological constructs delivers unprecedented R&D acceleration.
Performance Metrics
Correct feature counts with diverse homology and AF3 multimers
Pfam-hit rate vs 18% for previous models
Single-nucleotide resolution context window
Predictable log-linear relationship between beam width and AUROC
Business Impact
Generate therapeutic candidates 36x faster than traditional R&D
Fusion Workflow
Complete workflow combining discriminative and generative AI for therapeutic discovery
Fusion Workflow: End-to-End Therapeutic Pipeline
Complete RUO workflow combining discriminative and generative AI for therapeutic discovery, from problem framing to validated designs ready for wet-lab validation.
Problem Framing & Data Curation
Assemble genomic loci, clinical variants, DMS datasets, and assay priors
Process Details
- Genomic loci identification
- Clinical variant collection
- DMS dataset integration
- Assay prior establishment
Expected Outputs
- Curated dataset
- Problem statement
- Success criteria
Target Assessment (Discriminative)
Score disease-relevant variants with CrisPRO.ai ΔLL and specialist ensemble
Process Details
- CrisPRO.ai zero-shot ΔLL scoring (8,192 bp context)
- AlphaMissense/GPN-MSA ensemble
- Noncoding and splice variant analysis
- Confidence score generation
Expected Outputs
- Variant scores
- Confidence metrics
- Evidence tiers
Mechanistic Triage & Hypothesis
Use CrisPRO.ai embeddings for exon/intron features and region ranking
Process Details
- CrisPRO.ai embedding analysis
- Exon/intron classification
- Motif feature extraction
- Perturbation region ranking
Expected Outputs
- Mechanistic insights
- Hypothesis ranking
- Feature importance
Design (Generative)
CrisPRO.ai sequence proposals with epigenomic guidance and structural validation
Process Details
- CrisPRO.ai sequence generation
- Enformer+Borzoi epigenomic guidance
- AlphaFold 3 structural validation
- Sequence naturalness screening
Expected Outputs
- Design candidates
- Structural models
- Epigenomic scores
In-Silico Validation
Aggregate scores and prioritize designs for wet-lab validation
Process Details
- ΔLL score aggregation
- Splice and regulatory AUROC
- Structure metrics (pLDDT/PAE)
- Pfam hit analysis
Expected Outputs
- Validation scores
- Priority ranking
- Minipool candidates
Feedback & Calibration
Fit supervised heads and calibrate by cohort for continuous improvement
Process Details
- Lightweight supervised head training
- CrisPRO.ai embedding calibration
- Cohort-specific adjustment
- Platt/isotonic calibration
Expected Outputs
- Calibrated models
- Performance metrics
- Updated thresholds
Reporting & Provenance
Generate evidence reports with traceable citations and audit trails
Process Details
- Evidence report generation
- Traceable citation linking
- Audit trail documentation
- RUO compliance verification
Expected Outputs
- Final report
- Provenance log
- Compliance certificate
This workflow is designed for research purposes. All outputs require independent validation and regulatory review before any clinical application. Wet-lab validation is mandatory for designed sequences before scale-up.
The Fusion Approach: Why We Win
The competitive advantage of CrisPRO.ai lies in our fusion approach. We combine the generalist genome foundation model with specialist models to achieve SOTA across the entire R&D continuum.
Key Points
CrisPRO baseline: 95.7% AUROC ClinVar validation on 53,210 samples
Specialist integration: AlphaMissense for coding SNVs, GPN-MSA for specialized tasks
Cross-species capability: 0.82-0.99 AUROC range across 8 species
CrisPRO generation: 1M token context window for comprehensive sequence design
Functional scoring: Enformer/Borzoi for epigenomic validation
Structural validation: AlphaFold 3 for 3D structure prediction
Business Impact
This approach gives us Breadth (covering all variant types), Depth (achieving SOTA on key targets like BRCA1), and Control (designing sequences with predictable functional properties).
Transform Drug Development from Gambling to Engineering
Six core capabilities that eliminate the $2.6B gamble: from clinical decision support to therapeutic design, all powered by transparent AI with complete audit trails.
Chemo Co‑Pilot: In‑Silico Chemotherapy Guidance
Turn genetics into plain, useful guidance for chemo planning: a ranked drug hypothesis, a confidence hint, and an audit‑ready summary you can share with your team.
AgenticEMR™: Intelligent Clinical Data Management
Our vision is to solve the clinical data complexity challenge. We deploy specialized AI agents that process unstructured notes, labs, and genomic reports, integrating them into a unified, queryable intelligence platform. We streamline workflows and create an intelligent system for clinical and research operations.
Oracle Intelligence: Multi-Modal AI Validation Platform
Our vision is to solve the AI reliability problem in genomics. We deploy a three-signal validation framework that combines genomic sequence analysis with biological pathway mapping and evidence synthesis, ensuring every prediction is transparent, auditable, and clinically actionable. We provide confidence scores that clinicians can trust for life-changing decisions.
Forge Intelligence: Generative Therapeutic Design Platform
Our vision is to eliminate the guesswork from therapeutic design. We deploy generative AI agents that design precision interventions from molecular first principles, validated through structural modeling and optimized for clinical success. Every therapeutic is engineered, not discovered.
Scribe Intelligence: Conversational AI Co-Pilot
Our vision is to eliminate the technical barrier between complex genomic intelligence and clinical decision-making. We deploy conversational AI that understands context, provides progressive disclosure, and delivers audience-appropriate explanations. We make advanced AI accessible to every clinician and researcher.
CRISPR Intelligence: Advanced Therapeutic R&D Platform
To create a world where CRISPR-based therapies are designed and validated with computational certainty, eliminating guesswork and accelerating the path to cures.
Business Value: From Research to Revenue
Our results demonstrate that this fusion approach achieves 95.7% AUROC ClinVar validation on 53,210 samples, resolves 73% of Variants of Uncertain Significance (VUS), and provides a comprehensive, transparent, and controllable system for in-silico drug discovery.
Key Points
Accelerate R&D from years to weeks
Reduce experimental costs by $2.1M per program
Transform 40% VUS rate to 15% with validated predictions
Enable precision therapeutic design with predictable quality scaling
Provide comprehensive, transparent, and controllable system
Business Impact
Transform 40% VUS rate to 15% with validated predictions, accelerating target selection
Research Use Only (RUO)
All capabilities and performance metrics are designed for research purposes. Not intended for diagnostic or therapeutic decision-making without independent validation and regulatory review. All results should be validated through appropriate experimental and clinical studies.