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Models

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  • binders
  • codons
  • developability
  • enzyme
  • expression
  • folding
  • foundation model
  • function
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  • interaction
  • interpretability
  • kinetics
  • localization
  • naturalness
  • oligomer
  • oracle
  • pH
  • platform
  • property prediction
  • protein design
  • protein language model
  • protein language models
  • quality
  • quality control
  • representation learning
  • solubility
  • stability
  • structure
  • taxonomy
  • test-time compute
  • transformers

Showing 23 of 23 models

Foundation Models

cdsBERT

A codon-aware protein modeling research direction for understanding coding-sequence effects.

  • codons
  • CDS
  • foundation model

Dual Triangle Attention

A foundation-model research direction for stronger position-aware bidirectional sequence modeling.

  • attention
  • transformers
  • foundation model

ESMC

EvolutionaryScale Biohub's ESM Cambrian model family, exposed through FastPLMs as ESM++ checkpoints.

  • protein language model
  • ESMC
  • ESM++
  • foundation model

Vec2Vec

Aligns protein, annotation, and language-model representations so biological knowledge can move between spaces.

  • representation learning
  • alignment
  • annotation

Platforms

Protify

A low-code platform for evaluating and building protein property prediction workflows.

  • benchmarking
  • platform
  • protein language models

Interaction Models

Atlas CAMP

Connects protein sequences to structured functional annotation space for search, triage, and interpretation.

  • annotation
  • CAMP
  • function
  • Atlas

Atlas

Maps protein interactions, ligand relationships, and functional annotation context from sequence.

  • Atlas
  • PPI
  • PLI
  • CAMP
  • interaction
  • annotation

Oracle Models

EC General

Suggests broad enzyme-class hypotheses from protein sequence.

  • oracle
  • enzyme
  • annotation

EC Rigor

Provides stricter enzyme-function hypotheses when higher-confidence EC assignment is needed.

  • oracle
  • enzyme
  • annotation

E. coli Expression

Prioritizes proteins that are more likely to express successfully in E. coli workflows.

  • oracle
  • expression
  • developability

Homodimer

Estimates whether a protein sequence is likely to self-associate as a homodimer.

  • oracle
  • interaction
  • oligomer

Atlas Oracle Suite

A set of fast protein property predictors for triaging sequence quality, function, localization, and developability.

  • oracle
  • property prediction
  • interpretability
  • Atlas

kcat

Estimates enzyme turnover potential from protein sequence.

  • oracle
  • enzyme
  • kinetics

pH Preference

Estimates the pH range where a protein may be most compatible or active.

  • oracle
  • pH
  • enzyme

Realness

Scores whether a sequence looks like a natural protein rather than random or poorly formed sequence.

  • oracle
  • quality
  • naturalness

Solubility

Prioritizes protein sequences that are more likely to remain soluble.

  • oracle
  • solubility
  • developability

SoluProt

Provides a complementary solubility-style readout for protein developability triage.

  • oracle
  • solubility
  • developability

Subcellular Localization

Predicts likely cellular localization signals from protein sequence.

  • oracle
  • localization
  • annotation

Taxon

Estimates taxonomic signal in a protein sequence for context, quality control, and dataset review.

  • oracle
  • taxonomy
  • quality control

Temperature Stability

Estimates whether a protein sequence is likely to tolerate higher-temperature conditions.

  • oracle
  • stability
  • developability

Translator

Turns protein sequences into structured functional annotation hypotheses.

  • annotation
  • function
  • Translator
  • Atlas

Structure Models

ESMFold2 (Test-Time Compute)

Uses inference-time compute scaling to improve structure hypotheses in Atlas structure workflows.

  • structure
  • folding
  • test-time compute
  • Atlas

Generation Models

DSM

Generates and prioritizes protein sequences for design campaigns, including binder discovery.

  • generation
  • protein design
  • DSM
  • binders

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