GYDE (Collaborative Protein Design Platform)

GYDE (Guide Your Design and Engineering) is an open-source, web-based collaboration platform that makes computational analyses of proteins and antibodies accessible to bench scientists. Published as a bioRxiv preprint in March 2026.

Key Capabilities

flowchart TD
    ALPHA_SYNUCLEIN["ALPHA-SYNUCLEIN"] -->|"associated with"| Parkinson["Parkinson"]
    ALPHA_SYNUCLEIN["ALPHA-SYNUCLEIN"] -->|"therapeutic target"| Parkinson["Parkinson"]
    ALPHA_SYNUCLEIN["ALPHA-SYNUCLEIN"] -->|"activates"| Neurodegeneration["Neurodegeneration"]
    ALPHA_SYNUCLEIN["ALPHA-SYNUCLEIN"] -->|"activates"| Parkinson["Parkinson"]
    ALPHA_SYNUCLEIN["ALPHA-SYNUCLEIN"] -->|"activates"| Inflammation["Inflammation"]
    ALPHA_SYNUCLEIN["ALPHA-SYNUCLEIN"] -->|"associated with"| PARKINSON_S_DISEASE["PARKINSON'S DISEASE"]
    ALPHA_SYNUCLEIN["ALPHA-SYNUCLEIN"] -->|"associated with"| Als["Als"]
    ALPHA_SYNUCLEIN["ALPHA-SYNUCLEIN"] -->|"therapeutic target"| Neurodegeneration["Neurodegeneration"]
    ALPHA_SYNUCLEIN["ALPHA-SYNUCLEIN"] -->|"activates"| Als["Als"]
    PARKINSON_S_DISEASE["PARKINSON'S DISEASE"] -->|"associated with"| ALPHA_SYNUCLEIN["ALPHA-SYNUCLEIN"]
    PARKINSON_S_DISEASE["PARKINSON'S DISEASE"] -->|"therapeutic target"| ALPHA_SYNUCLEIN["ALPHA-SYNUCLEIN"]
    PARKINSON_S_DISEASE["PARKINSON'S DISEASE"] -->|"activates"| ALPHA_SYNUCLEIN["ALPHA-SYNUCLEIN"]
    NEURODEGENERATION["NEURODEGENERATION"] -->|"activates"| ALPHA_SYNUCLEIN["ALPHA-SYNUCLEIN"]
    PARKINSON["PARKINSON"] -->|"associated with"| ALPHA_SYNUCLEIN["ALPHA-SYNUCLEIN"]
    PARKINSON["PARKINSON"] -->|"therapeutic target"| ALPHA_SYNUCLEIN["ALPHA-SYNUCLEIN"]
    SNCA["SNCA"] -->|"produces"| alpha_synuclein["alpha-synuclein"]
    LAG3["LAG3"] -->|"interacts with"| alpha_synuclein["alpha-synuclein"]
    PARKIN["PARKIN"] -->|"regulates"| ALPHA_SYNUCLEIN["ALPHA-SYNUCLEIN"]
    style ALPHA_SYNUCLEIN fill:#ce93d8,stroke:#333,color:#000
    style Parkinson fill:#ef5350,stroke:#333,color:#000
    style Neurodegeneration fill:#ef5350,stroke:#333,color:#000
    style Inflammation fill:#ef5350,stroke:#333,color:#000
    style PARKINSON_S_DISEASE fill:#ce93d8,stroke:#333,color:#000
    style Als fill:#ef5350,stroke:#333,color:#000
    style NEURODEGENERATION fill:#ce93d8,stroke:#333,color:#000
    style PARKINSON fill:#ce93d8,stroke:#333,color:#000
    style SNCA fill:#ce93d8,stroke:#333,color:#000
    style alpha_synuclein fill:#4fc3f7,stroke:#333,color:#000
    style LAG3 fill:#4fc3f7,stroke:#333,color:#000
    style PARKIN fill:#ce93d8,stroke:#333,color:#000

Structure prediction: Integrates AlphaFold2, Chai, Boltz, OpenFold, and emerging co-folding methods
Sequence-structure-function exploration: Tightly integrated visual interface for exploring protein functional determinants
Collaborative sessions: Saved sessions enable researchers to share findings with other users
Extensible architecture: Easy addition of new tools and models via the Slivka compute API
Assay data integration: Explore relationships through real experimental assay data or computational predictions

Architecture

Web-based platform using the Slivka compute API for flexible tool integration. Supports growing list of structure prediction methods and downstream analyses. Designed for both academic and industry protein scientists to build customized drug discovery analytics workflows.

Relevance to SciDEX

GYDE represents the kind of specialized, open-source tool that SciDEX’s Forge layer could integrate — particularly for neurodegeneration targets like tau, amyloid-beta, and alpha-synuclein structure analysis. Its collaborative session model parallels SciDEX’s artifact sharing approach.

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