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| license: cc-by-4.0 |
| language: |
| - en |
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| |
| # Proteus Structures |
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| Computationally generated and predicted molecular structures from **Project Proteus**, the biological discovery research program of **Inserloft Research**. |
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| > **AI for the next generation of biological discovery.** |
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| This repository contains structural representations associated with computational protein-design experiments conducted within Project Proteus. |
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| ## About |
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| **Proteus Structures** is a structural repository for molecular candidates generated or investigated through the Proteus research program. |
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| The structures in this repository are intended to support: |
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| * Structural inspection |
| * Computational analysis |
| * Protein-design research |
| * Reproducibility |
| * Visualization |
| * Further experimental investigation |
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| Unless explicitly stated otherwise, structures contained here are **computational models** and should not be interpreted as experimentally determined structures. |
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| ## Repository Structure |
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| ```text |
| Proteus-Structures/ |
| │ |
| ├── CNB-1/ |
| │ ├── Macromolecular_PET_Hydrolase_Alpha.pdb |
| │ ├── Alanine-Glycine-Aspartate.pdb |
| │ └── ... |
| │ |
| └── README.md |
| ``` |
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| Additional structures may be added as Proteus research progresses. |
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| ## CNB-1 |
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| The first experimental model developed for Project Proteus is **Caelis Neural Base-1 (CNB-1)**. |
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| CNB-1 has been used to investigate computational protein design and generate defined molecular candidates for further structural and biological analysis. |
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| ### Documented candidates |
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| #### Macromolecular PET Hydrolase Alpha |
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| A computationally designed protein candidate of approximately **350 amino acids**. |
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| The candidate was generated around a structural design seed associated with natural PET-degrading enzymes and was investigated as a potential hydrolytic enzyme candidate targeting polyethylene terephthalate (PET). |
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| The computational hypothesis involves PET hydrolysis toward: |
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| * Terephthalic acid |
| * Ethylene glycol |
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| Proposed catalytic features remain hypotheses requiring further structural, biochemical, and experimental validation. |
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| #### AGD-F1 |
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| **AGD-F1 — Alanine–Glycine–Aspartate Structural Candidate** is a **377-amino-acid** computationally designed protein candidate generated by CNB-1. |
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| Its structure was computationally predicted using **ESMFold**. |
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| Current characterization: |
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| | Property | Status | |
| | ----------------------- | -------------------- | |
| | Length | 377 aa | |
| | Generation model | Caelis Neural Base-1 | |
| | Structure prediction | ESMFold | |
| | Experimental structure | Not determined | |
| | Biological function | Uncharacterized | |
| | Experimental stability | Not determined | |
| | Experimental validation | Not performed | |
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| The AGD-F1 designation reflects prominent amino-acid representation in the candidate sequence and does **not** imply a demonstrated biochemical function. |
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| ## Structure Prediction |
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| Some structures in this repository are computational predictions rather than experimentally determined structures. |
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| For predicted structures, the corresponding metadata should identify: |
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| * The generation model |
| * The structure-prediction method |
| * The associated candidate |
| * The computational nature of the structure |
| * Relevant attribution |
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| Computational structure predictions should therefore be treated as **structural hypotheses**. |
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| A predicted structure does not establish: |
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| * Biological function |
| * Experimental stability |
| * Enzymatic activity |
| * Binding affinity |
| * Folding behavior in vivo |
| * Experimental structure |
| * Biological efficacy |
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| ## PDB Files |
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| The repository uses the **Protein Data Bank (PDB)** format for molecular structure representation. |
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| PDB files can be inspected with molecular visualization software such as: |
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| * PyMOL |
| * UCSF ChimeraX |
| * VMD |
| * Mol* |
| * 3Dmol.js |
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| Web-based Proteus structure viewers may also be provided by Inserloft Research. |
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| ## Research Philosophy |
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| Proteus is built around a simple research principle: |
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| **Generate. Structure. Analyze. Validate. Repeat.** |
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| Computational generation is only one stage of the process. |
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| The long-term objective is to move from computational molecular hypotheses toward rigorous structural and experimental investigation. |
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| Proteus explores how AI can assist researchers in investigating biological structures and designing candidate molecules relevant to difficult scientific problems. |
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| **For a better world. |
| For a better life.** |
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| ## Scientific Status |
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| The structures in this repository represent ongoing research. |
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| Computational results should not be interpreted as established biological discoveries unless explicitly supported by experimental evidence. |
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| Where experimental validation has not been performed, the relevant structure or candidate should be considered a **computational research candidate**. |
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| ## Attribution |
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| **Inserloft Research** |
| Project Proteus |
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| Research and computational modeling by Inserloft Research. |
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| Where third-party models, predictors, datasets, or software are used, their respective authors, publications, and licensing terms remain applicable. |
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| ## License |
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| Unless a specific file or directory states otherwise, the repository's licensing terms apply to the structural files and accompanying documentation. |
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| Third-party components, predicted structures, models, datasets, and software may be subject to their own licenses and attribution requirements. |
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| See the individual files and repository metadata for applicable terms. |
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| ## Disclaimer |
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| These structures are provided for **research and computational analysis purposes**. |
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| Computationally generated or predicted molecular structures are not equivalent to experimentally determined structures. |
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| Nothing in this repository constitutes a claim that a candidate protein has a validated biological function, therapeutic effect, environmental effect, safety profile, or experimental activity unless such evidence is explicitly documented. |
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| ## Project |
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| **Project Proteus** |
| Inserloft Research |
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| > **AI for the next generation of biological discovery.** |
