| --- |
| license: apache-2.0 |
| pipeline_tag: tabular-regression |
| tags: |
| - biology |
| datasets: |
| - Allanatrix/ProtienBank |
| metrics: |
| - accuracy |
| --- |
| |
| # NexaBio: Advanced Protein Structure Prediction Models |
|
|
| **NexaBio** is a sophisticated two-stage model suite designed for high-accuracy protein structure prediction from amino acid sequences. It comprises two complementary models: |
|
|
| - **NexaBio_1**: A Convolutional Neural Network (CNN) and Bidirectional LSTM (BiLSTM) model for secondary structure prediction. |
| - **NexaBio_2**: A Variational Autoencoder (VAE) and Diffusion-based model for tertiary (3D) structure prediction. |
|
|
| NexaBio is a core component of the [Nexa Scientific Model Suite](https://huggingface.co/spaces/Allanatrix/NexaHub), a collection of machine learning models advancing scientific discovery. |
|
|
| ## Model Overview |
|
|
| ### NexaBio_1: Secondary Structure Prediction |
| - **Architecture**: CNN combined with BiLSTM for robust sequence modeling. |
| - **Input**: Amino acid sequence (one-hot encoded or embedded). |
| - **Output**: Secondary structure classifications (e.g., Helix, Sheet, Coil). |
| - **Use Case**: Identification of local structural motifs and protein folding patterns. |
| |
| ### NexaBio_2: Tertiary Structure Prediction |
| - **Architecture**: VAE integrated with a Diffusion Model for generative 3D modeling. |
| - **Input**: Amino acid sequence (optionally augmented with secondary structure predictions). |
| - **Output**: 3D coordinates of protein backbone atoms. |
| - **Use Case**: Full tertiary structure prediction for structural analysis and design. |
|
|
| ## Applications |
| - **Structural Bioinformatics**: Enabling precise protein structure analysis for research. |
| - **Drug Discovery**: Supporting protein-ligand interaction studies and therapeutic design. |
| - **Protein Engineering**: Facilitating the design of novel proteins for industrial and medical applications. |
| - **Synthetic Biology**: Generating protein structures for biotechnological innovation. |
| - **Academic Research**: Serving as a tool for educational and exploratory studies. |
|
|
| ## Getting Started |
|
|
| ### Example Usage |
| ```python |
| from transformers import AutoModel |
| |
| # Initialize the secondary structure prediction model |
| model_sec = AutoModel.from_pretrained("Allanatrix/NexaBio_1") |
| |
| # Initialize the tertiary structure prediction model |
| model_ter = AutoModel.from_pretrained("Allanatrix/NexaBio_2") |
| |
| # Process an amino acid sequence (refer to model documentation for input formatting) |
| ``` |
|
|
| For comprehensive instructions, including inference APIs and preprocessing details, consult the individual model cards on Hugging Face. |
|
|
| ## Citation and License |
| If you utilize NexaBio in your research or applications, please cite this repository and include a link to the [Nexa R&D Space](https://huggingface.co/spaces/Allanatrix/NexaR&D). |
| The models and associated code are licensed under the **Boost Software License 1.1 (BSL-1.1)**. |
|
|
| ## Part of the Nexa Scientific Ecosystem |
| Discover other components of the Nexa Scientific Stack: |
| - [Nexa Data Studio](https://huggingface.co/spaces/Allanatrix/NexaDataStudio): Data processing and visualization tools. |
| - [Nexa R&D](https://huggingface.co/spaces/Allanatrix/NexaR&D): Research-focused model development environment. |
| - [Nexa Infrastructure](https://huggingface.co/spaces/Allanatrix/NexaInfrastructure): Scalable ML deployment solutions. |
| - [Nexa Hub](https://huggingface.co/spaces/Allanatrix/NexaHub): Central portal for Nexa resources. |
|
|
| --- |
|
|
| *Developed and maintained by [Allan](https://huggingface.co/Allanatrix), an independent machine learning researcher specializing in scientific AI and infrastructure.* |
