# Protein Secondary Structure Predictor AI Agent Connect

> Predict protein secondary structures like alpha-helices and beta-sheets from amino acid sequences.

## Overview
- **Category:** science
- **Price:** Free
- **Endpoint:** https://edge.vinkius.com/vk_preview_ikmfZm8xYgozQnq0BgBnevedFolkZQC9ZWtLxBQb/ai-agent-connect
- **Tags:** protein, amino-acid, structure, bioinformatics, biology

## Description

This MCP server provides specialized tools for analyzing protein primary sequences to predict their secondary structural elements. Using established scientific methods, it calculates the distribution of alpha-helices, beta-sheets, and coils. Researchers can use `predict_structure_chou_fasman` for statistical propensity-based analysis or `predict_structure_gor` for information theory-based predictions. The tool also allows for direct comparison of these methods using `compare_prediction_methods` to identify specific structural biases.

## Tools

### get_amino_acid_propensities
Retrieves the specific propensity values for amino acids used in secondary structure prediction

### compare_prediction_methods
Compares the results of Chou-Fasman and GOR methods for a single sequence

### predict_structure_chou_fasman
Predicts the secondary structure of a protein sequence using the Chou-Fasman statistical propensity method

### predict_structure_gor
Note that GOR requires a minimum sequence length for window calculation.

Predicts the secondary structure of a protein sequence using the GOR (information theory) approach

## Prompt Examples

**Prompt:** 
```
Predict the secondary structure for the sequence MVLSAALALAL.
```

**Response:** 
```
The predicted structure for the sequence MVLSAALALAL is 45% alpha-helix, 15% beta-sheet, and 40% coil.
```

**Prompt:** 
```
Compare the Chou-Fasman and GOR predictions for the sequence MAVS.
```

**Response:** 
```
Chou-Fasman predicts 25% alpha-helix and 25% beta-sheet, while GOR predicts 30% alpha-helix and 20% beta-sheet. The difference in helix is 5% and the difference in sheet is 5%.
```

**Prompt:** 
```
What are the propensity values for the chou_fasman method?
```

**Response:** 
```
The Chou-Fasman propensity values include: Alanine (A) has a high helix propensity, while Proline (P) acts as a helix breaker.
```

## Frequently Asked Questions

**What methods are used for prediction?**
The server implements the Chou-Fasman statistical propensity method and the GOR (Garnier-Osguthorpe-Robson) information theory approach.

**How can I compare different prediction results?**
You can use the `compare_prediction_methods` tool to run both Chou-Fasman and GOR algorithms on the same sequence and see the differences in helix and sheet percentages.

**What input format is required?**
The tools require a string representing the primary amino acid sequence using standard single-letter codes (e.g., 'MVLSA').