# Protein Purification Yield Calculator AI Agent Connect

> Quantify protein purity and recovery efficiency across purification steps.

## Overview
- **Category:** biochemistry
- **Price:** Free
- **Endpoint:** https://edge.vinkius.com/vk_preview_PCkBPpWfbuJDzR2btC3kknTGYgdFLMktgLrG0wow/ai-agent-connect
- **Tags:** protein, purification, biochemistry, yield, purity

## Description

This MCP server provides a specialized calculation engine for biochemical researchers to track protein purification progress. It allows AI agents to calculate essential metrics such as specific activity, yield percentage, and purification factor. Researchers can use `calculate_step_metrics` to evaluate individual steps, `compare_purification_stages` to assess transitions between stages, and `getMethodEfficiencyThresholds` to compare experimental results against theoretical standards for methods like affinity or ion exchange. Additionally, `validate_purification_log` helps identify experimental anomalies in a sequence of purification steps.

## Tools

### compare_purification_stages
Compares two different stages of a purification process

### get_method_efficiency_thresholds
Provides expected yield and purification factor ranges for a specific purification method

### validate_purification_log
Checks a sequence of purification steps for logical consistency

### calculate_step_metrics
Calculates the essential purity and recovery metrics for a single purification step

## Prompt Examples

**Prompt:** 
```
Calculate the metrics for a step with 5mg total protein, 100 units of activity, and 10ml volume, given a baseline of 500 units activity and 10mg protein.
```

**Response:** 
```
The specific activity is 10 U/mg, the yield is 20%, and the purification factor is 2.0.
```

**Prompt:** 
```
What are the expected yield and fold ranges for affinity chromatography?
```

**Response:** 
```
For affinity chromatography, the expected yield range is typically 40-80% and the expected fold range is 10-100x.
```

**Prompt:** 
```
Compare a starting stage with 5 U/mg specific activity and 100% yield to a final stage with 50 U/mg specific activity and 70% yield.
```

**Response:** 
```
The transition shows a 10-fold increase in specific activity, a 30% yield loss, and a purity improvement of 45 U/mg.
```

## Frequently Asked Questions

**How do I calculate the purification factor?**
You can use the `calculate_step_metrics` tool. Provide the current step's protein and activity data along with the baseline values to receive the purification factor.

**Can I check if my purification results are within expected ranges?**
Yes, use the `getMethodEfficiencyThresholds` tool. It provides expected yield and fold ranges for methods like affinity, ion_exchange, and size_exclusion.

**How can I detect errors in my purification data?**
The `validate_purification_log` tool analyzes your sequence of steps to flag anomalies, such as unexpected increases in total activity.