# Protein Molecular Weight Calculator AI Agent Connect

> Calculate protein mass, extinction coefficient, and isoelectric point from sequences or compositions.

## Overview
- **Category:** biochemistry
- **Price:** Free
- **Endpoint:** https://edge.vinkius.com/vk_preview_KpNXZJZV15NIoDyTL3EWBDF30pED19EMgTDgirut/ai-agent-connect
- **Tags:** protein, molecular-weight, biochemistry, pi, amino-acid

## Description

This MCP server provides specialized biochemical tools for protein characterization. Use `calculate_sequence_properties` to derive a full suite of physical properties including molecular weight, UV absorption, and pI from a single-letter amino acid sequence. For mass calculations based on residue counts, use `calculate_composition_mass`. You can also isolate specific properties using `get_extinction_coefficient` for UV absorption at 280nm or `estimate_isoelectric_point` to find the neutral pH of a protein sequence. The tools account for post-translational modifications to ensure accurate biochemical modeling.

## Tools

### calculate_composition_mass
Calculates the total molecular weight based only on the counts of each amino acid present

### calculate_sequence_properties
Calculates a full suite of physical properties for a specific protein sequence

### estimate_isoelectric_point
Estimates the pH at which the protein is electrically neutral

### get_extinction_coefficient
Determines the UV absorption capability of a protein at 280nm

## Prompt Examples

**Prompt:** 
```
What is the molecular weight and pI of the sequence MKWVTFISLLFLFSSAYSRGVFRR?
```

**Response:** 
```
The protein has a molecular weight of approximately 2543.2 Da and an estimated isoelectric point of 5.2.
```

**Prompt:** 
```
Calculate the mass for a composition of 10 Alanine (A) and 5 Glycine (G).
```

**Response:** 
```
The total molecular weight for this composition is 185.15 Da.
```

**Prompt:** 
```
What is the extinction coefficient for the sequence WYYW?
```

**Response:** 
```
The molar extinction coefficient (ε280) for the sequence WYYW is 12450.5.
```

## Frequently Asked Questions

**How do I calculate the mass of a protein using a composition?**
You can use the `calculate_composition_mass` tool by providing a JSON mapping of amino acid single-letter codes to their respective counts.

**Can I include post-translational modifications in the calculation?**
Yes, both `calculate_sequence_properties` and `calculate_composition_mass` accept an optional modifications parameter to account for added mass.

**What is the purpose of the extinction coefficient tool?**
The `get_extinction_coefficient` tool determines the UV absorption capability of a protein at 280nm based on its aromatic amino acid content.