Secondary Structure Determination by Nuclear Magnetic Resonance (SSD-NMR)

Introduction SSD-NMR is a method for determining the secondary structure composition of proteins using a single unassigned 1D ¹³C NMR spectrum. This repository contains the implementation of the SSD-NMR algorithm, along with example datasets and Google Colab notebooks to reproduce the results presented in our manuscript.

Features

• Rapid and accurate determination of protein secondary structure composition
• Requires only a single unassigned 1D ¹³C NMR spectrum and the protein's primary sequence
• Applicable to proteins in solution, solid-state, and other complex environments
• Robust performance for a wide range of experimental conditions and spectral qualities

Getting Started

Google Colab Notebook

For a quick and easy way to try SSD-NMR, check out our Google Colab Notebook

Local Installation

To run SSD-NMR locally, first clone this repository and install the required dependencies:

cd SSD-NMR
pip install -r requirements.txt

Usage

SSD-NMR can be run from the command line with the following syntax:

python GD.py <spectrum_file> <ppm_column> <protein_name> <sequence> <self_reference>

For example:

python GD.py MDT_gb1_referenced.csv ppm gb1 MQYKLILNGKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVT True

Examples

The "Examples" folder contains a set of pre-configured Google Colab notebooks and sample spectra that reproduce the results presented in our manuscript.

Citation

For references, a preprint of this work is available: Li H, Tuttle M, Zilm K, Batista V. Rapid Quantification of Protein Secondary Structure Composition from a Single Unassigned 1D 13C NMR Spectrum. ChemRxiv. 2024; doi:10.26434/chemrxiv-2024-qt9g4

For questions, comments, or support, please contact the authors:

• Haote Li (haote.li@yale.edu)
• Marcus D. Tuttle (marcus.tuttle@yale.edu)