melodia-py 0.1.5

Differential Geometry of Proteins Backbones

Melodia_py

Protein Structure Analysis

Melodia_py is a Python library for computing Differential Geometry and Knot Theory descriptors of protein structures.

Installation

1. Open the terminal.
2. Run pip install melodia-py for the installation.

Installation in Anaconda Python

We recommend using Miniforge and Mamba for installation (optional). Miniforge is an Anaconda Python-compatible distribution with a faster and more reliable package manager (Mamba). It is as simple to install as the Anaconda distribution.

We start with creation of a new environment for Melodia_py.

conda create -n melodia_py

or (optionally, but highly recommended) replace conda for Miniforge's mamba command.

mamba create -n melodia_py

Next step is to activate the Melodia_py environment

conda activate melodia_py
pip install melodia-py

Or for building and installing Melodia_py for source. The first step is to clone Melodia_py's repository.

git clone https://github.com/rwmontalvao/Melodia.git
cd ./Melodia_py

conda env create -f environment.yml
conda activate melodia_py

python setup.py install

Documentation

The examples folder contains Jupyter Notebooks, with tutorials explaining Melodia_py's functionalities.

• Getting Started:
• Alignment Basics:
• Basic Similarity Analysis:
• Advanced Similarity Analysis:
• Machine Leaning Ensemble Analysis:
• Alignment Clustering and PDB Superimposition:
• RNA Differential Geometry Analysis:

Authors

• Rinaldo W. Montalvão, PhD
• Antonio Marinho da Silva Neto, PhD
• William R. Pitt, PhD

Publication

Melodia: a Python library for protein structure analysis

References

• Montalvão R, Smith R, Lovell S, Blundell T: CHORAL: a differential geometry approach to the prediction of the cores of protein structures. Bioinformatics. 2005, 21: 3719-3725.
• Chang PL, Rinne AW, Dewey TG: Structure alignment based on coding of local geometric measures. BMC Bioinformatics. 2006, 7:346.
• Leung H, Montaño B, Blundell T, Vendruscolo M, Montalvão R: ARABESQUE: A tool for protein structural comparison using differential geometry and knot theory. World Res J Peptide Protein. 2012, 1: 33-40.
• Pitt WR, Montalvão R, Blundell T: Polyphony: superposition independent methods for ensemble-based drug discovery. BMC Bioinformatics. 2014, 15:324
• Marinho da Silva Neto A, Reghim Silva S, Vendruscolo M, Camilloni C, Montalvão R: A Superposition Free Method for Protein Conformational Ensemble Analyses and Local Clustering Based on a Differential Geometry Representation of Backbone. Proteins: Structure, Function, and Bioinformatics. 2018, 87(4):302-312
• Marinho da Silva Neto A, Montalvão R, Gondim Martins DB, Lima Filho JL, Madeiros Castelletti CH: A model of key residues interactions for HPVs E1 DNA binding domain-DNA interface based on HPVs residues conservation profiles and molecular dynamics simulations, Journal of Biomolecular Structure and Dynamics. 2019, 38(12):3720-3729.