Awesome
Melodia_py
Protein Structure Analysis
Melodia_py is a Python library for computing Differential Geometry and Knot Theory descriptors of protein structures.
Installation
- Open the terminal.
- 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:
Authors
- Rinaldo W. Montalvão, PhD
- Antonio Marinho da Silva Neto, PhD
- William R. Pitt, PhD
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.