Protein-protein interaction Binding Affinity Prediction

Framework for benchmarking RNA secondary structure prediction algorithms.

Welcome to the Open Source Computational Biology Master's

This repository contains different scripts used for the normal mode analysis of biomolecules with known crystal structures.

Scripts for analysing MD simulations of nanopores and DNA translocation (ionic current, translocation rate, pore hydrophobicity).

Micelle Maker source code

Complete implementation with 3 methods, sensitivity analysis, and comprehensive visualizations. Reference: doi.org/10.1002/advs.202407641"

Curated Portfolio For A 100-Module Graduate Curriculum in ML/AI Ops Engineering Development of Soil Quality Laboratory Foundation Models Using A Set Of 100 Foundational Model Concepts

FELBuilder is an automated Python pipeline that automates the complex workflow of Principal Component Analysis (PCA) and Free Energy Landscape (FEL) analysis from Molecular Dynamics (MD) trajectories.

This GitHub repository contains the code and data for the manuscript "Dynamical control enables the formation of demixed biomolecular condensates" (BioRxiv link: https://www.biorxiv.org/content/10.1101/2023.01.04.522702v1)

Computational Molecular Biophysics Scripts

A tool that locates and lists the intramolecular interactions in each frame of a NetCDF MD trajectory file

Using graph-theory descriptors to classify the binding affinity of a protein dimer.

A graph-based approach to investigate protein contacts evolution during a Molecular Dynamics simulation

🧠🔬At the Cordeiro Lab, we investigate how intrinsically disordered proteins and biomolecular assemblies orchestrate cellular organization, pathogenic survival, and biotechnological innovation.

A protocol to evaluate near-native antibody–antigen docking poses using radially distributed statistical potentials via a matricial and graph-based approach.