Tracking publications on AlphaFold 2 and its applications.

Structural Bioinformatics Course @UAM

Optimal AlphaMissense threshold based on VKGL variant classifications

Plot AlphaFold2-based pathogenicity prediction scores for a particular gene and suggest a gene-specific threshold for separating pathogenic from benign variants.

Predicting changes in neutralizing antibody activity for SARS-CoV-2 XBB.1.5 using in silico protein modeling.

Prediction of possible paths of gene mutation using AlphaFold

In this research project a standardised AlphaFold 2-based molecular replacement strategy is developed and implemented in an existing biomolecule structure solution pipeline at MAX IV Laboratory. It can be run on high performance clusters similar to the LUNARC (https://www.lunarc.lu.se/). A standalone and implemented version of the pipeline exists.

Annotating cysteines part of disulfides and metal binding sites in AlphaFold2 predictions

Structure-informed MLDE of GB1

Jupyter notebook examples of Scop3P REST API services

AlphaFold Unofficial Wiki

Individual project for 5th year where models were trained to predict whether a drug and a protein bind together using their chemical properties and protein structural embeddings extracted from AlphaFold. Notebooks & Streamlit App Available

The provided code snippet forms a critical component of an automated script aimed at facilitating the prediction of protein structures using the AlphaFold model within a Google Colab environment. The script is tailored to handle the simultaneous upload of multiple input files, each containing multiple protein sequences for prediction.

Protein folding on VKGL data using FoldX and AlphaFold2

Automated generation of immunogenic peptides from protein structures and molecular docking analysis using AlphaFold2 and AutodockVina.

Implementation of Alphafold 2 monomer to run only with MSAs

Large scale, in silico interaction analyses of SARS-CoV-2 nucleocapsid protein variants against human cytokines.

A python software to parse AlphaFold/ColabFold results into PyMOL PSE and PAE plots.

Repository with scripts and data generated during my internship at Institut Pasteur of Paris