AlphaFold 2's confidence scores put into context
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Updated
Jul 5, 2023 - Jupyter Notebook
AlphaFold 2's confidence scores put into context
The Python software re-glycosylates protein structures using MD simulation results from the glycoshape database. It takes alphafold protein structures as input and outputs modified structures with glycans added at appropriate sites.
An implementation of Invariant Point Attention from Alphafold 2
Using AlphaFold Artificial Intelligence for prediction Coronavirus glycoprotein structures
Large scale, in silico interaction analyses of SARS-CoV-2 nucleocapsid protein variants against human cytokines.
Automated generation of immunogenic peptides from protein structures and molecular docking analysis using AlphaFold2 and AutodockVina.
This Google colab notebook, allows for conservation analysis of user input genes, on their local machine. It relies on the MMSeq2 introduced by https://www.nature.com/articles/s41592-022-01488-1
Tracking publications on AlphaFold 2 and its applications.
Implementation of Alphafold 2 monomer to run only with MSAs
A program that compares a protein structure prediction to a solved structure and evaluates the prediction's accuracy using RMSD.
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.
LightMHC: A Light Model for pMHC Structure Prediction with Graph Neural Networks
Prediction of possible paths of gene mutation using AlphaFold
A python software to parse AlphaFold/ColabFold results into PyMOL PSE and PAE plots.
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.
GUI for running jobs with a local installation of AlphaFold2. Supports submission to queuing systems.
Repository with scripts and data generated during my internship at Institut Pasteur of Paris
A Tufts Research Technology Workshop detailing how to use AlphaFold 2 on the Tufts HPC cluster
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