3D Protein Lab - Open Sourced

 Last year we placed all of the code for 3D protein lab into an GitHub repository and released it as an open-source project. It has not been put into the Pisabarro group GitHub organisation.

Please go through the README file to install and use. You will need a copy of the database to make use of the application.

In an ideal world someone will pick up the mantle and convert a more recent version of the protein structure databases into the format required for 3D Protein Lab to work.

Reduced False Positives in PDZ Binding Prediction using Sequence and Structural Descriptors

At last our paper on predicting PDZ binding has been published. In this work we built a custom machine learning model to identify peptides that are likely ligands of a given PDZ domain.

PDZs are a very common structural protein units that are involved in cell signalling pathways. The binding occurs in a cleft between an alpha helix and beta sheet, typically by turning the ligand into an additional strand at the end of the sheet.

In this work we showed how the number of false positive predictions could be reduced by making a consensus predictor that combines a number of individual machine learning components. They are joined by a voting mechanism, and then made turned into a rational number using probability distributions over the residues at each of the binding positions.

Unfortunately the process is too complicated to automate at this stage.

You can find it here:Reduced False Positives in PDZ Binding Prediction using Sequence and Structural Descriptors

Welcome to Protein Lab

I will be using this blog to post updates on some of the bioinformatics software that I have made available during my research career. In addition I will post a few general notes on research topics that are of interest to me.