Home ~ Citing ~ LeucipPy ~ LeucipPlus ~ DensityFlight

These projects have been developed as a result of studying Bioinformatics at Birkbeck College, University of London, UK
The current projects are under active resaerch as part of my PhD project.

Leucippus (2021 +): A webserver exploring protein structure and electron density

Leucippus is the integrated environment of LeucipPlus and LeucipPy operating as a webserver on the university servers.
Currently in its very early stages it allows the browsing of electron density values and peaks of x-ray solved structures.
It also provides adjusted pdb files based on electron density maxima (active research).

Click here for Leucipus webserver for protein structure exploration

LeucipPlus (2021 +): A C++ utility for protein structure analysis and re-refinement

A c++ utility to analyse protein structures, including re-refinement and electron density and structure factor analysis.
This is in under active research and is part of my PhD project.

LeucipPy (2020 +): A python library for protein geometry correlations

This is a python library to produce geoemntric analyses of protein structures, including the secondary structure information from dssp and the electron density information from ccp4 files where available. The images produced range from a simple Ramachandran plot than can be coloured on for example secondary structure, electron density or B-Factor, to say, a correlation of number of electrons against B-Factor. The library contains some pre-defined reports so the code to create some fairly involved reports is minimal.

The library relies on these Bioinformatics librararies:

• BioPython for protein structure coordinates
• PDB EDA for loading the electron density
• DSSP for asigning secondary structure

Density Flight (2020 + ): An interactive C# windows app to explore electron density maps

Density Flight is a windows application to view the inside of an electron density matrix. The application allows you to navigate around like a flight simulator, viewing atoms, bonds between atoms, finding density peaks, rotateing in the space to seek planar atoms.
The application can currently be downloaded from github and built in Vsiual Studio 2019 (C#)
It will be available for beta testing shortly on request.

Density Flight help and documentation is here

Protein Structure Utility - Birkbeck MSc (2019-2020)

This website and database was developed as part of an MSc thesis in Bioinformatics and Systems Biology (2020), supervisor Mark Williams
The database contains 3434 high resolution structures with resolution <= 1.3Å and 2697 structures from 2019 > 1.3Å
The website allows production of geometric plots and statistical analyses using these structures and selected criteria.

PSU Birkbeck help and documentation is here

The Website hosted on the Birkbeck College servers is here

A highlight is the demonstration of the bimodal nature of tau.

Created by: Rachel Alcraft ~ Home page: Leucippus ~ Supervisor: Mark A. Williams ~ Birkbeck, University of London (2021)