Welcome to BcompB on GitHub

BcompB or the Bristol Computational Biochemistry group is a grouping of University of Bristol researchers in Computational Biochemistry, in particular in biomolecular simulation and computational biomolecular design. The group has members across several Schools and Faculties, primarily in the faculties of Science and Life Sciences. We meet up regularly to discuss topics of interest to the group and host seminars in computational biochemistry.

Computational Resources Created by Members of BcompB

This section contains a list of computational resources created by members of BcompB. Check out the links for more information.

BioSimSpace (Woods Group)

Available here.

BioSimSpace is an interoperable framework for biomolecular simulation. With it you can:

Write robust and portable biomolecular workflow components that work on different hardware, with different software packages, and that can be run in different ways, e.g. command-line, Jupyter.
Interact with running molecular simulation processes in real-time within a Jupyter notebook.

BUDE (Sessions Group)

Available here.

BUDE is a general purpose molecular docking program written in C++, OpenMP and OpenCL that uses GPU acceleration to perform:

Virtual screening by docking of millions of small-molecule ligands
Ligand binding site identification on protein surfaces
Protein-protein docking in real space

CCBuilder 2 (Woolfson Group)

Available here (source).

CCBuilder 2 is an interactive web app for atomistic modelling of coiled coils and collagens. It has a simple user interface for creating and evaluating models that can be used in simulation, for solving structural data or for aiding protein design.

Elfin (Parmeggiani Group)

Available here.

Elfin is a computational protein design tool based on repeat protein module construction. The main idea of Elfin is to use repeat proteins as rigid construction modules (much like how Lego works) and build 3D shapes that are as close to the user’s input description as possible.

Enlighten (van der Kamp Group)

Available here.

Protocols and tools to run (automated) atomistic simulations of enzyme-ligand systems. For the PyMOL plugin, see here.

ISAMBARD (Woolfson Group)

Available here.

ISAMBARD is a Python-based framework for structural analysis and rational design of biomolecules, with a particular focus on parametric modelling of proteins.