ISAMBARD: A Python-based API for Biomolecular Structure Analysis and Parametric Design of Protein Structures

Aimed at:

Researchers wanting to perform biomolecular structure analysis and/or de novo modelling of parameterizable protein folds such as coiled coils or other repeat proteins.

Requirements:

A basic knowledge of Python is required and familiarity with Jupyter Notebooks is useful.

Abstract:

ISAMBARD is an open-source Python package for structural analysis and rational design of biomolecules. This workshop will cover an overview of the basic functionality included in ISAMBARD and comprises of three parts:

1. A basic overview of biomolecules in ISAMBARD: This session will be an introduction to structure representation in ISAMBARD through the AMPAL (Atom, Monomer, Polymer, Assembly, Ligand) framework, and will demonstrate how to perform selection and analysis of structural elements.

2. Modelling and analysis of coiled-coil structures: We will perform analysis of natural coiled coils to extract structural parameters, as well as create models de novo using ISAMBARD specifications, which can be extended to allow users to create their own parameterisations.

3. Optimization of the structural parameters of models: We will give a brief introduction to meta-heuristics, basic optimization of parametric models and how to analyse and interpret the results.

References:

ISAMBARD: an open-source computational environment for biomolecular analysis, modelling and design. Bioinformatics 2017. doi: 10.1093/bioinformatics/btx352

CCBuilder 2.0: Powerful and accessible coiled-coil modelling, Protein Science 2017. doi: 10.1002/pro.3279

Training Material

The workshop consists of a series of Jupyter notebooks. These are available below, and can be run using the workshop jupyter server.

Once you have started the server, navigate to the isambard_workshop directory and you will find the notebooks there.

Contents

• tutorial1/Tutorial001.ipynb
• tutorial2/Tutorial002.ipynb
• tutorial3/Tutorial003.ipynb