Christopher W Wood1, Amaurys A Ibarra2, Gail J Bartlett3, Andrew J Wilson4,5, Derek N Woolfson2,3,6, Richard B Sessions2,6. 1. School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, UK. 2. School of Biochemistry, University of Bristol, Medical Sciences Building, University Walk, Bristol BS8 1TD, UK. 3. School of Chemistry, University of Bristol, Bristol BS8 1TS, UK. 4. School of Chemistry. 5. Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, UK. 6. BrisSynBio, University of Bristol, Life Sciences Building, Bristol BS8 1TQ, UK.
Abstract
MOTIVATION: In experimental protein engineering, alanine-scanning mutagenesis involves the replacement of selected residues with alanine to determine the energetic contribution of each side chain to forming an interaction. For example, it is often used to study protein-protein interactions. However, such experiments can be time-consuming and costly, which has led to the development of programmes for performing computational alanine-scanning mutagenesis (CASM) to guide experiments. While programmes are available for this, there is a need for a real-time web application that is accessible to non-expert users. RESULTS: Here, we present BAlaS, an interactive web application for performing CASM via BudeAlaScan and visualizing its results. BAlaS is interactive and intuitive to use. Results are displayed directly in the browser for the structure being interrogated enabling their rapid inspection. BAlaS has broad applications in areas, such as drug discovery and protein-interface design. AVAILABILITY AND IMPLEMENTATION: BAlaS works on all modern browsers and is available through the following website: https://balas.app. The project is open source, distributed using an MIT license and is available on GitHub (https://github.com/wells-wood-research/balas).
MOTIVATION: In experimental protein engineering, alanine-scanning mutagenesis involves the replacement of selected residues with alanine to determine the energetic contribution of each side chain to forming an interaction. For example, it is often used to study protein-protein interactions. However, such experiments can be time-consuming and costly, which has led to the development of programmes for performing computational alanine-scanning mutagenesis (CASM) to guide experiments. While programmes are available for this, there is a need for a real-time web application that is accessible to non-expert users. RESULTS: Here, we present BAlaS, an interactive web application for performing CASM via BudeAlaScan and visualizing its results. BAlaS is interactive and intuitive to use. Results are displayed directly in the browser for the structure being interrogated enabling their rapid inspection. BAlaS has broad applications in areas, such as drug discovery and protein-interface design. AVAILABILITY AND IMPLEMENTATION: BAlaS works on all modern browsers and is available through the following website: https://balas.app. The project is open source, distributed using an MIT license and is available on GitHub (https://github.com/wells-wood-research/balas).
Authors: Fruzsina Hóbor; Zsófia Hegedüs; Amaurys Avila Ibarra; Vencel L Petrovicz; Gail J Bartlett; Richard B Sessions; Andrew J Wilson; Thomas A Edwards Journal: RSC Chem Biol Date: 2022-04-11
Authors: A Sofia F Oliveira; Amaurys Avila Ibarra; Isabel Bermudez; Lorenzo Casalino; Zied Gaieb; Deborah K Shoemark; Timothy Gallagher; Richard B Sessions; Rommie E Amaro; Adrian J Mulholland Journal: Biophys J Date: 2021-02-18 Impact factor: 4.033
Authors: Sarah M Smith; Gabrielle Larocque; Katherine M Wood; Kyle L Morris; Alan M Roseman; Richard B Sessions; Stephen J Royle; Corinne J Smith Journal: EMBO J Date: 2021-09-06 Impact factor: 11.598
Authors: Jack M O'Shea; Angeliki Goutou; Jack Brydon; Cyrus R Sethna; Christopher W Wood; Sebastian Greiss Journal: Chembiochem Date: 2022-07-07 Impact factor: 3.461
Authors: Sergio Celis; Fruzsina Hobor; Thomas James; Gail J Bartlett; Amaurys A Ibarra; Deborah K Shoemark; Zsófia Hegedüs; Kristina Hetherington; Derek N Woolfson; Richard B Sessions; Thomas A Edwards; David M Andrews; Adam Nelson; Andrew J Wilson Journal: Chem Sci Date: 2021-03-02 Impact factor: 9.825