BAlaS: Fast, interactive and accessible computational alanine-scanning using BudeAlaScan

Christopher W. Wood; Amaurys A. Ibarra; Gail J. Bartlett; Andrew J. Wilson; Derek N. Woolfson; Richard B. Sessions

doi:10.1093/bioinformatics/btaa026

BAlaS: Fast, interactive and accessible computational alanine-scanning using BudeAlaScan

Christopher W. Wood^*, Amaurys A. Ibarra, Gail J. Bartlett, Andrew J. Wilson, Derek N. Woolfson, Richard B. Sessions^*

^*Corresponding author for this work

Chemistry

Research output: Contribution to journal › Article › peer-review

29 Citations (Scopus)

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.

Original language	English
Pages (from-to)	2917-2919
Number of pages	3
Journal	Bioinformatics
Volume	36
Issue number	9
DOIs	https://doi.org/10.1093/bioinformatics/btaa026
Publication status	Published - 1 May 2020

Bibliographical note

Funding Information:
This work was supported by an Engineering and Physical Sciences Research Council Fellowship [EP/S003002/1 to C.W.W.]; a European Research Council Advanced Grant [340764], a Biotechnology and Biological Sciences Research Council Research Grant [BB/R00661X/1] and a Royal Society Wolfson Research Merit Award to D.N.W; and an Engineering and Physical Sciences Research Council Programme Grant [PoPPI, EP/N013573/1 to G.J.B., A.A.I., R.B.S., A.J.W. and D.N.W.].

Publisher Copyright:
© 2020 The Author(s). Published by Oxford University Press. All rights reserved.

ASJC Scopus subject areas

Statistics and Probability
Biochemistry
Molecular Biology
Computer Science Applications
Computational Theory and Mathematics
Computational Mathematics

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title = "BAlaS: Fast, interactive and accessible computational alanine-scanning using BudeAlaScan",

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.",

author = "Wood, {Christopher W.} and Ibarra, {Amaurys A.} and Bartlett, {Gail J.} and Wilson, {Andrew J.} and Woolfson, {Derek N.} and Sessions, {Richard B.}",

note = "Funding Information: This work was supported by an Engineering and Physical Sciences Research Council Fellowship [EP/S003002/1 to C.W.W.]; a European Research Council Advanced Grant [340764], a Biotechnology and Biological Sciences Research Council Research Grant [BB/R00661X/1] and a Royal Society Wolfson Research Merit Award to D.N.W; and an Engineering and Physical Sciences Research Council Programme Grant [PoPPI, EP/N013573/1 to G.J.B., A.A.I., R.B.S., A.J.W. and D.N.W.]. Publisher Copyright: {\textcopyright} 2020 The Author(s). Published by Oxford University Press. All rights reserved.",

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AU - Woolfson, Derek N.

AU - Sessions, Richard B.

N1 - Funding Information: This work was supported by an Engineering and Physical Sciences Research Council Fellowship [EP/S003002/1 to C.W.W.]; a European Research Council Advanced Grant [340764], a Biotechnology and Biological Sciences Research Council Research Grant [BB/R00661X/1] and a Royal Society Wolfson Research Merit Award to D.N.W; and an Engineering and Physical Sciences Research Council Programme Grant [PoPPI, EP/N013573/1 to G.J.B., A.A.I., R.B.S., A.J.W. and D.N.W.]. Publisher Copyright: © 2020 The Author(s). Published by Oxford University Press. All rights reserved.

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N2 - 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.

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BAlaS: Fast, interactive and accessible computational alanine-scanning using BudeAlaScan

Abstract

Bibliographical note

ASJC Scopus subject areas

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