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

Christopher W  Wood; Amaurys Avila Ibarra; Gail J Bartlett; Dek N Woolfson; Richard B Sessions

doi:10.1093/bioinformatics/btaa026

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

Christopher W Wood^*, Amaurys Avila Ibarra, Gail J Bartlett, Dek N Woolfson, Richard B Sessions^*

^*Corresponding author for this work

Research output: Contribution to journal › Article (Academic Journal) › peer-review

46 Citations (Scopus)

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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 programs for performing computational alanine-scanning mutagenesis (CASM) to guide experiments. While programs are available for this, there is a need for a real-time web application that is accessible to non-expert users.

Original language	English
Article number	btaa026
Pages (from-to)	2917-2919
Number of pages	3
Journal	Bioinformatics
Volume	36
Issue number	9
Early online date	13 Jan 2020
DOIs	https://doi.org/10.1093/bioinformatics/btaa026
Publication status	Published - 1 May 2020

Research Groups and Themes

Bristol BioDesign Institute

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10.1093/bioinformatics/btaa026

Full-text PDF (author’s accepted manuscript)
This is the author accepted manuscript (AAM). The final published version (version of record) is available online via Oxford University Press at https://doi.org/10.1093/bioinformatics/btaa026 . Please refer to any applicable terms of use of the publisher.
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Rational computational protein design in ISAMBARD: new approaches, folds and functions
Woolfson, D. N. (Principal Investigator)
1/05/18 → 30/04/23
Project: Research
8043 EPSRC VIA LEEDS EP/N013573/1 (closed)
Woolfson, D. N. (Principal Investigator)
1/02/16 → 31/01/22
Project: Research

HPC (High Performance Computing) and HTC (High Throughput Computing) Facilities
Alam, S. R. (Manager), Williams, D. A. G. (Manager), Eccleston, P. E. (Manager) & Greene, D. (Manager)
Facility/equipment: Facility

Cite this

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

abstract = "MotivationIn 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 programs for performing computational alanine-scanning mutagenesis (CASM) to guide experiments. While programs are available for this, there is a need for a real-time web application that is accessible to non-expert users.",

author = "Wood, {Christopher W} and {Avila Ibarra}, Amaurys and Bartlett, {Gail J} and Woolfson, {Dek N} and Sessions, {Richard B}",

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AU - Avila Ibarra, Amaurys

AU - Bartlett, Gail J

AU - Woolfson, Dek N

AU - Sessions, Richard B

PY - 2020/5/1

Y1 - 2020/5/1

N2 - MotivationIn 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 programs for performing computational alanine-scanning mutagenesis (CASM) to guide experiments. While programs are available for this, there is a need for a real-time web application that is accessible to non-expert users.

AB - MotivationIn 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 programs for performing computational alanine-scanning mutagenesis (CASM) to guide experiments. While programs are available for this, there is a need for a real-time web application that is accessible to non-expert users.

U2 - 10.1093/bioinformatics/btaa026

DO - 10.1093/bioinformatics/btaa026

M3 - Article (Academic Journal)

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SN - 1367-4811

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JO - Bioinformatics

JF - Bioinformatics

IS - 9

M1 - btaa026

ER -

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

Abstract

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Projects

Rational computational protein design in ISAMBARD: new approaches, folds and functions

8043 EPSRC VIA LEEDS EP/N013573/1 (closed)

Equipment

HPC (High Performance Computing) and HTC (High Throughput Computing) Facilities

Cite this