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

被引：52

作者：

Wood, Christopher W. ^{[1
]}

Ibarra, Amaurys A. ^{[2
]}

Bartlett, Gail J. ^{[3
]}

Wilson, Andrew J. ^{[4
,5
]}

Woolfson, Derek N. ^{[6
]}

Sessions, Richard B. ^{[2
,6
]}

机构：

[1] Univ Edinburgh, Sch Biol Sci, Edinburgh EH9 3FF, Midlothian, Scotland

[2] Univ Bristol, Sch Biochem, Med Sci Bldg, Bristol BS8 1TD, Avon, England

[3] Univ Bristol, Sch Chem, Bristol BS8 1TS, Avon, England

[4] Univ Leeds, Sch Chem, Leeds LS2 9JT, W Yorkshire, England

[5] Univ Leeds, Astbury Ctr Struct Mol Biol, Leeds LS2 9JT, W Yorkshire, England

[6] Univ Bristol, BrisSynBio, Life Sci Bldg, Leeds LS2 9JT, W Yorkshire, England

来源：

BIOINFORMATICS | 2020年 / 36卷 / 09期

基金：

英国生物技术与生命科学研究理事会; 英国工程与自然科学研究理事会; 欧洲研究理事会;

关键词：

PROTEIN-PROTEIN INTERACTIONS; HOT-SPOT; ENERGY;

D O I：

10.1093/bioinformatics/btaa026

中图分类号：

Q5 [生物化学];

学科分类号：

070307 [化学生物学];

摘要：

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.

引用

页码：2917 / 2919

页数：3

共 15 条

[11]

Effect of the MDM2 antagonist RG7112 on the P53 pathway in patients with MDM2-amplified, well-differentiated or dedifferentiated liposarcoma: an exploratory proof-of-mechanism study [J].

Ray-Coquard, Isabelle ;

Blay, Jean-Yves ;

Italiano, Antoine ;

Le Cesne, Axel ;

Penel, Nicolas ;

Zhi, Jianguo ;

Heil, Florian ;

Rueger, Ruediger ;

Graves, Bradford ;

Ding, Meichun ;

Geho, David ;

Middleton, Steven A. ;

Vassilev, Lyubomir T. ;

Nichols, Gwen L. ;

Binh Nguyen Bui .

LANCET ONCOLOGY, 2012, 13 (11) :1133-1140

[12]

Hot-spot analysis for drug discovery targeting protein-protein interactions [J].

Rosell, Mireia ;

Fernandez-Recio, Juan .

EXPERT OPINION ON DRUG DISCOVERY, 2018, 13 (04) :327-338

[13]

The FoldX web server: an online force field [J].

Schymkowitz, J ;

Borg, J ;

Stricher, F ;

Nys, R ;

Rousseau, F ;

Serrano, L .

NUCLEIC ACIDS RESEARCH, 2005, 33 :W382-W388

[14]

ABT-199, a potent and selective BCL-2 inhibitor, achieves antitumor activity while sparing platelets [J].

Souers, Andrew J. ;

Leverson, Joel D. ;

Boghaert, Erwin R. ;

Ackler, Scott L. ;

Catron, Nathaniel D. ;

Chen, Jun ;

Dayton, Brian D. ;

Ding, Hong ;

Enschede, Sari H. ;

Fairbrother, Wayne J. ;

Huang, David C. S. ;

Hymowitz, Sarah G. ;

Jin, Sha ;

Khaw, Seong Lin ;

Kovar, Peter J. ;

Lam, Lloyd T. ;

Lee, Jackie ;

Maecker, Heather L. ;

Marsh, Kennan C. ;

Mason, Kylie D. ;

Mitten, Michael J. ;

Nimmer, Paul M. ;

Oleksijew, Anatol ;

Park, Chang H. ;

Park, Cheol-Min ;

Phillips, Darren C. ;

Roberts, Andrew W. ;

Sampath, Deepak ;

Seymour, John F. ;

Smith, Morey L. ;

Sullivan, Gerard M. ;

Tahir, Stephen K. ;

Tse, Chris ;

Wendt, Michael D. ;

Xiao, Yu ;

Xue, John C. ;

Zhang, Haichao ;

Humerickhouse, Rod A. ;

Rosenberg, Saul H. ;

Elmore, Steven W. .

NATURE MEDICINE, 2013, 19 (02) :202-208

[15]

ISAMBARD: an open-source computational environment for biomolecular analysis, modelling and design [J].

Wood, Christopher W. ;

Heal, Jack W. ;

Thomson, Andrew R. ;

Bartlett, Gail J. ;

Ibarra, Amaurys A. ;

Brady, R. Leo ;

Sessions, Richard B. ;

Woolfson, Derek N. .

BIOINFORMATICS, 2017, 33 (19) :3043-3050

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