The curse of the protein ribbon diagram

被引：4

作者：

Bourne, Philip E. ^{[1
,2
]}

Draizen, Eli J. ^{[1
,2
]}

Mura, Cameron ^{[1
]}

机构：

[1] Univ Virginia, Sch Data Sci, Charlottesville, VA 22903 USA

[2] Univ Virginia, Dept Biomed Engn, Charlottesville, VA 22903 USA

来源：

PLOS BIOLOGY | 2022年 / 20卷 / 12期

关键词：

PREDICTION;

D O I：

10.1371/journal.pbio.3001901

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

Does reductionism, in the era of machine learning and now interpretable AI, facilitate or hinder scientific insight? The protein ribbon diagram, as a means of visual reductionism, is a case in point.

引用

页数：4

共 13 条

[1] Accurate prediction of protein structures and interactions using a three-track neural network [J].

Baek, Minkyung ;

DiMaio, Frank ;

Anishchenko, Ivan ;

Dauparas, Justas ;

Ovchinnikov, Sergey ;

Lee, Gyu Rie ;

Wang, Jue ;

Cong, Qian ;

Kinch, Lisa N. ;

Schaeffer, R. Dustin ;

Millan, Claudia ;

Park, Hahnbeom ;

Adams, Carson ;

Glassman, Caleb R. ;

DeGiovanni, Andy ;

Pereira, Jose H. ;

Rodrigues, Andria V. ;

van Dijk, Alberdina A. ;

Ebrecht, Ana C. ;

Opperman, Diederik J. ;

Sagmeister, Theo ;

Buhlheller, Christoph ;

Pavkov-Keller, Tea ;

Rathinaswamy, Manoj K. ;

Dalwadi, Udit ;

Yip, Calvin K. ;

Burke, John E. ;

Garcia, K. Christopher ;

Grishin, Nick V. ;

Adams, Paul D. ;

Read, Randy J. ;

Baker, David .

SCIENCE, 2021, 373 (6557) :871-+

[2]

Draizen EJ., 2022, DEEP GENERATIVE MODE, DOI [10.1101/2022.07.29.501943, DOI 10.1101/2022.07.29.501943]

[3] Highly accurate protein structure prediction with AlphaFold [J].

Jumper, John ;

Evans, Richard ;

Pritzel, Alexander ;

Green, Tim ;

Figurnov, Michael ;

Ronneberger, Olaf ;

Tunyasuvunakool, Kathryn ;

Bates, Russ ;

Zidek, Augustin ;

Potapenko, Anna ;

Bridgland, Alex ;

Meyer, Clemens ;

Kohl, Simon A. A. ;

Ballard, Andrew J. ;

Cowie, Andrew ;

Romera-Paredes, Bernardino ;

Nikolov, Stanislav ;

Jain, Rishub ;

Adler, Jonas ;

Back, Trevor ;

Petersen, Stig ;

Reiman, David ;

Clancy, Ellen ;

Zielinski, Michal ;

Steinegger, Martin ;

Pacholska, Michalina ;

Berghammer, Tamas ;

Bodenstein, Sebastian ;

Silver, David ;

Vinyals, Oriol ;

Senior, Andrew W. ;

Kavukcuoglu, Koray ;

Kohli, Pushmeet ;

Hassabis, Demis .

NATURE, 2021, 596 (7873) :583-+

[4] A LARGE-SCALE EXPERIMENT TO ASSESS PROTEIN-STRUCTURE PREDICTION METHODS [J].

MOULT, J ;

PEDERSEN, JT ;

JUDSON, R ;

FIDELIS, K .

PROTEINS-STRUCTURE FUNCTION AND GENETICS, 1995, 23 (03) :R2-R4

[5] The Urfold: Structural similarity just above the superfold level? [J].

Mura, Cameron ;

Veretnik, Stella ;

Bourne, Philip E. .

PROTEIN SCIENCE, 2019, 28 (12) :2119-2126

[6]

Raymond E.S., 1999, CATHEDRAL BAZAAR, V1st, P268

[7]

Richardson J S, 1981, Adv Protein Chem, V34, P167, DOI 10.1016/S0065-3233(08)60520-3

[8] Early ribbon drawings of proteins [J].

Richardson, JS .

NATURE STRUCTURAL BIOLOGY, 2000, 7 (08) :624-625

[9] Discrete-continuous duality of protein structure space [J].

Sadreyev, Ruslan I. ;

Kim, Bong-Hyun ;

Grishin, Nick V. .

CURRENT OPINION IN STRUCTURAL BIOLOGY, 2009, 19 (03) :321-328

[10] Improved protein structure prediction using potentials from deep learning [J].

Senior, Andrew W. ;

Evans, Richard ;

Jumper, John ;

Kirkpatrick, James ;

Sifre, Laurent ;

Green, Tim ;

Qin, Chongli ;

Zidek, Augustin ;

Nelson, Alexander W. R. ;

Bridgland, Alex ;

Penedones, Hugo ;

Petersen, Stig ;

Simonyan, Karen ;

Crossan, Steve ;

Kohli, Pushmeet ;

Jones, David T. ;

Silver, David ;

Kavukcuoglu, Koray ;

Hassabis, Demis .

NATURE, 2020, 577 (7792) :706-+

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