Literature DB >> 34533838

Critical assessment of methods of protein structure prediction (CASP)-Round XIV.

Andriy Kryshtafovych1, Torsten Schwede2, Maya Topf3, Krzysztof Fidelis1, John Moult4,5.   

Abstract

Critical assessment of structure prediction (CASP) is a community experiment to advance methods of computing three-dimensional protein structure from amino acid sequence. Core components are rigorous blind testing of methods and evaluation of the results by independent assessors. In the most recent experiment (CASP14), deep-learning methods from one research group consistently delivered computed structures rivaling the corresponding experimental ones in accuracy. In this sense, the results represent a solution to the classical protein-folding problem, at least for single proteins. The models have already been shown to be capable of providing solutions for problematic crystal structures, and there are broad implications for the rest of structural biology. Other research groups also substantially improved performance. Here, we describe these results and outline some of the many implications. Other related areas of CASP, including modeling of protein complexes, structure refinement, estimation of model accuracy, and prediction of inter-residue contacts and distances, are also described.
© 2021 Wiley Periodicals LLC.

Entities:  

Keywords:  Alphafold; CASP; community wide experiment; protein folding; protein structure prediction

Mesh:

Substances:

Year:  2021        PMID: 34533838      PMCID: PMC8726744          DOI: 10.1002/prot.26237

Source DB:  PubMed          Journal:  Proteins        ISSN: 0887-3585


  47 in total

1.  An improved protein decoy set for testing energy functions for protein structure prediction.

Authors:  Jerry Tsai; Richard Bonneau; Alexandre V Morozov; Brian Kuhlman; Carol A Rohl; David Baker
Journal:  Proteins       Date:  2003-10-01

2.  Principles that govern the folding of protein chains.

Authors:  C B Anfinsen
Journal:  Science       Date:  1973-07-20       Impact factor: 47.728

3.  Prediction of protein assemblies, the next frontier: The CASP14-CAPRI experiment.

Authors:  Marc F Lensink; Guillaume Brysbaert; Théo Mauri; Nurul Nadzirin; Sameer Velankar; Raphael A G Chaleil; Tereza Clarence; Paul A Bates; Ren Kong; Bin Liu; Guangbo Yang; Ming Liu; Hang Shi; Xufeng Lu; Shan Chang; Raj S Roy; Farhan Quadir; Jian Liu; Jianlin Cheng; Anna Antoniak; Cezary Czaplewski; Artur Giełdoń; Mateusz Kogut; Agnieszka G Lipska; Adam Liwo; Emilia A Lubecka; Martyna Maszota-Zieleniak; Adam K Sieradzan; Rafał Ślusarz; Patryk A Wesołowski; Karolina Zięba; Carlos A Del Carpio Muñoz; Eiichiro Ichiishi; Ameya Harmalkar; Jeffrey J Gray; Alexandre M J J Bonvin; Francesco Ambrosetti; Rodrigo Vargas Honorato; Zuzana Jandova; Brian Jiménez-García; Panagiotis I Koukos; Siri Van Keulen; Charlotte W Van Noort; Manon Réau; Jorge Roel-Touris; Sergei Kotelnikov; Dzmitry Padhorny; Kathryn A Porter; Andrey Alekseenko; Mikhail Ignatov; Israel Desta; Ryota Ashizawa; Zhuyezi Sun; Usman Ghani; Nasser Hashemi; Sandor Vajda; Dima Kozakov; Mireia Rosell; Luis A Rodríguez-Lumbreras; Juan Fernandez-Recio; Agnieszka Karczynska; Sergei Grudinin; Yumeng Yan; Hao Li; Peicong Lin; Sheng-You Huang; Charles Christoffer; Genki Terashi; Jacob Verburgt; Daipayan Sarkar; Tunde Aderinwale; Xiao Wang; Daisuke Kihara; Tsukasa Nakamura; Yuya Hanazono; Ragul Gowthaman; Johnathan D Guest; Rui Yin; Ghazaleh Taherzadeh; Brian G Pierce; Didier Barradas-Bautista; Zhen Cao; Luigi Cavallo; Romina Oliva; Yuanfei Sun; Shaowen Zhu; Yang Shen; Taeyong Park; Hyeonuk Woo; Jinsol Yang; Sohee Kwon; Jonghun Won; Chaok Seok; Yasuomi Kiyota; Shinpei Kobayashi; Yoshiki Harada; Mayuko Takeda-Shitaka; Petras J Kundrotas; Amar Singh; Ilya A Vakser; Justas Dapkūnas; Kliment Olechnovič; Česlovas Venclovas; Rui Duan; Liming Qiu; Xianjin Xu; Shuang Zhang; Xiaoqin Zou; Shoshana J Wodak
Journal:  Proteins       Date:  2021-09-13

4.  Topology evaluation of models for difficult targets in the 14th round of the critical assessment of protein structure prediction (CASP14).

Authors:  Lisa N Kinch; Jimin Pei; Andriy Kryshtafovych; R Dustin Schaeffer; Nick V Grishin
Journal:  Proteins       Date:  2021-07-23

5.  Assessing the binding properties of CASP14 targets and models.

Authors:  Megan Egbert; Usman Ghani; Ryota Ashizawa; Sergei Kotelnikov; Thu Nguyen; Israel Desta; Nasser Hashemi; Dzmitry Padhorny; Dima Kozakov; Sandor Vajda
Journal:  Proteins       Date:  2021-08-19

6.  Applying and improving AlphaFold at CASP14.

Authors:  John Jumper; Richard Evans; Alexander Pritzel; Tim Green; Michael Figurnov; Olaf Ronneberger; Kathryn Tunyasuvunakool; Russ Bates; Augustin Žídek; Anna Potapenko; Alex Bridgland; Clemens Meyer; Simon A A Kohl; Andrew J Ballard; Andrew Cowie; Bernardino Romera-Paredes; Stanislav Nikolov; Rishub Jain; Jonas Adler; Trevor Back; Stig Petersen; David Reiman; Ellen Clancy; Michal Zielinski; Martin Steinegger; Michalina Pacholska; Tamas Berghammer; David Silver; Oriol Vinyals; Andrew W Senior; Koray Kavukcuoglu; Pushmeet Kohli; Demis Hassabis
Journal:  Proteins       Date:  2021-12

7.  Accurate prediction of protein structures and interactions using a three-track neural network.

Authors:  Minkyung Baek; Frank DiMaio; Ivan Anishchenko; Justas Dauparas; Sergey Ovchinnikov; Gyu Rie Lee; Jue Wang; Qian Cong; Lisa N Kinch; R Dustin Schaeffer; Claudia Millán; Hahnbeom Park; Carson Adams; Caleb R Glassman; Andy DeGiovanni; Jose H Pereira; Andria V Rodrigues; Alberdina A van Dijk; Ana C Ebrecht; Diederik J Opperman; Theo Sagmeister; Christoph Buhlheller; Tea Pavkov-Keller; Manoj K Rathinaswamy; Udit Dalwadi; Calvin K Yip; John E Burke; K Christopher Garcia; Nick V Grishin; Paul D Adams; Randy J Read; David Baker
Journal:  Science       Date:  2021-07-15       Impact factor: 47.728

8.  Target highlights in CASP14: Analysis of models by structure providers.

Authors:  Leila T Alexander; Rosalba Lepore; Andriy Kryshtafovych; Athanassios Adamopoulos; Markus Alahuhta; Ann M Arvin; Yannick J Bomble; Bettina Böttcher; Cécile Breyton; Valerio Chiarini; Naga Babu Chinnam; Wah Chiu; Krzysztof Fidelis; Rhys Grinter; Gagan D Gupta; Marcus D Hartmann; Christopher S Hayes; Tatjana Heidebrecht; Andrea Ilari; Andrzej Joachimiak; Youngchang Kim; Romain Linares; Andrew L Lovering; Vladimir V Lunin; Andrei N Lupas; Cihan Makbul; Karolina Michalska; John Moult; Prasun K Mukherjee; William Sam Nutt; Stefan L Oliver; Anastassis Perrakis; Lucy Stols; John A Tainer; Maya Topf; Susan E Tsutakawa; Mauricio Valdivia-Delgado; Torsten Schwede
Journal:  Proteins       Date:  2021-10-10

9.  Protein oligomer modeling guided by predicted interchain contacts in CASP14.

Authors:  Minkyung Baek; Ivan Anishchenko; Hahnbeom Park; Ian R Humphreys; David Baker
Journal:  Proteins       Date:  2021-08-23

10.  Target classification in the 14th round of the critical assessment of protein structure prediction (CASP14).

Authors:  Lisa N Kinch; R Dustin Schaeffer; Andriy Kryshtafovych; Nick V Grishin
Journal:  Proteins       Date:  2021-08-19
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  33 in total

1.  Harnessing protein folding neural networks for peptide-protein docking.

Authors:  Tomer Tsaban; Julia K Varga; Orly Avraham; Ziv Ben-Aharon; Alisa Khramushin; Ora Schueler-Furman
Journal:  Nat Commun       Date:  2022-01-10       Impact factor: 14.919

2.  GPU-I-TASSER: a GPU accelerated I-TASSER protein structure prediction tool.

Authors:  Elijah A MacCarthy; Chengxin Zhang; Yang Zhang; K C Dukka
Journal:  Bioinformatics       Date:  2022-01-03       Impact factor: 6.937

Review 3.  I-TASSER-MTD: a deep-learning-based platform for multi-domain protein structure and function prediction.

Authors:  Xiaogen Zhou; Wei Zheng; Yang Li; Robin Pearce; Chengxin Zhang; Eric W Bell; Guijun Zhang; Yang Zhang
Journal:  Nat Protoc       Date:  2022-08-05       Impact factor: 17.021

4.  Computational models in the service of X-ray and cryo-electron microscopy structure determination.

Authors:  Andriy Kryshtafovych; John Moult; Reinhard Albrecht; Geoffrey A Chang; Kinlin Chao; Alec Fraser; Julia Greenfield; Marcus D Hartmann; Osnat Herzberg; Inokentijs Josts; Petr G Leiman; Sara B Linden; Andrei N Lupas; Daniel C Nelson; Steven D Rees; Xiaoran Shang; Maria L Sokolova; Henning Tidow
Journal:  Proteins       Date:  2021-09-06

Review 5.  An Outlook on the Complexity of Protein Morphogenesis in Health and Disease.

Authors:  Maurizio Brunori; Stefano Gianni
Journal:  Front Mol Biosci       Date:  2022-06-13

6.  Editorial: Influence of Protein-Protein Interactions (PPIs) on the Outcome of Viral Infections.

Authors:  Rohit K Jangra; Mercè Llabrés; Pablo Guardado-Calvo; Eva Mittler; Gorka Lasso
Journal:  Front Microbiol       Date:  2022-06-27       Impact factor: 6.064

7.  CRFalign: A Sequence-Structure Alignment of Proteins Based on a Combination of HMM-HMM Comparison and Conditional Random Fields.

Authors:  Sung Jong Lee; Keehyoung Joo; Sangjin Sim; Juyong Lee; In-Ho Lee; Jooyoung Lee
Journal:  Molecules       Date:  2022-06-09       Impact factor: 4.927

8.  AlphaFold Models of Small Proteins Rival the Accuracy of Solution NMR Structures.

Authors:  Roberto Tejero; Yuanpeng Janet Huang; Theresa A Ramelot; Gaetano T Montelione
Journal:  Front Mol Biosci       Date:  2022-06-13

9.  Applying and improving AlphaFold at CASP14.

Authors:  John Jumper; Richard Evans; Alexander Pritzel; Tim Green; Michael Figurnov; Olaf Ronneberger; Kathryn Tunyasuvunakool; Russ Bates; Augustin Žídek; Anna Potapenko; Alex Bridgland; Clemens Meyer; Simon A A Kohl; Andrew J Ballard; Andrew Cowie; Bernardino Romera-Paredes; Stanislav Nikolov; Rishub Jain; Jonas Adler; Trevor Back; Stig Petersen; David Reiman; Ellen Clancy; Michal Zielinski; Martin Steinegger; Michalina Pacholska; Tamas Berghammer; David Silver; Oriol Vinyals; Andrew W Senior; Koray Kavukcuoglu; Pushmeet Kohli; Demis Hassabis
Journal:  Proteins       Date:  2021-12

Review 10.  Evolving Perspective on the Origin and Diversification of Cellular Life and the Virosphere.

Authors:  Anja Spang; Tara A Mahendrarajah; Pierre Offre; Courtney W Stairs
Journal:  Genome Biol Evol       Date:  2022-05-31       Impact factor: 4.065

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