Literature DB >> 33639355

Deep learning techniques have significantly impacted protein structure prediction and protein design.

Robin Pearce1, Yang Zhang2.   

Abstract

Protein structure prediction and design can be regarded as two inverse processes governed by the same folding principle. Although progress remained stagnant over the past two decades, the recent application of deep neural networks to spatial constraint prediction and end-to-end model training has significantly improved the accuracy of protein structure prediction, largely solving the problem at the fold level for single-domain proteins. The field of protein design has also witnessed dramatic improvement, where noticeable examples have shown that information stored in neural-network models can be used to advance functional protein design. Thus, incorporation of deep learning techniques into different steps of protein folding and design approaches represents an exciting future direction and should continue to have a transformative impact on both fields.
Copyright © 2021 Elsevier Ltd. All rights reserved.

Entities:  

Mesh:

Substances:

Year:  2021        PMID: 33639355      PMCID: PMC8222070          DOI: 10.1016/j.sbi.2021.01.007

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN: 0959-440X            Impact factor:   7.786


  61 in total

1.  Improved protein structure prediction using predicted interresidue orientations.

Authors:  Jianyi Yang; Ivan Anishchenko; Hahnbeom Park; Zhenling Peng; Sergey Ovchinnikov; David Baker
Journal:  Proc Natl Acad Sci U S A       Date:  2020-01-02       Impact factor: 11.205

2.  EvoEF2: accurate and fast energy function for computational protein design.

Authors:  Xiaoqiang Huang; Robin Pearce; Yang Zhang
Journal:  Bioinformatics       Date:  2020-02-15       Impact factor: 6.937

3.  Improved protein structure prediction using potentials from deep learning.

Authors:  Andrew W Senior; Richard Evans; John Jumper; James Kirkpatrick; Laurent Sifre; Tim Green; Chongli Qin; Augustin Žídek; Alexander W R Nelson; Alex Bridgland; Hugo Penedones; Stig Petersen; Karen Simonyan; Steve Crossan; Pushmeet Kohli; David T Jones; David Silver; Koray Kavukcuoglu; Demis Hassabis
Journal:  Nature       Date:  2020-01-15       Impact factor: 49.962

4.  De novo design of protein logic gates.

Authors:  Zibo Chen; Ryan D Kibler; Andrew Hunt; Florian Busch; Jocelynn Pearl; Mengxuan Jia; Zachary L VanAernum; Basile I M Wicky; Galen Dods; Hanna Liao; Matthew S Wilken; Christie Ciarlo; Shon Green; Hana El-Samad; John Stamatoyannopoulos; Vicki H Wysocki; Michael C Jewett; Scott E Boyken; David Baker
Journal:  Science       Date:  2020-04-03       Impact factor: 47.728

5.  A novel side-chain orientation dependent potential derived from random-walk reference state for protein fold selection and structure prediction.

Authors:  Jian Zhang; Yang Zhang
Journal:  PLoS One       Date:  2010-10-27       Impact factor: 3.240

6.  RosettaRemodel: a generalized framework for flexible backbone protein design.

Authors:  Po-Ssu Huang; Yih-En Andrew Ban; Florian Richter; Ingemar Andre; Robert Vernon; William R Schief; David Baker
Journal:  PLoS One       Date:  2011-08-31       Impact factor: 3.240

7.  Accurate De Novo Prediction of Protein Contact Map by Ultra-Deep Learning Model.

Authors:  Sheng Wang; Siqi Sun; Zhen Li; Renyu Zhang; Jinbo Xu
Journal:  PLoS Comput Biol       Date:  2017-01-05       Impact factor: 4.475

8.  Computational Design of SARS-CoV-2 Spike Glycoproteins to Increase Immunogenicity by T Cell Epitope Engineering.

Authors:  Edison Ong; Xiaoqiang Huang; Robin Pearce; Yang Zhang; Yongqun He
Journal:  Comput Struct Biotechnol J       Date:  2020-12-31       Impact factor: 7.271

9.  De novo design of picomolar SARS-CoV-2 miniprotein inhibitors.

Authors:  Longxing Cao; Inna Goreshnik; Brian Coventry; James Brett Case; Lauren Miller; Lisa Kozodoy; Rita E Chen; Lauren Carter; Alexandra C Walls; Young-Jun Park; Eva-Maria Strauch; Lance Stewart; Michael S Diamond; David Veesler; David Baker
Journal:  Science       Date:  2020-09-09       Impact factor: 47.728

10.  De novo design of a four-fold symmetric TIM-barrel protein with atomic-level accuracy.

Authors:  Po-Ssu Huang; Kaspar Feldmeier; Fabio Parmeggiani; D Alejandro Fernandez Velasco; Birte Höcker; David Baker
Journal:  Nat Chem Biol       Date:  2015-11-23       Impact factor: 15.040

View more
  10 in total

Review 1.  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

2.  Whole-Genome Sequencing of a Potential Ester-Synthesizing Bacterium Isolated from Fermented Golden Pomfret and Identification of Its Lipase Encoding Genes.

Authors:  Huifang Wang; Yanyan Wu; Yueqi Wang
Journal:  Foods       Date:  2022-06-30

Review 3.  Protein Design with Deep Learning.

Authors:  Marianne Defresne; Sophie Barbe; Thomas Schiex
Journal:  Int J Mol Sci       Date:  2021-10-29       Impact factor: 5.923

4.  DeepVASP-E: A Flexible Analysis of Electrostatic Isopotentials for Finding and Explaining Mechanisms that Control Binding Specificity.

Authors:  Felix M Quintana; Zhaoming Kong; Lifang He; Brian Y Chen
Journal:  Pac Symp Biocomput       Date:  2022

5.  Proteome-Wide Profiling of the Covalent-Druggable Cysteines with a Structure-Based Deep Graph Learning Network.

Authors:  Hongyan Du; Dejun Jiang; Junbo Gao; Xujun Zhang; Lingxiao Jiang; Yundian Zeng; Zhenxing Wu; Chao Shen; Lei Xu; Dongsheng Cao; Tingjun Hou; Peichen Pan
Journal:  Research (Wash D C)       Date:  2022-07-21

Review 6.  AlphaFold, Artificial Intelligence (AI), and Allostery.

Authors:  Ruth Nussinov; Mingzhen Zhang; Yonglan Liu; Hyunbum Jang
Journal:  J Phys Chem B       Date:  2022-08-17       Impact factor: 3.466

7.  Energy Profile Bayes and Thompson Optimized Convolutional Neural Network protein structure prediction.

Authors:  Varanavasi Nallasamy; Malarvizhi Seshiah
Journal:  Neural Comput Appl       Date:  2022-10-07       Impact factor: 5.102

8.  Fast and accurate Ab Initio Protein structure prediction using deep learning potentials.

Authors:  Robin Pearce; Yang Li; Gilbert S Omenn; Yang Zhang
Journal:  PLoS Comput Biol       Date:  2022-09-16       Impact factor: 4.779

Review 9.  Recent Advances in Protein Homology Detection Propelled by Inter-Residue Interaction Map Threading.

Authors:  Sutanu Bhattacharya; Rahmatullah Roche; Md Hossain Shuvo; Debswapna Bhattacharya
Journal:  Front Mol Biosci       Date:  2021-05-11

10.  Highly accurate protein structure prediction with AlphaFold.

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; Demis Hassabis; Jonas Adler; Trevor Back; Stig Petersen; David Reiman; Ellen Clancy; Michal Zielinski; Martin Steinegger; Michalina Pacholska; Tamas Berghammer; Sebastian Bodenstein; David Silver; Oriol Vinyals; Andrew W Senior; Koray Kavukcuoglu; Pushmeet Kohli
Journal:  Nature       Date:  2021-07-15       Impact factor: 49.962

  10 in total

北京卡尤迪生物科技股份有限公司 © 2022-2023.