Fast protein structure comparison through effective representation learning with contrastive graph neural networks.

Autor: Chunqiu Xia, Shi-Hao Feng, Ying Xia, Xiaoyong Pan, Hong-Bin Shen

Publikováno v: PLoS Computational Biology, Vol 18, Iss 3, p e1009986 (2022)

Protein structure alignment algorithms are often time-consuming, resulting in challenges for large-scale protein structure similarity-based retrieval. There is an urgent need for more efficient structure comparison approaches as the number of protein

Externí odkaz: https://doaj.org/article/55959f429b074711b63306a7c7ca9a5c

Ab-Initio Membrane Protein Amphipathic Helix Structure Prediction Using Deep Neural Networks

Autor: Hong-Bin Shen, Shi-Hao Feng, Chun-Qiu Xia, Peidong Zhang

Publikováno v: IEEE/ACM Transactions on Computational Biology and Bioinformatics. 19:795-805

Amphipathic helix (AH)features the segregation of polar and nonpolar residues and plays important roles in many membrane-associated biological processes through interacting with both the lipid and the soluble phases. Although the AH structure has bee

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::4933d5d3a2214b3c189d637ce071986d
https://doi.org/10.1109/tcbb.2020.3029274

CoCoPRED: coiled-coil protein structural feature prediction from amino acid sequence using deep neural networks

Autor: Chun-Qiu Xia, Hong-Bin Shen, Shi-Hao Feng

Publikováno v: Bioinformatics. 38:720-729

Motivation Coiled-coil is composed of two or more helices that are wound around each other. It widely exists in proteins and has been discovered to play a variety of critical roles in biology processes. Generally, there are three types of structural

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::cefd997a41a300c23383777ebf3a4f47
https://doi.org/10.1093/bioinformatics/btab744

Fast protein structure comparison through effective representation learning with contrastive graph neural networks

Autor: Chunqiu Xia, Shi-Hao Feng, Ying Xia, Xiaoyong Pan, Hong-Bin Shen

Publikováno v: PLoS computational biology. 18(3)

Protein structure alignment algorithms are often time-consuming, resulting in challenges for large-scale protein structure similarity-based retrieval. There is an urgent need for more efficient structure comparison approaches as the number of protein

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_dedup___::301a090f1e99b0878a53b0ddac79ab0f
https://pubmed.ncbi.nlm.nih.gov/35324898

Contributors

Autor: Oguz Akbilgic, Turki AlAnzi, Xiangdong An, Jorge R. Barrio, Alessandra Bertoldo, Lei Bi, Sheng Bin, Weidong Cai, Longbing Cao, Hao Chen, Robert Clarke, Claudio Cobelli, Hui Cui, Qi Dou, Yiping P. Du, Stefan Eberl, Ming Fan, Shi-Hao Feng, David Dagan Feng, Gregory S. Fischer, Yi Fu, Michael J. Fulham, Fan Gao, Manzhao Hao, Pheng-Ann Heng, Sung-Cheng Huang, H.K. Huang, Jimmy Xiangji Huang, Robert S.H. Istepanian, Younhyun Jung, Rishikesan Kamaleswaran, Peter Kazanzides, Jinman Kim, Minjeong Kim, Bin Kong, Ashnil Kumar, Ning Lan, Zhongyu Li, Lihua Li, Brent J. Liu, Junbo Ma, Chunhong Mao, Saleha Masood, Seong K. Mun, Yuxiang Pan, Jing Qin, Habtom W. Ressom, Caroline Schoenewald, Arash Shaban-Nejad, Hong-Bin Shen, Eun Kyong Shin, Nabil Simaan, Nadine Smith, Yang Song, Russell H. Taylor, Tsung-Heng Tsai, Jiawei Tu, Michael A. Urbin, Hao Wan, Hao Wang, Yuqi Wang, Qian Wang, Xiuying Wang, Minkun Wang, Ping Wang, Yue Wang, Andrew Webb, Douglas J. Weber, Lingfeng Wen, Anna M. Wu, Guorong Wu, Jia-Yan Xu, Chenggang Yan, Ke Yan, Defu Yang, Xiaofeng Zhang, Shaoting Zhang, Bin Zhang, Zhen Zhang, Yitan Zhu, Liujing Zhuang, Wangmeng Zuo

Externí odkaz: https://explore.openaire.eu/search/publication?articleId=doi_________::52a8a55b64f633ac0720740bb48c7b1b
https://doi.org/10.1016/b978-0-12-816034-3.01002-6