Deep graph learning to estimate protein model quality using structural constraints from multiple sequence alignments

Author:

Rahbar Mahdi1,Chauhan Rahul Kumar1,Shah Pankil Nimeshbhai1,Cao Renzhi2,Si Dong3,Hou Jie1

Affiliation:

1. Saint Louis University

2. Pacific Lutheran University

3. University of Washington

Funder

Saint Louis University

Publisher

ACM

Reference51 articles.

1. 2021. UniProt: the universal protein knowledgebase in 2021 . Nucleic acids research 49, D1 (2021), D480--D489. 2021. UniProt: the universal protein knowledgebase in 2021. Nucleic acids research 49, D1 (2021), D480--D489.

2. Badri Adhikari and Jianlin Cheng . 2016. Protein Residue Contacts and Prediction Methods. Methods in molecular biology (Clifton , N.J.) 1415 ( 2016 ), 463--76. Badri Adhikari and Jianlin Cheng. 2016. Protein Residue Contacts and Prediction Methods. Methods in molecular biology (Clifton, N.J.) 1415 (2016), 463--76.

3. DNCON2: improved protein contact prediction using two-level deep convolutional neural networks

4. Minkyung Baek , Frank DiMaio , Ivan Anishchenko , Justas Dauparas , Sergey Ovchinnikov , Gyu Rie Lee , Jue Wang, Qian Cong, Lisa N Kinch, R Dustin Schaeffer, et al. 2021 . Accurate prediction of protein structures and interactions using a three-track neural network. Science 373, 6557 (2021), 871--876. Minkyung Baek, Frank DiMaio, Ivan Anishchenko, Justas Dauparas, Sergey Ovchinnikov, Gyu Rie Lee, Jue Wang, Qian Cong, Lisa N Kinch, R Dustin Schaeffer, et al. 2021. Accurate prediction of protein structures and interactions using a three-track neural network. Science 373, 6557 (2021), 871--876.

5. Renzhi Cao , Debswapna Bhattacharya , Jie Hou , and Jianlin Cheng . 2016. DeepQA: improving the estimation of single protein model quality with deep belief networks. BMC bioinformatics 17, 1 ( 2016 ), 1--9. Renzhi Cao, Debswapna Bhattacharya, Jie Hou, and Jianlin Cheng. 2016. DeepQA: improving the estimation of single protein model quality with deep belief networks. BMC bioinformatics 17, 1 (2016), 1--9.

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