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Number Cited by Other Article(s)
101
Suh D, Lee JW, Choi S, Lee Y. Recent Applications of Deep Learning Methods on Evolution- and Contact-Based Protein Structure Prediction. Int J Mol Sci 2021;22:6032. [PMID: 34199677 PMCID: PMC8199773 DOI: 10.3390/ijms22116032] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2021] [Revised: 05/29/2021] [Accepted: 05/29/2021] [Indexed: 01/23/2023]  Open
102
Wang X, Zhang Y, Yu B, Salhi A, Chen R, Wang L, Liu Z. Prediction of protein-protein interaction sites through eXtreme gradient boosting with kernel principal component analysis. Comput Biol Med 2021;134:104516. [PMID: 34119922 DOI: 10.1016/j.compbiomed.2021.104516] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Revised: 05/24/2021] [Accepted: 05/24/2021] [Indexed: 12/22/2022]
103
Görmez Y, Sabzekar M, Aydın Z. IGPRED: Combination of convolutional neural and graph convolutional networks for protein secondary structure prediction. Proteins 2021;89:1277-1288. [PMID: 33993559 DOI: 10.1002/prot.26149] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Revised: 04/21/2021] [Accepted: 05/11/2021] [Indexed: 11/10/2022]
104
Zhang S, Wang L, Zhao L, Li M, Liu M, Li K, Bin Y, Xia J. An improved DNA-binding hot spot residues prediction method by exploring interfacial neighbor properties. BMC Bioinformatics 2021;22:253. [PMID: 34000983 PMCID: PMC8130120 DOI: 10.1186/s12859-020-03871-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 11/09/2020] [Indexed: 11/29/2022]  Open
105
Remodelling structure-based drug design using machine learning. Emerg Top Life Sci 2021;5:13-27. [PMID: 33825834 DOI: 10.1042/etls20200253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/17/2021] [Accepted: 03/30/2021] [Indexed: 12/13/2022]
106
Hu J, Zheng LL, Bai YS, Zhang KW, Yu DJ, Zhang GJ. Accurate prediction of protein-ATP binding residues using position-specific frequency matrix. Anal Biochem 2021;626:114241. [PMID: 33971164 DOI: 10.1016/j.ab.2021.114241] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 04/27/2021] [Accepted: 05/01/2021] [Indexed: 10/21/2022]
107
Xu Y, Cheng J. Secondary structure prediction of protein based on multi scale convolutional attention neural networks. MATHEMATICAL BIOSCIENCES AND ENGINEERING : MBE 2021;18:3404-3422. [PMID: 34198392 DOI: 10.3934/mbe.2021170] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
108
Fogalli GB, Line SRP. Estimating the Influence of Physicochemical and Biochemical Property Indexes on Selection for Amino Acids Usage in Eukaryotic Cells. J Mol Evol 2021;89:257-268. [PMID: 33760966 DOI: 10.1007/s00239-021-10003-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 03/10/2021] [Indexed: 11/26/2022]
109
Wang J, Zhao Y, Gong W, Liu Y, Wang M, Huang X, Tan J. EDLMFC: an ensemble deep learning framework with multi-scale features combination for ncRNA-protein interaction prediction. BMC Bioinformatics 2021;22:133. [PMID: 33740884 PMCID: PMC7980572 DOI: 10.1186/s12859-021-04069-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 03/05/2021] [Indexed: 11/29/2022]  Open
110
Li Z, Zhang H. Automatic Detection for Multi-Labeled Cardiac Arrhythmia Based on Frame Blocking Preprocessing and Residual Networks. Front Cardiovasc Med 2021;8:616585. [PMID: 33816573 PMCID: PMC8017170 DOI: 10.3389/fcvm.2021.616585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Accepted: 02/15/2021] [Indexed: 11/20/2022]  Open
111
Liu Z, Gong Y, Guo Y, Zhang X, Lu C, Zhang L, Wang H. TMP- SSurface2: A Novel Deep Learning-Based Surface Accessibility Predictor for Transmembrane Protein Sequence. Front Genet 2021;12:656140. [PMID: 33790952 PMCID: PMC8006303 DOI: 10.3389/fgene.2021.656140] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 02/22/2021] [Indexed: 12/13/2022]  Open
112
Bhasin M, Varadarajan R. Prediction of Function Determining and Buried Residues Through Analysis of Saturation Mutagenesis Datasets. Front Mol Biosci 2021;8:635425. [PMID: 33778004 PMCID: PMC7991590 DOI: 10.3389/fmolb.2021.635425] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/25/2021] [Indexed: 11/13/2022]  Open
113
Shuvo MH, Bhattacharya S, Bhattacharya D. QDeep: distance-based protein model quality estimation by residue-level ensemble error classifications using stacked deep residual neural networks. Bioinformatics 2021;36:i285-i291. [PMID: 32657397 PMCID: PMC7355297 DOI: 10.1093/bioinformatics/btaa455] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
114
Kruglikov A, Rakesh M, Wei Y, Xia X. Applications of Protein Secondary Structure Algorithms in SARS-CoV-2 Research. J Proteome Res 2021;20:1457-1463. [PMID: 33617253 PMCID: PMC7927282 DOI: 10.1021/acs.jproteome.0c00734] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Indexed: 01/25/2023]
115
Roche R, Bhattacharya S, Bhattacharya D. Hybridized distance- and contact-based hierarchical structure modeling for folding soluble and membrane proteins. PLoS Comput Biol 2021;17:e1008753. [PMID: 33621244 PMCID: PMC7935296 DOI: 10.1371/journal.pcbi.1008753] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 03/05/2021] [Accepted: 01/31/2021] [Indexed: 11/18/2022]  Open
116
Bokor M, Tantos Á. Secondary Structures of Proteins: A Comparison of Models and Experimental Results. J Proteome Res 2021;20:1802-1808. [PMID: 33620224 PMCID: PMC8028322 DOI: 10.1021/acs.jproteome.0c00986] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
117
Guo Y, Wu J, Ma H, Wang S, Huang J. Comprehensive Study on Enhancing Low-Quality Position-Specific Scoring Matrix with Deep Learning for Accurate Protein Structure Property Prediction: Using Bagging Multiple Sequence Alignment Learning. J Comput Biol 2021;28:346-361. [PMID: 33617347 DOI: 10.1089/cmb.2020.0416] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]  Open
118
Uddin MR, Mahbub S, Rahman MS, Bayzid MS. SAINT: self-attention augmented inception-inside-inception network improves protein secondary structure prediction. Bioinformatics 2021;36:4599-4608. [PMID: 32437517 DOI: 10.1093/bioinformatics/btaa531] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Revised: 05/10/2020] [Accepted: 05/16/2020] [Indexed: 11/12/2022]  Open
119
Liu Z, Gong Y, Bao Y, Guo Y, Wang H, Lin GN. TMPSS: A Deep Learning-Based Predictor for Secondary Structure and Topology Structure Prediction of Alpha-Helical Transmembrane Proteins. Front Bioeng Biotechnol 2021;8:629937. [PMID: 33569377 PMCID: PMC7869861 DOI: 10.3389/fbioe.2020.629937] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 12/10/2020] [Indexed: 11/13/2022]  Open
120
Synergistic role of nucleotides and lipids for the self-assembly of Shs1 septin oligomers. Biochem J 2021;477:2697-2714. [PMID: 32726433 DOI: 10.1042/bcj20200199] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 07/07/2020] [Accepted: 07/09/2020] [Indexed: 12/25/2022]
121
Chen J, Zheng S, Zhao H, Yang Y. Structure-aware protein solubility prediction from sequence through graph convolutional network and predicted contact map. J Cheminform 2021;13:7. [PMID: 33557952 PMCID: PMC7869490 DOI: 10.1186/s13321-021-00488-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 01/20/2021] [Indexed: 11/26/2022]  Open
122
Eastwood EL, Jara KA, Bornelöv S, Munafò M, Frantzis V, Kneuss E, Barbar EJ, Czech B, Hannon GJ. Dimerisation of the PICTS complex via LC8/Cut-up drives co-transcriptional transposon silencing in Drosophila. eLife 2021;10:e65557. [PMID: 33538693 PMCID: PMC7861614 DOI: 10.7554/elife.65557] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 01/04/2021] [Indexed: 12/16/2022]  Open
123
Zhao Y, Liu Y. OCLSTM: Optimized convolutional and long short-term memory neural network model for protein secondary structure prediction. PLoS One 2021;16:e0245982. [PMID: 33534819 PMCID: PMC7857624 DOI: 10.1371/journal.pone.0245982] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 01/12/2021] [Indexed: 11/19/2022]  Open
124
Broad specificity of immune helminth scFv library to identify monoclonal antibodies targeting Strongyloides. Sci Rep 2021;11:2502. [PMID: 33510342 PMCID: PMC7843650 DOI: 10.1038/s41598-021-82125-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 01/04/2021] [Indexed: 12/24/2022]  Open
125
Runthala A. Probabilistic divergence of a template-based modelling methodology from the ideal protocol. J Mol Model 2021;27:25. [PMID: 33411019 DOI: 10.1007/s00894-020-04640-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 12/09/2020] [Indexed: 12/27/2022]
126
McGehee AJ, Bhattacharya S, Roche R, Bhattacharya D. PolyFold: An interactive visual simulator for distance-based protein folding. PLoS One 2020;15:e0243331. [PMID: 33270805 PMCID: PMC7714222 DOI: 10.1371/journal.pone.0243331] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2020] [Accepted: 11/18/2020] [Indexed: 11/18/2022]  Open
127
Izumi H, Nafie LA, Dukor RK. SSSCPreds: Deep Neural Network-Based Software for the Prediction of Conformational Variability and Application to SARS-CoV-2. ACS OMEGA 2020;5:30556-30567. [PMID: 33283104 PMCID: PMC7687297 DOI: 10.1021/acsomega.0c04472] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 11/05/2020] [Indexed: 05/05/2023]
128
HACS1 signaling adaptor protein recognizes a motif in the paired immunoglobulin receptor B cytoplasmic domain. Commun Biol 2020;3:672. [PMID: 33188360 PMCID: PMC7666139 DOI: 10.1038/s42003-020-01397-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 10/22/2020] [Indexed: 12/30/2022]  Open
129
Enhancing protein backbone angle prediction by using simpler models of deep neural networks. Sci Rep 2020;10:19430. [PMID: 33173130 PMCID: PMC7655839 DOI: 10.1038/s41598-020-76317-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 10/23/2020] [Indexed: 11/09/2022]  Open
130
Jing X, Dong Q, Hong D, Lu R. Amino Acid Encoding Methods for Protein Sequences: A Comprehensive Review and Assessment. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020;17:1918-1931. [PMID: 30998480 DOI: 10.1109/tcbb.2019.2911677] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
131
Wen B, Zeng W, Liao Y, Shi Z, Savage SR, Jiang W, Zhang B. Deep Learning in Proteomics. Proteomics 2020;20:e1900335. [PMID: 32939979 PMCID: PMC7757195 DOI: 10.1002/pmic.201900335] [Citation(s) in RCA: 78] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 09/14/2020] [Indexed: 12/17/2022]
132
Predicting Hot Spot Residues at Protein-DNA Binding Interfaces Based on Sequence Information. Interdiscip Sci 2020;13:1-11. [PMID: 33068261 DOI: 10.1007/s12539-020-00399-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 09/27/2020] [Accepted: 10/01/2020] [Indexed: 10/23/2022]
133
Kotowski K, Smolarczyk T, Roterman-Konieczna I, Stapor K. ProteinUnet-An efficient alternative to SPIDER3-single for sequence-based prediction of protein secondary structures. J Comput Chem 2020;42:50-59. [PMID: 33058261 PMCID: PMC7756333 DOI: 10.1002/jcc.26432] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Revised: 09/21/2020] [Accepted: 09/23/2020] [Indexed: 12/16/2022]
134
Valeri JA, Collins KM, Ramesh P, Alcantar MA, Lepe BA, Lu TK, Camacho DM. Sequence-to-function deep learning frameworks for engineered riboregulators. Nat Commun 2020;11:5058. [PMID: 33028819 PMCID: PMC7541510 DOI: 10.1038/s41467-020-18676-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 09/02/2020] [Indexed: 12/26/2022]  Open
135
Urban G, Torrisi M, Magnan CN, Pollastri G, Baldi P. Protein profiles: Biases and protocols. Comput Struct Biotechnol J 2020;18:2281-2289. [PMID: 32994887 PMCID: PMC7486441 DOI: 10.1016/j.csbj.2020.08.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/14/2020] [Accepted: 08/15/2020] [Indexed: 11/13/2022]  Open
136
Ding W, Gong H. Predicting the Real-Valued Inter-Residue Distances for Proteins. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020;7:2001314. [PMID: 33042750 PMCID: PMC7539185 DOI: 10.1002/advs.202001314] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/06/2020] [Indexed: 05/04/2023]
137
Pan Y, Zhou S, Guan J. Computationally identifying hot spots in protein-DNA binding interfaces using an ensemble approach. BMC Bioinformatics 2020;21:384. [PMID: 32938375 PMCID: PMC7495898 DOI: 10.1186/s12859-020-03675-3] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]  Open
138
Guo Z, Hou J, Cheng J. DNSS2: Improved ab initio protein secondary structure prediction using advanced deep learning architectures. Proteins 2020;89:207-217. [PMID: 32893403 DOI: 10.1002/prot.26007] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 07/07/2020] [Accepted: 09/02/2020] [Indexed: 12/27/2022]
139
Hanson J, Litfin T, Paliwal K, Zhou Y. Identifying molecular recognition features in intrinsically disordered regions of proteins by transfer learning. Bioinformatics 2020;36:1107-1113. [PMID: 31504193 DOI: 10.1093/bioinformatics/btz691] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 07/24/2019] [Accepted: 08/31/2019] [Indexed: 11/12/2022]  Open
140
Ranjan A, Fahad MS, Fernandez-Baca D, Deepak A, Tripathi S. Deep Robust Framework for Protein Function Prediction Using Variable-Length Protein Sequences. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020;17:1648-1659. [PMID: 30998479 DOI: 10.1109/tcbb.2019.2911609] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
141
Sequence-Based Prediction of Metamorphic Behavior in Proteins. Biophys J 2020;119:1380-1390. [PMID: 32937108 PMCID: PMC7567988 DOI: 10.1016/j.bpj.2020.07.034] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 07/07/2020] [Accepted: 07/23/2020] [Indexed: 12/24/2022]  Open
142
Visibelli A, Bongini P, Rossi A, Niccolai N, Bianchini M. A deep attention network for predicting amino acid signals in the formation of [Formula: see text]-helices. J Bioinform Comput Biol 2020;18:2050028. [PMID: 32757808 DOI: 10.1142/s0219720020500286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
143
Jing R, Li Y, Xue L, Liu F, Li M, Luo J. autoBioSeqpy: A Deep Learning Tool for the Classification of Biological Sequences. J Chem Inf Model 2020;60:3755-3764. [PMID: 32786512 DOI: 10.1021/acs.jcim.0c00409] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
144
Xu G, Wang Q, Ma J. OPUS-TASS: a protein backbone torsion angles and secondary structure predictor based on ensemble neural networks. Bioinformatics 2020;36:5021-5026. [DOI: 10.1093/bioinformatics/btaa629] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 06/25/2020] [Accepted: 07/10/2020] [Indexed: 11/13/2022]  Open
145
Sun J, Frishman D. DeepHelicon: Accurate prediction of inter-helical residue contacts in transmembrane proteins by residual neural networks. J Struct Biol 2020;212:107574. [PMID: 32663598 DOI: 10.1016/j.jsb.2020.107574] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/03/2020] [Accepted: 07/07/2020] [Indexed: 01/16/2023]
146
Shi Q, Chen W, Huang S, Jin F, Dong Y, Wang Y, Xue Z. DNN-Dom: predicting protein domain boundary from sequence alone by deep neural network. Bioinformatics 2020;35:5128-5136. [PMID: 31197306 DOI: 10.1093/bioinformatics/btz464] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 05/07/2019] [Accepted: 06/05/2019] [Indexed: 11/13/2022]  Open
147
Taherzadeh G, Dehzangi A, Golchin M, Zhou Y, Campbell MP. SPRINT-Gly: predicting N- and O-linked glycosylation sites of human and mouse proteins by using sequence and predicted structural properties. Bioinformatics 2020;35:4140-4146. [PMID: 30903686 DOI: 10.1093/bioinformatics/btz215] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 03/03/2019] [Accepted: 03/21/2019] [Indexed: 12/19/2022]  Open
148
Chopra K, Burdak B, Sharma K, Kembhavi A, Mande SC, Chauhan R. CoRNeA: A Pipeline to Decrypt the Inter-Protein Interfaces from Amino Acid Sequence Information. Biomolecules 2020;10:biom10060938. [PMID: 32580303 PMCID: PMC7356028 DOI: 10.3390/biom10060938] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2020] [Revised: 05/26/2020] [Accepted: 05/27/2020] [Indexed: 12/27/2022]  Open
149
Wu X, Siggel M, Ovchinnikov S, Mi W, Svetlov V, Nudler E, Liao M, Hummer G, Rapoport TA. Structural basis of ER-associated protein degradation mediated by the Hrd1 ubiquitin ligase complex. Science 2020;368:368/6489/eaaz2449. [PMID: 32327568 DOI: 10.1126/science.aaz2449] [Citation(s) in RCA: 152] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2019] [Revised: 01/18/2020] [Accepted: 03/11/2020] [Indexed: 12/13/2022]
150
Shapovalov M, Dunbrack RL, Vucetic S. Multifaceted analysis of training and testing convolutional neural networks for protein secondary structure prediction. PLoS One 2020;15:e0232528. [PMID: 32374785 PMCID: PMC7202669 DOI: 10.1371/journal.pone.0232528] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 04/16/2020] [Indexed: 11/30/2022]  Open
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