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For: Cozzetto D, Minneci F, Currant H, Jones DT. FFPred 3: feature-based function prediction for all Gene Ontology domains. Sci Rep 2016;6:31865. [PMID: 27561554 PMCID: PMC4999993 DOI: 10.1038/srep31865] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 07/25/2016] [Indexed: 11/09/2022]  Open
Number Cited by Other Article(s)
1
Tariq TB, Munir F, Jabeen I, Gul A, Amir R. Molecular modelling and gene expression analysis to probe the GT-γ trihelix transcription factors in Solanum tuberosum under drought stress. Sci Rep 2025;15:12471. [PMID: 40216884 PMCID: PMC11992213 DOI: 10.1038/s41598-025-96485-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Accepted: 03/28/2025] [Indexed: 04/14/2025]  Open
2
Li J, Chen X, Huang H, Zeng M, Yu J, Gong X, Ye Q. $\mathcal{S}$ able: bridging the gap in protein structure understanding with an empowering and versatile pre-training paradigm. Brief Bioinform 2025;26:bbaf120. [PMID: 40163822 PMCID: PMC11957296 DOI: 10.1093/bib/bbaf120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2024] [Revised: 01/23/2025] [Accepted: 02/23/2025] [Indexed: 04/02/2025]  Open
3
Yadav DK, Srivastava GP, Singh A, Singh M, Yadav N, Tuteja N. Proteome-wide analysis reveals G protein-coupled receptor-like proteins in rice (Oryza sativa). PLANT SIGNALING & BEHAVIOR 2024;19:2365572. [PMID: 38904257 PMCID: PMC11195488 DOI: 10.1080/15592324.2024.2365572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 06/04/2024] [Indexed: 06/22/2024]
4
Ahmad EM, Abdelsamad A, El-Shabrawi HM, El-Awady MAM, Aly MAM, El-Soda M. In-silico identification of putatively functional intergenic small open reading frames in the cucumber genome and their predicted response to biotic and abiotic stresses. PLANT, CELL & ENVIRONMENT 2024;47:5330-5342. [PMID: 39189930 DOI: 10.1111/pce.15104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2024] [Revised: 07/13/2024] [Accepted: 08/10/2024] [Indexed: 08/28/2024]
5
Li C, Luo Y, Xie Y, Zhang Z, Liu Y, Zou L, Xiao F. Structural and functional prediction, evaluation, and validation in the post-sequencing era. Comput Struct Biotechnol J 2024;23:446-451. [PMID: 38223342 PMCID: PMC10787220 DOI: 10.1016/j.csbj.2023.12.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/16/2024]  Open
6
Breimann S, Kamp F, Steiner H, Frishman D. AAontology: An Ontology of Amino Acid Scales for Interpretable Machine Learning. J Mol Biol 2024;436:168717. [PMID: 39053689 DOI: 10.1016/j.jmb.2024.168717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/15/2024] [Accepted: 07/19/2024] [Indexed: 07/27/2024]
7
Buchan DWA, Moffat L, Lau A, Kandathil S, Jones D. Deep learning for the PSIPRED Protein Analysis Workbench. Nucleic Acids Res 2024;52:W287-W293. [PMID: 38747351 PMCID: PMC11223827 DOI: 10.1093/nar/gkae328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 04/08/2024] [Accepted: 04/24/2024] [Indexed: 07/06/2024]  Open
8
Ye B, Liang J. Predicting Functional Surface Topographies Combining Topological Data Analysis and Deep Learning Across the Human Protein Universe. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2024;2024:1-4. [PMID: 40039158 DOI: 10.1109/embc53108.2024.10782681] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/06/2025]
9
Duo H, Chhabra R, Muthusamy V, Zunjare RU, Hossain F. Assessing sequence variation, haplotype analysis and molecular characterisation of aspartate kinase2 (ask2) gene regulating methionine biosynthesis in diverse maize inbreds. Mol Genet Genomics 2024;299:7. [PMID: 38349549 DOI: 10.1007/s00438-024-02096-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Accepted: 11/02/2023] [Indexed: 02/15/2024]
10
Hannon Bozorgmehr J. Four classic "de novo" genes all have plausible homologs and likely evolved from retro-duplicated or pseudogenic sequences. Mol Genet Genomics 2024;299:6. [PMID: 38315248 DOI: 10.1007/s00438-023-02090-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 10/15/2023] [Indexed: 02/07/2024]
11
Dagher SF, Vaishnav A, Stanley CB, Meilleur F, Edwards BFP, Bruno-Bárcena JM. Structural analysis and functional evaluation of the disordered ß-hexosyltransferase region from Hamamotoa (Sporobolomyces) singularis. Front Bioeng Biotechnol 2023;11:1291245. [PMID: 38162180 PMCID: PMC10755861 DOI: 10.3389/fbioe.2023.1291245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 11/16/2023] [Indexed: 01/03/2024]  Open
12
Krishnamoorthy S, Muruganantham B, Yu JR, Park WY, Muthusami S. Exploring the utility of FTS as a bonafide binding partner for EGFR: A potential drug target for cervical cancer. Comput Biol Med 2023;167:107592. [PMID: 37976824 DOI: 10.1016/j.compbiomed.2023.107592] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/25/2023] [Accepted: 10/17/2023] [Indexed: 11/19/2023]
13
Chen J, Gu Z, Lai L, Pei J. In silico protein function prediction: the rise of machine learning-based approaches. MEDICAL REVIEW (2021) 2023;3:487-510. [PMID: 38282798 PMCID: PMC10808870 DOI: 10.1515/mr-2023-0038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 10/11/2023] [Indexed: 01/30/2024]
14
Hartke J, Ceron-Noriega A, Stoldt M, Sistermans T, Kever M, Fuchs J, Butter F, Foitzik S. Long live the host! Proteomic analysis reveals possible strategies for parasitic manipulation of its social host. Mol Ecol 2023;32:5877-5889. [PMID: 37795937 DOI: 10.1111/mec.17155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 09/15/2023] [Accepted: 09/19/2023] [Indexed: 10/06/2023]
15
Li W, Yu Y, Zhou G, Hu G, Li B, Ma H, Yan W, Pei H. Large-scale ORF screening based on LC-MS to discover novel lncRNA-encoded peptides responding to ionizing radiation and microgravity. Comput Struct Biotechnol J 2023;21:5201-5211. [PMID: 37928948 PMCID: PMC10624585 DOI: 10.1016/j.csbj.2023.10.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 10/12/2023] [Accepted: 10/18/2023] [Indexed: 11/07/2023]  Open
16
Boadu F, Cao H, Cheng J. Combining protein sequences and structures with transformers and equivariant graph neural networks to predict protein function. Bioinformatics 2023;39:i318-i325. [PMID: 37387145 DOI: 10.1093/bioinformatics/btad208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/01/2023]  Open
17
Wang Z, Deng Z, Zhang W, Lou Q, Choi KS, Wei Z, Wang L, Wu J. MMSMAPlus: a multi-view multi-scale multi-attention embedding model for protein function prediction. Brief Bioinform 2023:7187109. [PMID: 37258453 DOI: 10.1093/bib/bbad201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 04/16/2023] [Accepted: 05/08/2023] [Indexed: 06/02/2023]  Open
18
Boadu F, Cao H, Cheng J. Combining protein sequences and structures with transformers and equivariant graph neural networks to predict protein function. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.17.524477. [PMID: 36711471 PMCID: PMC9882282 DOI: 10.1101/2023.01.17.524477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
19
Systems biology's role in leveraging microalgal biomass potential: Current status and future perspectives. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
20
Zhu YH, Zhang C, Yu DJ, Zhang Y. Integrating unsupervised language model with triplet neural networks for protein gene ontology prediction. PLoS Comput Biol 2022;18:e1010793. [PMID: 36548439 PMCID: PMC9822105 DOI: 10.1371/journal.pcbi.1010793] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 01/06/2023] [Accepted: 12/05/2022] [Indexed: 12/24/2022]  Open
21
Gupta N, Reddy K, Gnanasekaran P, Zhai Y, Chakraborty S, Pappu HR. Functional characterization of a new ORF βV1 encoded by radish leaf curl betasatellite. FRONTIERS IN PLANT SCIENCE 2022;13:972386. [PMID: 36212370 PMCID: PMC9546537 DOI: 10.3389/fpls.2022.972386] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Accepted: 08/10/2022] [Indexed: 05/26/2023]
22
Ramola R, Friedberg I, Radivojac P. The field of protein function prediction as viewed by different domain scientists. BIOINFORMATICS ADVANCES 2022;2:vbac057. [PMID: 36699361 PMCID: PMC9710704 DOI: 10.1093/bioadv/vbac057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/14/2022] [Indexed: 01/28/2023]
23
Almutairi ZM. In Silico Identification and Characterization of B12D Family Proteins in Viridiplantae. Evol Bioinform Online 2022;18:11769343221106795. [PMID: 35721582 PMCID: PMC9201304 DOI: 10.1177/11769343221106795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 05/12/2022] [Indexed: 11/16/2022]  Open
24
Lai B, Xu J. Accurate protein function prediction via graph attention networks with predicted structure information. Brief Bioinform 2022;23:bbab502. [PMID: 34882195 PMCID: PMC8898000 DOI: 10.1093/bib/bbab502] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 10/13/2021] [Accepted: 11/02/2021] [Indexed: 12/27/2022]  Open
25
Matkovic R, Morel M, Lanciano S, Larrous P, Martin B, Bejjani F, Vauthier V, Hansen MMK, Emiliani S, Cristofari G, Gallois-Montbrun S, Margottin-Goguet F. TASOR epigenetic repressor cooperates with a CNOT1 RNA degradation pathway to repress HIV. Nat Commun 2022;13:66. [PMID: 35013187 PMCID: PMC8748822 DOI: 10.1038/s41467-021-27650-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 11/30/2021] [Indexed: 12/17/2022]  Open
26
Greener JG, Kandathil SM, Moffat L, Jones DT. A guide to machine learning for biologists. Nat Rev Mol Cell Biol 2022;23:40-55. [PMID: 34518686 DOI: 10.1038/s41580-021-00407-0] [Citation(s) in RCA: 782] [Impact Index Per Article: 260.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/23/2021] [Indexed: 02/08/2023]
27
Törönen P, Holm L. PANNZER-A practical tool for protein function prediction. Protein Sci 2022;31:118-128. [PMID: 34562305 PMCID: PMC8740830 DOI: 10.1002/pro.4193] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 09/22/2021] [Accepted: 09/22/2021] [Indexed: 01/03/2023]
28
Protein function prediction using functional inter-relationship. Comput Biol Chem 2021;95:107593. [PMID: 34736126 DOI: 10.1016/j.compbiolchem.2021.107593] [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: 04/21/2021] [Revised: 08/25/2021] [Accepted: 10/03/2021] [Indexed: 11/23/2022]
29
Zhang F, Song H, Zeng M, Wu FX, Li Y, Pan Y, Li M. A Deep Learning Framework for Gene Ontology Annotations With Sequence- and Network-Based Information. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2021;18:2208-2217. [PMID: 31985440 DOI: 10.1109/tcbb.2020.2968882] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
30
Elhaj-Abdou MEM, El-Dib H, El-Helw A, El-Habrouk M. Deep_CNN_LSTM_GO: Protein function prediction from amino-acid sequences. Comput Biol Chem 2021;95:107584. [PMID: 34601431 DOI: 10.1016/j.compbiolchem.2021.107584] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 09/08/2021] [Accepted: 09/21/2021] [Indexed: 11/15/2022]
31
Vu TTD, Jung J. Protein function prediction with gene ontology: from traditional to deep learning models. PeerJ 2021;9:e12019. [PMID: 34513334 PMCID: PMC8395570 DOI: 10.7717/peerj.12019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 07/29/2021] [Indexed: 11/25/2022]  Open
32
Unveiling the structure of GPI-anchored protein of Malassezia globosa and its pathogenic role in pityriasis versicolor. J Mol Model 2021;27:246. [PMID: 34379190 DOI: 10.1007/s00894-021-04853-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2021] [Accepted: 07/07/2021] [Indexed: 10/20/2022]
33
Kulmanov M, Smaili FZ, Gao X, Hoehndorf R. Semantic similarity and machine learning with ontologies. Brief Bioinform 2021;22:bbaa199. [PMID: 33049044 PMCID: PMC8293838 DOI: 10.1093/bib/bbaa199] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 08/03/2020] [Accepted: 08/04/2020] [Indexed: 12/13/2022]  Open
34
Kulmanov M, Zhapa-Camacho F, Hoehndorf R. DeepGOWeb: fast and accurate protein function prediction on the (Semantic) Web. Nucleic Acids Res 2021;49:W140-W146. [PMID: 34019664 PMCID: PMC8262746 DOI: 10.1093/nar/gkab373] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/18/2021] [Accepted: 04/26/2021] [Indexed: 11/24/2022]  Open
35
Structure-based protein function prediction using graph convolutional networks. Nat Commun 2021;12:3168. [PMID: 34039967 PMCID: PMC8155034 DOI: 10.1038/s41467-021-23303-9] [Citation(s) in RCA: 337] [Impact Index Per Article: 84.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 04/22/2021] [Indexed: 02/04/2023]  Open
36
Villegas-Morcillo A, Makrodimitris S, van Ham RCHJ, Gomez AM, Sanchez V, Reinders MJT. Unsupervised protein embeddings outperform hand-crafted sequence and structure features at predicting molecular function. Bioinformatics 2021;37:162-170. [PMID: 32797179 PMCID: PMC8055213 DOI: 10.1093/bioinformatics/btaa701] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 07/10/2020] [Accepted: 08/12/2020] [Indexed: 12/19/2022]  Open
37
Ofer D, Brandes N, Linial M. The language of proteins: NLP, machine learning & protein sequences. Comput Struct Biotechnol J 2021;19:1750-1758. [PMID: 33897979 PMCID: PMC8050421 DOI: 10.1016/j.csbj.2021.03.022] [Citation(s) in RCA: 145] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 03/19/2021] [Accepted: 03/19/2021] [Indexed: 12/12/2022]  Open
38
Seyyedsalehi SF, Soleymani M, Rabiee HR, Mofrad MRK. PFP-WGAN: Protein function prediction by discovering Gene Ontology term correlations with generative adversarial networks. PLoS One 2021;16:e0244430. [PMID: 33630862 PMCID: PMC7906332 DOI: 10.1371/journal.pone.0244430] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 12/09/2020] [Indexed: 12/12/2022]  Open
39
Barot M, Gligorijević V, Cho K, Bonneau R. NetQuilt: Deep Multispecies Network-based Protein Function Prediction using Homology-informed Network Similarity. Bioinformatics 2021;37:2414-2422. [PMID: 33576802 PMCID: PMC8388039 DOI: 10.1093/bioinformatics/btab098] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 02/04/2021] [Accepted: 02/09/2021] [Indexed: 02/02/2023]  Open
40
Venko K, Novič M, Stoka V, Žerovnik E. Prediction of Transmembrane Regions, Cholesterol, and Ganglioside Binding Sites in Amyloid-Forming Proteins Indicate Potential for Amyloid Pore Formation. Front Mol Neurosci 2021;14:619496. [PMID: 33642992 PMCID: PMC7902868 DOI: 10.3389/fnmol.2021.619496] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 01/12/2021] [Indexed: 12/26/2022]  Open
41
Littmann M, Heinzinger M, Dallago C, Olenyi T, Rost B. Embeddings from deep learning transfer GO annotations beyond homology. Sci Rep 2021;11:1160. [PMID: 33441905 PMCID: PMC7806674 DOI: 10.1038/s41598-020-80786-0] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 12/24/2020] [Indexed: 11/09/2022]  Open
42
Wu F, Ma J, Cha Y, Lu D, Li Z, Zhuo M, Luo X, Li S, Zhu M. Using inexpensive substrate to achieve high-level lipase A secretion by Bacillus subtilis through signal peptide and promoter screening. Process Biochem 2020. [DOI: 10.1016/j.procbio.2020.08.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Semwal R, Varadwaj PK. HumDLoc: Human Protein Subcellular Localization Prediction Using Deep Neural Network. Curr Genomics 2020;21:546-557. [PMID: 33214771 PMCID: PMC7604748 DOI: 10.2174/1389202921999200528160534] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 03/27/2020] [Accepted: 03/30/2020] [Indexed: 11/24/2022]  Open
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Du Z, He Y, Li J, Uversky VN. DeepAdd: Protein function prediction from k-mer embedding and additional features. Comput Biol Chem 2020;89:107379. [PMID: 33011616 DOI: 10.1016/j.compbiolchem.2020.107379] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 09/15/2020] [Accepted: 09/17/2020] [Indexed: 10/23/2022]
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Zhang C, Zheng W, Mortuza SM, Li Y, Zhang Y. DeepMSA: constructing deep multiple sequence alignment to improve contact prediction and fold-recognition for distant-homology proteins. Bioinformatics 2020;36:2105-2112. [PMID: 31738385 DOI: 10.1093/bioinformatics/btz863] [Citation(s) in RCA: 110] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 10/17/2019] [Accepted: 11/15/2019] [Indexed: 12/23/2022]  Open
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Dahal S, Yurkovich JT, Xu H, Palsson BO, Yang L. Synthesizing Systems Biology Knowledge from Omics Using Genome-Scale Models. Proteomics 2020;20:e1900282. [PMID: 32579720 PMCID: PMC7501203 DOI: 10.1002/pmic.201900282] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Revised: 06/13/2020] [Indexed: 12/18/2022]
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Stamboulian M, Guerrero RF, Hahn MW, Radivojac P. The ortholog conjecture revisited: the value of orthologs and paralogs in function prediction. Bioinformatics 2020;36:i219-i226. [PMID: 32657391 PMCID: PMC7355290 DOI: 10.1093/bioinformatics/btaa468] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
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Koo DCE, Bonneau R. Towards region-specific propagation of protein functions. Bioinformatics 2020;35:1737-1744. [PMID: 30304483 PMCID: PMC6513163 DOI: 10.1093/bioinformatics/bty834] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 08/23/2018] [Accepted: 10/08/2018] [Indexed: 01/06/2023]  Open
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Buchan DWA, Jones DT. The PSIPRED Protein Analysis Workbench: 20 years on. Nucleic Acids Res 2020;47:W402-W407. [PMID: 31251384 PMCID: PMC6602445 DOI: 10.1093/nar/gkz297] [Citation(s) in RCA: 917] [Impact Index Per Article: 183.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/02/2019] [Accepted: 04/15/2019] [Indexed: 02/07/2023]  Open
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Strodthoff N, Wagner P, Wenzel M, Samek W. UDSMProt: universal deep sequence models for protein classification. Bioinformatics 2020;36:2401-2409. [PMID: 31913448 PMCID: PMC7178389 DOI: 10.1093/bioinformatics/btaa003] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 12/13/2019] [Accepted: 01/02/2020] [Indexed: 01/03/2023]  Open
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