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For: Uziela K, Menéndez Hurtado D, Shu N, Wallner B, Elofsson A. ProQ3D: improved model quality assessments using deep learning. Bioinformatics 2018;33:1578-1580. [PMID: 28052925 DOI: 10.1093/bioinformatics/btw819] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/20/2016] [Indexed: 11/14/2022]  Open
Number Cited by Other Article(s)
1
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
2
Nandigrami P, Goldman ID, Fiser A. Mechanistic insights into mutation in the proton-coupled folate transporter (SLC46A1) causing hereditary folate malabsorption. J Biol Chem 2025;301:108280. [PMID: 39924111 PMCID: PMC11929075 DOI: 10.1016/j.jbc.2025.108280] [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: 08/04/2024] [Revised: 01/17/2025] [Accepted: 01/31/2025] [Indexed: 02/11/2025]  Open
3
Liang F, Sun M, Xie L, Zhao X, Liu D, Zhao K, Zhang G. Recent advances and challenges in protein complex model accuracy estimation. Comput Struct Biotechnol J 2024;23:1824-1832. [PMID: 38707538 PMCID: PMC11066466 DOI: 10.1016/j.csbj.2024.04.049] [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: 01/27/2024] [Revised: 04/18/2024] [Accepted: 04/18/2024] [Indexed: 05/07/2024]  Open
4
Matinja AI, Kamarudin NHA, Leow ATC, Oslan SN, Ali MSM. Structural Insights into Cold-Active Lipase from Glaciozyma antarctica PI12: Alphafold2 Prediction and Molecular Dynamics Simulation. J Mol Evol 2024;92:944-963. [PMID: 39549052 DOI: 10.1007/s00239-024-10219-3] [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: 12/22/2023] [Accepted: 11/06/2024] [Indexed: 11/18/2024]
5
McGuffin LJ, Alharbi SMA. ModFOLD9: A Web Server for Independent Estimates of 3D Protein Model Quality. J Mol Biol 2024;436:168531. [PMID: 39237204 DOI: 10.1016/j.jmb.2024.168531] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Revised: 02/19/2024] [Accepted: 03/06/2024] [Indexed: 09/07/2024]
6
Liu J, Liu D, He G, Zhang G. Estimating protein complex model accuracy based on ultrafast shape recognition and deep learning in CASP15. Proteins 2023;91:1861-1870. [PMID: 37553848 DOI: 10.1002/prot.26564] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2023] [Revised: 07/05/2023] [Accepted: 07/11/2023] [Indexed: 08/10/2023]
7
Yue T, Wang Y, Zhang L, Gu C, Xue H, Wang W, Lyu Q, Dun Y. Deep Learning for Genomics: From Early Neural Nets to Modern Large Language Models. Int J Mol Sci 2023;24:15858. [PMID: 37958843 PMCID: PMC10649223 DOI: 10.3390/ijms242115858] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 10/24/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023]  Open
8
Roy S, Ben-Hur A. Protein quality assessment with a loss function designed for high-quality decoys. FRONTIERS IN BIOINFORMATICS 2023;3:1198218. [PMID: 37915563 PMCID: PMC10616882 DOI: 10.3389/fbinf.2023.1198218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 09/29/2023] [Indexed: 11/03/2023]  Open
9
Liu J, Liu D, Zhang GJ. DeepUMQA3: a web server for accurate assessment of interface residue accuracy in protein complexes. Bioinformatics 2023;39:btad591. [PMID: 37740296 PMCID: PMC10560100 DOI: 10.1093/bioinformatics/btad591] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 08/21/2023] [Accepted: 09/21/2023] [Indexed: 09/24/2023]  Open
10
Perea‐Cabrera M, Granados‐Riveron JT, Segura‐Stanford B, Moreno‐Vargas LM, Prada‐Gracia D, Moran‐Espinosa MC, Erdmenger J, Diaz‐Garcia H, Sánchez‐Urbina R. Opitz GBBB syndrome with total anomalous pulmonary venous connection: A new MID1 gene variant. Mol Genet Genomic Med 2023;11:e2234. [PMID: 37498300 PMCID: PMC10496055 DOI: 10.1002/mgg3.2234] [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: 10/05/2022] [Revised: 06/12/2023] [Accepted: 06/28/2023] [Indexed: 07/28/2023]  Open
11
Wu F, Wu L, Radev D, Xu J, Li SZ. Integration of pre-trained protein language models into geometric deep learning networks. Commun Biol 2023;6:876. [PMID: 37626165 PMCID: PMC10457366 DOI: 10.1038/s42003-023-05133-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 07/11/2023] [Indexed: 08/27/2023]  Open
12
Gao Z, Jiang W, Zhang Y, Zhang L, Yi M, Wang H, Ma Z, Qu B, Ji X, Long H, Zhang S. Amphioxus adenosine-to-inosine tRNA-editing enzyme that can perform C-to-U and A-to-I deamination of DNA. Commun Biol 2023;6:744. [PMID: 37464027 PMCID: PMC10354150 DOI: 10.1038/s42003-023-05134-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Accepted: 07/11/2023] [Indexed: 07/20/2023]  Open
13
He G, Liu J, Liu D, Zhang G. GraphGPSM: a global scoring model for protein structure using graph neural networks. Brief Bioinform 2023:bbad219. [PMID: 37317619 DOI: 10.1093/bib/bbad219] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 04/14/2023] [Accepted: 05/22/2023] [Indexed: 06/16/2023]  Open
14
Deng L, Ly C, Abdollahi S, Zhao Y, Prinz I, Bonn S. Performance comparison of TCR-pMHC prediction tools reveals a strong data dependency. Front Immunol 2023;14:1128326. [PMID: 37143667 PMCID: PMC10152969 DOI: 10.3389/fimmu.2023.1128326] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Accepted: 03/24/2023] [Indexed: 05/06/2023]  Open
15
Zhang P, Xia C, Shen HB. High-accuracy protein model quality assessment using attention graph neural networks. Brief Bioinform 2023;24:7025462. [PMID: 36736352 DOI: 10.1093/bib/bbac614] [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: 09/23/2022] [Revised: 11/23/2022] [Accepted: 12/12/2022] [Indexed: 02/05/2023]  Open
16
Bhattacharya S, Roche R, Shuvo MH, Moussad B, Bhattacharya D. Contact-Assisted Threading in Low-Homology Protein Modeling. Methods Mol Biol 2023;2627:41-59. [PMID: 36959441 DOI: 10.1007/978-1-0716-2974-1_3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
17
Marin FI, Marcatili P. Computational Modeling of Antibody and T-Cell Receptor (CDR3 Loops). Methods Mol Biol 2023;2552:83-100. [PMID: 36346586 DOI: 10.1007/978-1-0716-2609-2_3] [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] [Indexed: 06/16/2023]
18
Maghrabi AHA, Aldowsari FMF, McGuffin LJ. Quality Estimates for 3D Protein Models. Methods Mol Biol 2023;2627:101-118. [PMID: 36959444 DOI: 10.1007/978-1-0716-2974-1_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/25/2023]
19
San A, Palmieri D, Saxena A, Singh S. In silico study predicts a key role of RNA-binding domains 3 and 4 in nucleolin-miRNA interactions. Proteins 2022;90:1837-1850. [PMID: 35514080 DOI: 10.1002/prot.26355] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 04/07/2022] [Accepted: 04/26/2022] [Indexed: 12/17/2023]
20
Kurniawan J, Ishida T. Protein Model Quality Estimation Using Molecular Dynamics Simulation. ACS OMEGA 2022;7:24274-24281. [PMID: 35874260 PMCID: PMC9301944 DOI: 10.1021/acsomega.2c01475] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
21
Chen X, Cheng J. DISTEMA: distance map-based estimation of single protein model accuracy with attentive 2D convolutional neural network. BMC Bioinformatics 2022;23:141. [PMID: 35439931 PMCID: PMC9019949 DOI: 10.1186/s12859-022-04683-1] [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: 04/08/2022] [Accepted: 04/11/2022] [Indexed: 01/25/2023]  Open
22
A Benchmark Dataset for Evaluating Practical Performance of Model Quality Assessment of Homology Models. Bioengineering (Basel) 2022;9:bioengineering9030118. [PMID: 35324806 PMCID: PMC8945737 DOI: 10.3390/bioengineering9030118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/08/2022] [Accepted: 03/11/2022] [Indexed: 11/25/2022]  Open
23
Sandoval K, McCormack GP. Actinoporin-like Proteins Are Widely Distributed in the Phylum Porifera. Mar Drugs 2022;20:md20010074. [PMID: 35049929 PMCID: PMC8778704 DOI: 10.3390/md20010074] [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: 12/15/2021] [Revised: 01/07/2022] [Accepted: 01/10/2022] [Indexed: 11/16/2022]  Open
24
Machine learning to estimate the local quality of protein crystal structures. Sci Rep 2021;11:23599. [PMID: 34880321 PMCID: PMC8654820 DOI: 10.1038/s41598-021-02948-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 11/24/2021] [Indexed: 11/23/2022]  Open
25
Jiang Z, Wang C, Wu Z, Chen K, Yang W, Deng H, Song H, Zhou X. Enzymatic deamination of the epigenetic nucleoside N6-methyladenosine regulates gene expression. Nucleic Acids Res 2021;49:12048-12068. [PMID: 34850126 PMCID: PMC8643624 DOI: 10.1093/nar/gkab1124] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 10/20/2021] [Accepted: 11/16/2021] [Indexed: 12/26/2022]  Open
26
Wang W, Wang J, Li Z, Xu D, Shang Y. MUfoldQA_G: High-accuracy protein model QA via retraining and transformation. Comput Struct Biotechnol J 2021;19:6282-6290. [PMID: 34900138 PMCID: PMC8636996 DOI: 10.1016/j.csbj.2021.11.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 11/10/2021] [Accepted: 11/14/2021] [Indexed: 11/21/2022]  Open
27
Proteomic Tools for the Analysis of Cytoskeleton Proteins. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2021;2364:363-425. [PMID: 34542864 DOI: 10.1007/978-1-0716-1661-1_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
28
Kong L, Ju F, Zhang H, Sun S, Bu D. FALCON2: a web server for high-quality prediction of protein tertiary structures. BMC Bioinformatics 2021;22:439. [PMID: 34525939 PMCID: PMC8444573 DOI: 10.1186/s12859-021-04353-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/01/2021] [Indexed: 11/21/2022]  Open
29
Komarevtsev SK, Evseev PV, Shneider MM, Popova EA, Tupikin AE, Stepanenko VN, Kabilov MR, Shabunin SV, Osmolovskiy AA, Miroshnikov KA. Gene Analysis, Cloning, and Heterologous Expression of Protease from a Micromycete Aspergillus ochraceus Capable of Activating Protein C of Blood Plasma. Microorganisms 2021;9:1936. [PMID: 34576831 PMCID: PMC8471544 DOI: 10.3390/microorganisms9091936] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/05/2021] [Accepted: 09/08/2021] [Indexed: 12/16/2022]  Open
30
Schaeffer RD, Kinch L, Kryshtafovych A, Grishin NV. Assessment of domain interactions in the fourteenth round of the Critical Assessment of Structure Prediction (CASP14). Proteins 2021;89:1700-1710. [PMID: 34455641 PMCID: PMC8616818 DOI: 10.1002/prot.26225] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 08/07/2021] [Accepted: 08/24/2021] [Indexed: 12/29/2022]
31
Bhattacharya S, Roche R, Shuvo MH, Bhattacharya D. Recent Advances in Protein Homology Detection Propelled by Inter-Residue Interaction Map Threading. Front Mol Biosci 2021;8:643752. [PMID: 34046429 PMCID: PMC8148041 DOI: 10.3389/fmolb.2021.643752] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 04/21/2021] [Indexed: 11/13/2022]  Open
32
Jiang V, Khare SD, Banta S. Computational structure prediction provides a plausible mechanism for electron transfer by the outer membrane protein Cyc2 from Acidithiobacillus ferrooxidans. Protein Sci 2021;30:1640-1652. [PMID: 33969560 DOI: 10.1002/pro.4106] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 04/30/2021] [Accepted: 05/03/2021] [Indexed: 12/14/2022]
33
Baldassarre F, Menéndez Hurtado D, Elofsson A, Azizpour H. GraphQA: protein model quality assessment using graph convolutional networks. Bioinformatics 2021;37:360-366. [PMID: 32780838 PMCID: PMC8058777 DOI: 10.1093/bioinformatics/btaa714] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 07/03/2020] [Accepted: 08/05/2020] [Indexed: 11/25/2022]  Open
34
Protein Structure Refinement Using Multi-Objective Particle Swarm Optimization with Decomposition Strategy. Int J Mol Sci 2021;22:ijms22094408. [PMID: 33922489 PMCID: PMC8122964 DOI: 10.3390/ijms22094408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 04/16/2021] [Accepted: 04/20/2021] [Indexed: 12/02/2022]  Open
35
Waman VP, Sen N, Varadi M, Daina A, Wodak SJ, Zoete V, Velankar S, Orengo C. The impact of structural bioinformatics tools and resources on SARS-CoV-2 research and therapeutic strategies. Brief Bioinform 2021;22:742-768. [PMID: 33348379 PMCID: PMC7799268 DOI: 10.1093/bib/bbaa362] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 11/06/2020] [Accepted: 11/09/2020] [Indexed: 01/18/2023]  Open
36
Takei Y, Ishida T. P3CMQA: Single-Model Quality Assessment Using 3DCNN with Profile-Based Features. Bioengineering (Basel) 2021;8:bioengineering8030040. [PMID: 33808604 PMCID: PMC8003382 DOI: 10.3390/bioengineering8030040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 03/12/2021] [Accepted: 03/16/2021] [Indexed: 11/16/2022]  Open
37
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
38
Hiranuma N, Park H, Baek M, Anishchenko I, Dauparas J, Baker D. Improved protein structure refinement guided by deep learning based accuracy estimation. Nat Commun 2021;12:1340. [PMID: 33637700 PMCID: PMC7910447 DOI: 10.1038/s41467-021-21511-x] [Citation(s) in RCA: 135] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 01/18/2021] [Indexed: 11/22/2022]  Open
39
Phan IQ, Subramanian S, Kim D, Murphy M, Pettie D, Carter L, Anishchenko I, Barrett LK, Craig J, Tillery L, Shek R, Harrington WE, Koelle DM, Wald A, Veesler D, King N, Boonyaratanakornkit J, Isoherranen N, Greninger AL, Jerome KR, Chu H, Staker B, Stewart L, Myler PJ, Van Voorhis WC. In silico detection of SARS-CoV-2 specific B-cell epitopes and validation in ELISA for serological diagnosis of COVID-19. Sci Rep 2021;11:4290. [PMID: 33619344 PMCID: PMC7900118 DOI: 10.1038/s41598-021-83730-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2020] [Accepted: 02/03/2021] [Indexed: 02/07/2023]  Open
40
Aguirre-Plans J, Meseguer A, Molina-Fernandez R, Marín-López MA, Jumde G, Casanova K, Bonet J, Fornes O, Fernandez-Fuentes N, Oliva B. SPServer: split-statistical potentials for the analysis of protein structures and protein-protein interactions. BMC Bioinformatics 2021;22:4. [PMID: 33407073 PMCID: PMC7788957 DOI: 10.1186/s12859-020-03770-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 09/20/2020] [Indexed: 12/13/2022]  Open
41
Studer G, Tauriello G, Bienert S, Biasini M, Johner N, Schwede T. ProMod3-A versatile homology modelling toolbox. PLoS Comput Biol 2021;17:e1008667. [PMID: 33507980 PMCID: PMC7872268 DOI: 10.1371/journal.pcbi.1008667] [Citation(s) in RCA: 177] [Impact Index Per Article: 44.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 02/09/2021] [Accepted: 01/03/2021] [Indexed: 11/18/2022]  Open
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Jing X, Xu J. Improved Protein Model Quality Assessment By Integrating Sequential And Pairwise Features Using Deep Learning. Bioinformatics 2020;36:5361-5367. [PMID: 33325480 PMCID: PMC8016469 DOI: 10.1093/bioinformatics/btaa1037] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 11/27/2020] [Accepted: 12/06/2020] [Indexed: 12/23/2022]  Open
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Ugarte-Alvarez O, Muñoz-López P, Moreno-Vargas LM, Prada-Gracia D, Mateos-Chávez AA, Becerra-Báez EI, Luria-Pérez R. Cell-Permeable Bak BH3 Peptide Induces Chemosensitization of Hematologic Malignant Cells. JOURNAL OF ONCOLOGY 2020;2020:2679046. [PMID: 33312200 PMCID: PMC7721494 DOI: 10.1155/2020/2679046] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/04/2020] [Accepted: 07/13/2020] [Indexed: 12/24/2022]
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Studer G, Rempfer C, Waterhouse AM, Gumienny R, Haas J, Schwede T. QMEANDisCo-distance constraints applied on model quality estimation. Bioinformatics 2020;36:1765-1771. [PMID: 31697312 PMCID: PMC7075525 DOI: 10.1093/bioinformatics/btz828] [Citation(s) in RCA: 527] [Impact Index Per Article: 105.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 10/24/2019] [Accepted: 11/06/2019] [Indexed: 01/13/2023]  Open
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Postic G, Janel N, Tufféry P, Moroy G. An information gain-based approach for evaluating protein structure models. Comput Struct Biotechnol J 2020;18:2228-2236. [PMID: 32837711 PMCID: PMC7431362 DOI: 10.1016/j.csbj.2020.08.013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 12/23/2022]  Open
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Pei J, Song LF, Merz KM. Pair Potentials as Machine Learning Features. J Chem Theory Comput 2020;16:5385-5400. [PMID: 32559380 DOI: 10.1021/acs.jctc.9b01246] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Liu T, Wang Z. MASS: predict the global qualities of individual protein models using random forests and novel statistical potentials. BMC Bioinformatics 2020;21:246. [PMID: 32631256 PMCID: PMC7336608 DOI: 10.1186/s12859-020-3383-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 01/22/2020] [Indexed: 11/10/2022]  Open
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Miranda MRA, Uchôa AF, Ferreira SR, Ventury KE, Costa EP, Carmo PRL, Machado OLT, Fernandes KVS, Amancio Oliveira AE. Chemical Modifications of Vicilins Interfere with Chitin-Binding Affinity and Toxicity to Callosobruchus maculatus (Coleoptera: Chrysomelidae) Insect: A Combined In Vitro and In Silico Analysis. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020;68:5596-5605. [PMID: 32343573 DOI: 10.1021/acs.jafc.9b08034] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
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Olechnovič K, Venclovas Č. VoroMQA web server for assessing three-dimensional structures of proteins and protein complexes. Nucleic Acids Res 2020;47:W437-W442. [PMID: 31073605 PMCID: PMC6602437 DOI: 10.1093/nar/gkz367] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 04/19/2019] [Accepted: 05/05/2019] [Indexed: 01/12/2023]  Open
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McGuffin LJ, Adiyaman R, Maghrabi AHA, Shuid AN, Brackenridge DA, Nealon JO, Philomina LS. IntFOLD: an integrated web resource for high performance protein structure and function prediction. Nucleic Acids Res 2020;47:W408-W413. [PMID: 31045208 PMCID: PMC6602432 DOI: 10.1093/nar/gkz322] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/05/2019] [Accepted: 04/23/2019] [Indexed: 12/14/2022]  Open
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