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For: Borkakoti N, Thornton JM. AlphaFold2 protein structure prediction: Implications for drug discovery. Curr Opin Struct Biol 2023;78:102526. [PMID: 36621153 PMCID: PMC7614146 DOI: 10.1016/j.sbi.2022.102526] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 12/01/2022] [Accepted: 12/03/2022] [Indexed: 01/09/2023]
Number Cited by Other Article(s)
1
Manna T, Dey S, Karmakar M, Panda AK, Ghosh C. Investigations on genomic, topological and structural properties of diguanylate cyclases involved in Vibrio cholerae biofilm signalling using in silico techniques: Promising drug targets in combating cholera. Curr Res Struct Biol 2025;9:100166. [PMID: 40330072 PMCID: PMC12051071 DOI: 10.1016/j.crstbi.2025.100166] [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: 12/10/2024] [Revised: 03/19/2025] [Accepted: 04/07/2025] [Indexed: 05/08/2025]  Open
2
Sarvepalli S, Vadarevu S. Role of artificial intelligence in cancer drug discovery and development. Cancer Lett 2025;627:217821. [PMID: 40414522 DOI: 10.1016/j.canlet.2025.217821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2024] [Revised: 04/17/2025] [Accepted: 05/23/2025] [Indexed: 05/27/2025]
3
Najar Najafi N, Karbassian R, Hajihassani H, Azimzadeh Irani M. Unveiling the influence of fastest nobel prize winner discovery: alphafold's algorithmic intelligence in medical sciences. J Mol Model 2025;31:163. [PMID: 40387957 DOI: 10.1007/s00894-025-06392-x] [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: 12/01/2024] [Accepted: 05/06/2025] [Indexed: 05/20/2025]
4
Jo HG, Seo J, Jang B, Kim Y, Kim H, Baek E, Park SY, Lee D. Integrating network pharmacology and experimental validation to advance psoriasis treatment: Multi-target mechanistic elucidation of medicinal herbs and natural compounds. Autoimmun Rev 2025;24:103836. [PMID: 40381707 DOI: 10.1016/j.autrev.2025.103836] [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: 04/02/2025] [Revised: 05/10/2025] [Accepted: 05/12/2025] [Indexed: 05/20/2025]
5
Ali S, Qadri YA, Ahmad K, Lin Z, Leung MF, Kim SW, Vasilakos AV, Zhou T. Large Language Models in Genomics-A Perspective on Personalized Medicine. Bioengineering (Basel) 2025;12:440. [PMID: 40428059 PMCID: PMC12108693 DOI: 10.3390/bioengineering12050440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2025] [Revised: 04/21/2025] [Accepted: 04/22/2025] [Indexed: 05/29/2025]  Open
6
Yates J, Van Allen EM. New horizons at the interface of artificial intelligence and translational cancer research. Cancer Cell 2025;43:708-727. [PMID: 40233719 PMCID: PMC12007700 DOI: 10.1016/j.ccell.2025.03.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2025] [Revised: 03/04/2025] [Accepted: 03/12/2025] [Indexed: 04/17/2025]
7
Agoni C, Fernández-Díaz R, Timmons PB, Adelfio A, Gómez H, Shields DC. Molecular Modelling in Bioactive Peptide Discovery and Characterisation. Biomolecules 2025;15:524. [PMID: 40305228 PMCID: PMC12025251 DOI: 10.3390/biom15040524] [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: 12/21/2024] [Revised: 03/12/2025] [Accepted: 04/01/2025] [Indexed: 05/02/2025]  Open
8
Malhotra Y, John J, Yadav D, Sharma D, Vanshika, Rawal K, Mishra V, Chaturvedi N. Advancements in protein structure prediction: A comparative overview of AlphaFold and its derivatives. Comput Biol Med 2025;188:109842. [PMID: 39970826 DOI: 10.1016/j.compbiomed.2025.109842] [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: 11/23/2024] [Revised: 02/07/2025] [Accepted: 02/10/2025] [Indexed: 02/21/2025]
9
Mao W, Rong Y, Zhang H, Yuan F, Wang Y, Wang M, Wang L, Wang PG, Chen M, Wang S, Kong Y. Characterization and application in recombinant N-GlcNAc-protein production of a novel endo-β-N-acetylglucosaminidase from Listeria booriae. Bioorg Chem 2025;157:108290. [PMID: 39983405 DOI: 10.1016/j.bioorg.2025.108290] [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: 01/09/2025] [Revised: 02/07/2025] [Accepted: 02/15/2025] [Indexed: 02/23/2025]
10
He XH, Li JR, Shen SY, Xu HE. AlphaFold3 versus experimental structures: assessment of the accuracy in ligand-bound G protein-coupled receptors. Acta Pharmacol Sin 2025;46:1111-1122. [PMID: 39643640 PMCID: PMC11950431 DOI: 10.1038/s41401-024-01429-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/13/2024] [Accepted: 11/11/2024] [Indexed: 12/09/2024]
11
Rosignoli S, Pacelli M, Manganiello F, Paiardini A. An outlook on structural biology after AlphaFold: tools, limits and perspectives. FEBS Open Bio 2025;15:202-222. [PMID: 39313455 PMCID: PMC11788754 DOI: 10.1002/2211-5463.13902] [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: 03/13/2024] [Revised: 08/19/2024] [Accepted: 09/13/2024] [Indexed: 09/25/2024]  Open
12
Duan SG, Mao L, Sun SF, Chen RD, Taha Abdelkhalek S, Wang MQ. Key site residues of Cnaphalocrocis medinalis odorant-binding protein 13 CmedOBP13 involved in interacting with rice plant volatiles. Int J Biol Macromol 2025;290:139007. [PMID: 39708865 DOI: 10.1016/j.ijbiomac.2024.139007] [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] [Revised: 12/03/2024] [Accepted: 12/18/2024] [Indexed: 12/23/2024]
13
Varadi M, Tsenkov M, Velankar S. Challenges in bridging the gap between protein structure prediction and functional interpretation. Proteins 2025;93:400-410. [PMID: 37850517 PMCID: PMC11623436 DOI: 10.1002/prot.26614] [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: 06/28/2023] [Revised: 09/26/2023] [Accepted: 10/04/2023] [Indexed: 10/19/2023]
14
Sánchez-Juárez C, Flores-López R, Sánchez-Pérez LDC, García-Gutiérrez P, Jiménez L, Landa A, Zubillaga RA. Discovery and Characterization of Two Selective Inhibitors for a Mu-Class Glutathione S-Transferase of 25 kDa from Taenia solium Using Computational and Bioinformatics Tools. Biomolecules 2024;15:7. [PMID: 39858402 PMCID: PMC11760891 DOI: 10.3390/biom15010007] [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: 11/13/2024] [Revised: 12/10/2024] [Accepted: 12/19/2024] [Indexed: 01/27/2025]  Open
15
Godinez-Macias KP, Chen D, Wallis JL, Siegel MG, Adam A, Bopp S, Carolino K, Coulson LB, Durst G, Thathy V, Esherick L, Farringer MA, Flannery EL, Forte B, Liu T, Magalhaes LG, Gupta AK, Istvan ES, Jiang T, Kumpornsin K, Lobb K, McLean K, Moura IMR, Okombo J, Payne NC, Plater A, Rao SPS, Siqueira-Neto JL, Somsen BA, Summers RL, Zhang R, Gilson MK, Gamo FJ, Campo B, Baragaña B, Duffy J, Gilbert IH, Lukens AK, Dechering KJ, Niles JC, McNamara CW, Cheng X, Birkholtz LM, Bronkhorst AW, Fidock DA, Wirth DF, Goldberg DE, Lee MCS, Winzeler EA. Revisiting the Plasmodium falciparum druggable genome using predicted structures and data mining. RESEARCH SQUARE 2024:rs.3.rs-5412515. [PMID: 39649165 PMCID: PMC11623766 DOI: 10.21203/rs.3.rs-5412515/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/10/2024]
16
Lau AM, Bordin N, Kandathil SM, Sillitoe I, Waman VP, Wells J, Orengo CA, Jones DT. Exploring structural diversity across the protein universe with The Encyclopedia of Domains. Science 2024;386:eadq4946. [PMID: 39480926 DOI: 10.1126/science.adq4946] [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: 05/21/2024] [Accepted: 08/30/2024] [Indexed: 11/02/2024]
17
Büttiker P, Boukherissa A, Weissenberger S, Ptacek R, Anders M, Raboch J, Stefano GB. Cognitive Impact of Neurotropic Pathogens: Investigating Molecular Mimicry through Computational Methods. Cell Mol Neurobiol 2024;44:72. [PMID: 39467848 PMCID: PMC11519248 DOI: 10.1007/s10571-024-01509-x] [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: 09/02/2024] [Accepted: 10/22/2024] [Indexed: 10/30/2024]
18
Eren AM, Banfield JF. Modern microbiology: Embracing complexity through integration across scales. Cell 2024;187:5151-5170. [PMID: 39303684 PMCID: PMC11450119 DOI: 10.1016/j.cell.2024.08.028] [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: 06/22/2024] [Revised: 08/14/2024] [Accepted: 08/14/2024] [Indexed: 09/22/2024]
19
Li B, Tan K, Lao AR, Wang H, Zheng H, Zhang L. A comprehensive review of artificial intelligence for pharmacology research. Front Genet 2024;15:1450529. [PMID: 39290983 PMCID: PMC11405247 DOI: 10.3389/fgene.2024.1450529] [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: 06/17/2024] [Accepted: 08/26/2024] [Indexed: 09/19/2024]  Open
20
Margelevičius M. GTalign: spatial index-driven protein structure alignment, superposition, and search. Nat Commun 2024;15:7305. [PMID: 39181863 PMCID: PMC11344802 DOI: 10.1038/s41467-024-51669-z] [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: 01/04/2024] [Accepted: 08/14/2024] [Indexed: 08/27/2024]  Open
21
Wang W, Li H, Liu Z, Xu D, Pu H, Hu L, Mo H. Identification of flavor peptides based on virtual screening and molecular docking from Hypsizygus marmoreuss. Food Chem 2024;448:139071. [PMID: 38552458 DOI: 10.1016/j.foodchem.2024.139071] [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: 12/01/2023] [Revised: 03/11/2024] [Accepted: 03/16/2024] [Indexed: 04/24/2024]
22
Abbas MKG, Rassam A, Karamshahi F, Abunora R, Abouseada M. The Role of AI in Drug Discovery. Chembiochem 2024;25:e202300816. [PMID: 38735845 DOI: 10.1002/cbic.202300816] [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: 12/03/2023] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/14/2024]
23
Desai D, Kantliwala SV, Vybhavi J, Ravi R, Patel H, Patel J. Review of AlphaFold 3: Transformative Advances in Drug Design and Therapeutics. Cureus 2024;16:e63646. [PMID: 39092344 PMCID: PMC11292590 DOI: 10.7759/cureus.63646] [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: 06/05/2024] [Accepted: 07/01/2024] [Indexed: 08/04/2024]  Open
24
Hallam TM, Andreadi A, Sharp SJ, Brocklebank V, Gardenal E, Dreismann A, Lotery AJ, Marchbank KJ, Harris CL, Jones AV, Kavanagh D. Comprehensive functional characterization of complement factor I rare variant genotypes identified in the SCOPE geographic atrophy cohort. J Biol Chem 2024;300:107452. [PMID: 38852887 PMCID: PMC11277764 DOI: 10.1016/j.jbc.2024.107452] [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: 04/10/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/11/2024]  Open
25
Nilsen P, Sundemo D, Heintz F, Neher M, Nygren J, Svedberg P, Petersson L. Towards evidence-based practice 2.0: leveraging artificial intelligence in healthcare. FRONTIERS IN HEALTH SERVICES 2024;4:1368030. [PMID: 38919828 PMCID: PMC11196845 DOI: 10.3389/frhs.2024.1368030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 05/31/2024] [Indexed: 06/27/2024]
26
Boland DJ, Ayres NM. Cracking AlphaFold2: Leveraging the power of artificial intelligence in undergraduate biochemistry curriculums. PLoS Comput Biol 2024;20:e1012123. [PMID: 38935611 PMCID: PMC11210786 DOI: 10.1371/journal.pcbi.1012123] [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] [Indexed: 06/29/2024]  Open
27
Woo H, Kim Y, Seok C. Protein loop structure prediction by community-based deep learning and its application to antibody CDR H3 loop modeling. PLoS Comput Biol 2024;20:e1012239. [PMID: 38913733 PMCID: PMC11226077 DOI: 10.1371/journal.pcbi.1012239] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Revised: 07/05/2024] [Accepted: 06/07/2024] [Indexed: 06/26/2024]  Open
28
Sethi A, Rathi B. Artificial intelligence in drug discovery: A mirage or an oasis? Drug Discov Today 2024;29:103994. [PMID: 38663577 DOI: 10.1016/j.drudis.2024.103994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 05/02/2024]
29
Wu Z, Chen S, Wang Y, Li F, Xu H, Li M, Zeng Y, Wu Z, Gao Y. Current perspectives and trend of computer-aided drug design: a review and bibliometric analysis. Int J Surg 2024;110:3848-3878. [PMID: 38502850 PMCID: PMC11175770 DOI: 10.1097/js9.0000000000001289] [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: 11/08/2023] [Accepted: 02/22/2024] [Indexed: 03/21/2024]
30
Lee S, Kim G, Karin EL, Mirdita M, Park S, Chikhi R, Babaian A, Kryshtafovych A, Steinegger M. Petabase-Scale Homology Search for Structure Prediction. Cold Spring Harb Perspect Biol 2024;16:a041465. [PMID: 38316555 PMCID: PMC11065157 DOI: 10.1101/cshperspect.a041465] [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] [Indexed: 02/07/2024]
31
Ghandikota SK, Jegga AG. Application of artificial intelligence and machine learning in drug repurposing. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024;205:171-211. [PMID: 38789178 DOI: 10.1016/bs.pmbts.2024.03.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
32
Monteiro da Silva G, Cui JY, Dalgarno DC, Lisi GP, Rubenstein BM. High-throughput prediction of protein conformational distributions with subsampled AlphaFold2. Nat Commun 2024;15:2464. [PMID: 38538622 PMCID: PMC10973385 DOI: 10.1038/s41467-024-46715-9] [Citation(s) in RCA: 56] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 02/28/2024] [Indexed: 04/12/2024]  Open
33
Kumar N, Srivastava R. Deep learning in structural bioinformatics: current applications and future perspectives. Brief Bioinform 2024;25:bbae042. [PMID: 38701422 PMCID: PMC11066934 DOI: 10.1093/bib/bbae042] [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: 08/17/2023] [Revised: 01/05/2024] [Accepted: 01/18/2024] [Indexed: 05/05/2024]  Open
34
Qiu X, Li H, Ver Steeg G, Godzik A. Advances in AI for Protein Structure Prediction: Implications for Cancer Drug Discovery and Development. Biomolecules 2024;14:339. [PMID: 38540759 PMCID: PMC10968151 DOI: 10.3390/biom14030339] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/04/2024] [Accepted: 03/06/2024] [Indexed: 11/11/2024]  Open
35
Yadhav Y, Selvaraj K, Ramasamy S, Venkataraman S. Computational studies on rep and capsid proteins of CRESS DNA viruses. Virusdisease 2024;35:17-26. [PMID: 38817400 PMCID: PMC11133267 DOI: 10.1007/s13337-024-00858-x] [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: 11/20/2023] [Accepted: 01/29/2024] [Indexed: 06/01/2024]  Open
36
Versini R, Sritharan S, Aykac Fas B, Tubiana T, Aimeur SZ, Henri J, Erard M, Nüsse O, Andreani J, Baaden M, Fuchs P, Galochkina T, Chatzigoulas A, Cournia Z, Santuz H, Sacquin-Mora S, Taly A. A Perspective on the Prospective Use of AI in Protein Structure Prediction. J Chem Inf Model 2024;64:26-41. [PMID: 38124369 DOI: 10.1021/acs.jcim.3c01361] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
37
Krokidis MG, Dimitrakopoulos GN, Vrahatis AG, Exarchos TP, Vlamos P. Challenges and limitations in computational prediction of protein misfolding in neurodegenerative diseases. Front Comput Neurosci 2024;17:1323182. [PMID: 38250244 PMCID: PMC10796696 DOI: 10.3389/fncom.2023.1323182] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 12/19/2023] [Indexed: 01/23/2024]  Open
38
Pham AC, Holstein SA, Borgstahl GE. Structural Insight into Geranylgeranyl Diphosphate Synthase (GGDPS) for Cancer Therapy. Mol Cancer Ther 2024;23:14-23. [PMID: 37756579 PMCID: PMC10762340 DOI: 10.1158/1535-7163.mct-23-0358] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 08/09/2023] [Accepted: 09/22/2023] [Indexed: 09/29/2023]
39
Roy BG, Choi J, Fuchs MF. Predictive Modeling of Proteins Encoded by a Plant Virus Sheds a New Light on Their Structure and Inherent Multifunctionality. Biomolecules 2024;14:62. [PMID: 38254661 PMCID: PMC10813169 DOI: 10.3390/biom14010062] [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: 11/29/2023] [Revised: 12/29/2023] [Accepted: 12/30/2023] [Indexed: 01/24/2024]  Open
40
Martin RL, Heifetz A, Bodkin MJ, Townsend-Nicholson A. High-Throughput Structure-Based Drug Design (HT-SBDD) Using Drug Docking, Fragment Molecular Orbital Calculations, and Molecular Dynamic Techniques. Methods Mol Biol 2024;2716:293-306. [PMID: 37702945 DOI: 10.1007/978-1-0716-3449-3_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
41
Radjasandirane R, de Brevern AG. AlphaFold2 for Protein Structure Prediction: Best Practices and Critical Analyses. Methods Mol Biol 2024;2836:235-252. [PMID: 38995544 DOI: 10.1007/978-1-0716-4007-4_13] [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: 07/13/2024]
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da Silva GM, Cui JY, Dalgarno DC, Lisi GP, Rubenstein BM. Predicting Relative Populations of Protein Conformations without a Physics Engine Using AlphaFold 2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.25.550545. [PMID: 37546747 PMCID: PMC10402055 DOI: 10.1101/2023.07.25.550545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
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Du K, Huang H. Development of anti-PD-L1 antibody based on structure prediction of AlphaFold2. Front Immunol 2023;14:1275999. [PMID: 37942332 PMCID: PMC10628240 DOI: 10.3389/fimmu.2023.1275999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/11/2023] [Indexed: 11/10/2023]  Open
44
Stuart DD, Guzman-Perez A, Brooijmans N, Jackson EL, Kryukov GV, Friedman AA, Hoos A. Precision Oncology Comes of Age: Designing Best-in-Class Small Molecules by Integrating Two Decades of Advances in Chemistry, Target Biology, and Data Science. Cancer Discov 2023;13:2131-2149. [PMID: 37712571 PMCID: PMC10551669 DOI: 10.1158/2159-8290.cd-23-0280] [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: 03/06/2023] [Revised: 04/27/2023] [Accepted: 07/28/2023] [Indexed: 09/16/2023]
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Wu K, Karapetyan E, Schloss J, Vadgama J, Wu Y. Advancements in small molecule drug design: A structural perspective. Drug Discov Today 2023;28:103730. [PMID: 37536390 PMCID: PMC10543554 DOI: 10.1016/j.drudis.2023.103730] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 07/19/2023] [Accepted: 07/27/2023] [Indexed: 08/05/2023]
46
Pathak RK, Kim JM. Identification of histidine kinase inhibitors through screening of natural compounds to combat mastitis caused by Streptococcus agalactiae in dairy cattle. J Biol Eng 2023;17:59. [PMID: 37752501 PMCID: PMC10523694 DOI: 10.1186/s13036-023-00378-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 09/18/2023] [Indexed: 09/28/2023]  Open
47
Lee S, Kim G, Karin EL, Mirdita M, Park S, Chikhi R, Babaian A, Kryshtafovych A, Steinegger M. Petascale Homology Search for Structure Prediction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.10.548308. [PMID: 37503235 PMCID: PMC10369885 DOI: 10.1101/2023.07.10.548308] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
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Bijak V, Szczygiel M, Lenkiewicz J, Gucwa M, Cooper DR, Murzyn K, Minor W. The current role and evolution of X-ray crystallography in drug discovery and development. Expert Opin Drug Discov 2023;18:1221-1230. [PMID: 37592849 PMCID: PMC10620067 DOI: 10.1080/17460441.2023.2246881] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 08/08/2023] [Indexed: 08/19/2023]
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Zheng LE, Barethiya S, Nordquist E, Chen J. Machine Learning Generation of Dynamic Protein Conformational Ensembles. Molecules 2023;28:4047. [PMID: 37241789 PMCID: PMC10220786 DOI: 10.3390/molecules28104047] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023]  Open
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