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For: Hegedűs T, Geisler M, Lukács GL, Farkas B. Ins and outs of AlphaFold2 transmembrane protein structure predictions. Cell Mol Life Sci 2022;79:73. [PMID: 35034173 PMCID: PMC8761152 DOI: 10.1007/s00018-021-04112-1] [Citation(s) in RCA: 64] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 11/25/2021] [Accepted: 12/20/2021] [Indexed: 12/20/2022]
Number Cited by Other Article(s)
1
Strieder Philippsen G, Augusto Vicente Seixas F. Computational approach based on freely accessible tools for antimicrobial drug design. Bioorg Med Chem Lett 2025;115:130010. [PMID: 39486485 DOI: 10.1016/j.bmcl.2024.130010] [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: 08/05/2024] [Revised: 10/15/2024] [Accepted: 10/28/2024] [Indexed: 11/04/2024]
2
Torres J, Pervushin K, Surya W. Prediction of conformational states in a coronavirus channel using Alphafold-2 and DeepMSA2: Strengths and limitations. Comput Struct Biotechnol J 2024;23:3730-3740. [PMID: 39525089 PMCID: PMC11543627 DOI: 10.1016/j.csbj.2024.10.021] [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: 06/15/2024] [Revised: 10/01/2024] [Accepted: 10/15/2024] [Indexed: 11/16/2024]  Open
3
Poudel B, Vanegas JM. Structural Rearrangement of the AT1 Receptor Modulated by Membrane Thickness and Tension. J Phys Chem B 2024;128:9470-9481. [PMID: 39298653 DOI: 10.1021/acs.jpcb.4c03325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2024]
4
Berta B, Tordai H, Lukács GL, Papp B, Enyedi Á, Padányi R, Hegedűs T. SARS-CoV-2 envelope protein alters calcium signaling via SERCA interactions. Sci Rep 2024;14:21200. [PMID: 39261533 PMCID: PMC11391011 DOI: 10.1038/s41598-024-71144-5] [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: 03/06/2024] [Accepted: 08/26/2024] [Indexed: 09/13/2024]  Open
5
Kroll A, Niebuhr N, Butler G, Lercher MJ. SPOT: A machine learning model that predicts specific substrates for transport proteins. PLoS Biol 2024;22:e3002807. [PMID: 39325691 PMCID: PMC11426516 DOI: 10.1371/journal.pbio.3002807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2024] [Accepted: 08/13/2024] [Indexed: 09/28/2024]  Open
6
Pala D, Clark DE. Caught between a ROCK and a hard place: current challenges in structure-based drug design. Drug Discov Today 2024;29:104106. [PMID: 39029868 DOI: 10.1016/j.drudis.2024.104106] [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: 04/11/2024] [Revised: 06/27/2024] [Accepted: 07/13/2024] [Indexed: 07/21/2024]
7
Agarwal V, McShan AC. The power and pitfalls of AlphaFold2 for structure prediction beyond rigid globular proteins. Nat Chem Biol 2024;20:950-959. [PMID: 38907110 DOI: 10.1038/s41589-024-01638-w] [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: 05/22/2023] [Accepted: 04/29/2024] [Indexed: 06/23/2024]
8
Zhang H, Lan J, Wang H, Lu R, Zhang N, He X, Yang J, Chen L. AlphaFold2 in biomedical research: facilitating the development of diagnostic strategies for disease. Front Mol Biosci 2024;11:1414916. [PMID: 39139810 PMCID: PMC11319189 DOI: 10.3389/fmolb.2024.1414916] [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: 04/09/2024] [Accepted: 07/15/2024] [Indexed: 08/15/2024]  Open
9
Laczkó-Dobos H, Bhattacharjee A, Maddali AK, Kincses A, Abuammar H, Sebők-Nagy K, Páli T, Dér A, Hegedűs T, Csordás G, Juhász G. PtdIns4P is required for the autophagosomal recruitment of STX17 (syntaxin 17) to promote lysosomal fusion. Autophagy 2024;20:1639-1650. [PMID: 38411137 PMCID: PMC11210929 DOI: 10.1080/15548627.2024.2322493] [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: 08/31/2023] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 02/28/2024]  Open
10
Duart G, Graña-Montes R, Pastor-Cantizano N, Mingarro I. Experimental and computational approaches for membrane protein insertion and topology determination. Methods 2024;226:102-119. [PMID: 38604415 DOI: 10.1016/j.ymeth.2024.03.012] [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: 11/07/2023] [Revised: 03/13/2024] [Accepted: 03/22/2024] [Indexed: 04/13/2024]  Open
11
Partipilo M, Slotboom DJ. The S-component fold: a link between bacterial transporters and receptors. Commun Biol 2024;7:610. [PMID: 38773269 PMCID: PMC11109136 DOI: 10.1038/s42003-024-06295-2] [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: 01/18/2024] [Accepted: 05/06/2024] [Indexed: 05/23/2024]  Open
12
Tordai H, Torres O, Csepi M, Padányi R, Lukács GL, Hegedűs T. Analysis of AlphaMissense data in different protein groups and structural context. Sci Data 2024;11:495. [PMID: 38744964 PMCID: PMC11094042 DOI: 10.1038/s41597-024-03327-8] [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: 12/04/2023] [Accepted: 04/29/2024] [Indexed: 05/16/2024]  Open
13
Doga H, Raubenolt B, Cumbo F, Joshi J, DiFilippo FP, Qin J, Blankenberg D, Shehab O. A Perspective on Protein Structure Prediction Using Quantum Computers. J Chem Theory Comput 2024;20:3359-3378. [PMID: 38703105 PMCID: PMC11099973 DOI: 10.1021/acs.jctc.4c00067] [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: 01/22/2024] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/06/2024]
14
Long XB, Yao CR, Li SY, Zhang JG, Lu ZJ, Ma DD, Chen CE, Ying GG, Shi WJ. Screening androgen receptor agonists of fish species using machine learning and molecular model in NORMAN water-relevant list. JOURNAL OF HAZARDOUS MATERIALS 2024;468:133844. [PMID: 38394900 DOI: 10.1016/j.jhazmat.2024.133844] [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: 12/05/2023] [Revised: 02/14/2024] [Accepted: 02/18/2024] [Indexed: 02/25/2024]
15
Li H, Sun X, Cui W, Xu M, Dong J, Ekundayo BE, Ni D, Rao Z, Guo L, Stahlberg H, Yuan S, Vogel H. Computational drug development for membrane protein targets. Nat Biotechnol 2024;42:229-242. [PMID: 38361054 DOI: 10.1038/s41587-023-01987-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 09/13/2023] [Indexed: 02/17/2024]
16
Speer NO, Braun RJ, Reynolds EG, Brudnicka A, Swanson JM, Henne WM. Tld1 is a regulator of triglyceride lipolysis that demarcates a lipid droplet subpopulation. J Cell Biol 2024;223:e202303026. [PMID: 37889293 PMCID: PMC10609110 DOI: 10.1083/jcb.202303026] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 09/09/2023] [Accepted: 10/06/2023] [Indexed: 10/28/2023]  Open
17
Caoili SEC. B-Cell Epitope Prediction for Antipeptide Paratopes with the HAPTIC2/HEPTAD User Toolkit (HUT). Methods Mol Biol 2024;2821:9-32. [PMID: 38997477 DOI: 10.1007/978-1-0716-3914-6_2] [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: 07/14/2024]
18
Topitsch A, Schwede T, Pereira J. Outer membrane β-barrel structure prediction through the lens of AlphaFold2. Proteins 2024;92:3-14. [PMID: 37465978 DOI: 10.1002/prot.26552] [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: 02/18/2023] [Revised: 06/26/2023] [Accepted: 07/01/2023] [Indexed: 07/20/2023]
19
Torres J, Surya W, Boonserm P. Channel Formation in Cry Toxins: An Alphafold-2 Perspective. Int J Mol Sci 2023;24:16809. [PMID: 38069132 PMCID: PMC10705909 DOI: 10.3390/ijms242316809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 11/23/2023] [Accepted: 11/24/2023] [Indexed: 12/18/2023]  Open
20
Peslalz P, Kraus F, Izzo F, Bleisch A, El Hamdaoui Y, Schulz I, Kany AM, Hirsch AKH, Friedland K, Plietker B. Selective Activation of a TRPC6 Ion Channel Over TRPC3 by Metalated Type-B Polycyclic Polyprenylated Acylphloroglucinols. J Med Chem 2023;66:15061-15072. [PMID: 37922400 DOI: 10.1021/acs.jmedchem.3c01170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2023]
21
Jambrich MA, Tusnady GE, Dobson L. How AlphaFold2 shaped the structural coverage of the human transmembrane proteome. Sci Rep 2023;13:20283. [PMID: 37985809 PMCID: PMC10662385 DOI: 10.1038/s41598-023-47204-7] [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: 10/09/2023] [Accepted: 11/10/2023] [Indexed: 11/22/2023]  Open
22
Desai SA. Unique Properties of Nutrient Channels on Plasmodium-Infected Erythrocytes. Pathogens 2023;12:1211. [PMID: 37887727 PMCID: PMC10610302 DOI: 10.3390/pathogens12101211] [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: 09/09/2023] [Revised: 09/26/2023] [Accepted: 09/30/2023] [Indexed: 10/28/2023]  Open
23
Wu T, Li J, Tian C. Fungal carboxylate transporters: recent manipulations and applications. Appl Microbiol Biotechnol 2023;107:5909-5922. [PMID: 37561180 DOI: 10.1007/s00253-023-12720-z] [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: 04/18/2023] [Revised: 07/24/2023] [Accepted: 07/31/2023] [Indexed: 08/11/2023]
24
Pogozheva ID, Cherepanov S, Park SJ, Raghavan M, Im W, Lomize AL. Structural Modeling of Cytokine-Receptor-JAK2 Signaling Complexes Using AlphaFold Multimer. J Chem Inf Model 2023;63:5874-5895. [PMID: 37694948 DOI: 10.1021/acs.jcim.3c00926] [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: 09/12/2023]
25
Sosnick TR. AlphaFold developers Demis Hassabis and John Jumper share the 2023 Albert Lasker Basic Medical Research Award. J Clin Invest 2023:e174915. [PMID: 37731359 DOI: 10.1172/jci174915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/22/2023]  Open
26
Sun J, Kulandaisamy A, Ru J, Gromiha MM, Cribbs AP. TMKit: a Python interface for computational analysis of transmembrane proteins. Brief Bioinform 2023;24:bbad288. [PMID: 37594311 PMCID: PMC10516361 DOI: 10.1093/bib/bbad288] [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: 04/17/2023] [Revised: 07/07/2023] [Accepted: 07/18/2023] [Indexed: 08/19/2023]  Open
27
Al-Masri C, Trozzi F, Lin SH, Tran O, Sahni N, Patek M, Cichonska A, Ravikumar B, Rahman R. Investigating the conformational landscape of AlphaFold2-predicted protein kinase structures. BIOINFORMATICS ADVANCES 2023;3:vbad129. [PMID: 37786533 PMCID: PMC10541651 DOI: 10.1093/bioadv/vbad129] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 07/28/2023] [Accepted: 09/13/2023] [Indexed: 10/04/2023]
28
Speer NO, Braun RJ, Reynolds E, Brudnicka A, Swanson J, Henne WM. Tld1 is a novel regulator of triglyceride lipolysis that demarcates a lipid droplet subpopulation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.07.531595. [PMID: 36945645 PMCID: PMC10028886 DOI: 10.1101/2023.03.07.531595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
29
Basu K, Krugliak M, Arkin IT. Viroporins of Mpox Virus. Int J Mol Sci 2023;24:13828. [PMID: 37762131 PMCID: PMC10530900 DOI: 10.3390/ijms241813828] [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: 08/01/2023] [Revised: 08/17/2023] [Accepted: 09/04/2023] [Indexed: 09/29/2023]  Open
30
Tipper DJ, Harley CA. Spf1 and Ste24: quality controllers of transmembrane protein topology in the eukaryotic cell. Front Cell Dev Biol 2023;11:1220441. [PMID: 37635876 PMCID: PMC10456885 DOI: 10.3389/fcell.2023.1220441] [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: 05/10/2023] [Accepted: 07/14/2023] [Indexed: 08/29/2023]  Open
31
Tam C, Iwasaki W. AlphaCutter: Efficient removal of non-globular regions from predicted protein structures. Proteomics 2023;23:e2300176. [PMID: 37309722 DOI: 10.1002/pmic.202300176] [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: 04/03/2023] [Revised: 05/24/2023] [Accepted: 05/26/2023] [Indexed: 06/14/2023]
32
Jiao Y, Xing Y, Sun Y. Impact of E484Q and L452R Mutations on Structure and Binding Behavior of SARS-CoV-2 B.1.617.1 Using Deep Learning AlphaFold2, Molecular Docking and Dynamics Simulation. Int J Mol Sci 2023;24:11564. [PMID: 37511322 PMCID: PMC10380202 DOI: 10.3390/ijms241411564] [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: 06/06/2023] [Revised: 07/04/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023]  Open
33
Krokengen OC, Raasakka A, Kursula P. The intrinsically disordered protein glue of the myelin major dense line: Linking AlphaFold2 predictions to experimental data. Biochem Biophys Rep 2023;34:101474. [PMID: 37153862 PMCID: PMC10160357 DOI: 10.1016/j.bbrep.2023.101474] [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: 10/07/2022] [Revised: 03/31/2023] [Accepted: 04/19/2023] [Indexed: 05/10/2023]  Open
34
Hammoudeh N, Soukkarieh C, Murphy DJ, Hanano A. Mammalian lipid droplets: structural, pathological, immunological and anti-toxicological roles. Prog Lipid Res 2023;91:101233. [PMID: 37156444 DOI: 10.1016/j.plipres.2023.101233] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 04/30/2023] [Accepted: 05/05/2023] [Indexed: 05/10/2023]
35
Pogozheva ID, Cherepanov S, Park SJ, Raghavan M, Im W, Lomize AL. Structural modeling of cytokine-receptor-JAK2 signaling complexes using AlphaFold Multimer. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.14.544971. [PMID: 37398331 PMCID: PMC10312770 DOI: 10.1101/2023.06.14.544971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
36
Gulsevin A, Han B, Porta JC, Mchaourab HS, Meiler J, Kenworthy AK. Template-free prediction of a new monotopic membrane protein fold and assembly by AlphaFold2. Biophys J 2023;122:2041-2052. [PMID: 36352786 PMCID: PMC10257013 DOI: 10.1016/j.bpj.2022.11.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Revised: 10/20/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022]  Open
37
Kotliar IB, Ceraudo E, Kemelmakher-Liben K, Oren DA, Lorenzen E, Dodig-Crnković T, Horioka-Duplix M, Huber T, Schwenk JM, Sakmar TP. Itch receptor MRGPRX4 interacts with the receptor activity-modifying proteins. J Biol Chem 2023;299:104664. [PMID: 37003505 PMCID: PMC10165273 DOI: 10.1016/j.jbc.2023.104664] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 04/03/2023]  Open
38
Teufel F, Refsgaard JC, Kasimova MA, Deibler K, Madsen CT, Stahlhut C, Grønborg M, Winther O, Madsen D. Deorphanizing Peptides Using Structure Prediction. J Chem Inf Model 2023;63:2651-2655. [PMID: 37092865 DOI: 10.1021/acs.jcim.3c00378] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
39
Nguyen PH, Sterpone F, Derreumaux P. Metastable alpha-rich and beta-rich conformations of small Aβ42 peptide oligomers. Proteins 2023. [PMID: 37038252 DOI: 10.1002/prot.26495] [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: 12/14/2022] [Revised: 02/15/2023] [Accepted: 03/23/2023] [Indexed: 04/12/2023]
40
Varadi M, Bordin N, Orengo C, Velankar S. The opportunities and challenges posed by the new generation of deep learning-based protein structure predictors. Curr Opin Struct Biol 2023;79:102543. [PMID: 36807079 DOI: 10.1016/j.sbi.2023.102543] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Revised: 01/04/2023] [Accepted: 01/13/2023] [Indexed: 02/21/2023]
41
de Brevern AG. An agnostic analysis of the human AlphaFold2 proteome using local protein conformations. Biochimie 2023;207:11-19. [PMID: 36417962 DOI: 10.1016/j.biochi.2022.11.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 10/14/2022] [Accepted: 11/17/2022] [Indexed: 11/21/2022]
42
Pakuła K, Sequeiros-Borja C, Biała-Leonhard W, Pawela A, Banasiak J, Bailly A, Radom M, Geisler M, Brezovsky J, Jasiński M. Restriction of access to the central cavity is a major contributor to substrate selectivity in plant ABCG transporters. Cell Mol Life Sci 2023;80:105. [PMID: 36952129 PMCID: PMC10036432 DOI: 10.1007/s00018-023-04751-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 02/22/2023] [Accepted: 03/06/2023] [Indexed: 03/24/2023]
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Gao T, Zhao Y, Zhang L, Wang H. Secondary and Topological Structural Merge Prediction of Alpha-Helical Transmembrane Proteins Using a Hybrid Model Based on Hidden Markov and Long Short-Term Memory Neural Networks. Int J Mol Sci 2023;24:ijms24065720. [PMID: 36982795 PMCID: PMC10057634 DOI: 10.3390/ijms24065720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/11/2023] [Accepted: 03/13/2023] [Indexed: 03/19/2023]  Open
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Yang Z, Zeng X, Zhao Y, Chen R. AlphaFold2 and its applications in the fields of biology and medicine. Signal Transduct Target Ther 2023;8:115. [PMID: 36918529 PMCID: PMC10011802 DOI: 10.1038/s41392-023-01381-z] [Citation(s) in RCA: 115] [Impact Index Per Article: 115.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/27/2022] [Accepted: 02/16/2023] [Indexed: 03/16/2023]  Open
45
Willems A, Kalaw A, Ecer A, Kotwal A, Roepe LD, Roepe PD. Structures of Plasmodium falciparum Chloroquine Resistance Transporter (PfCRT) Isoforms and Their Interactions with Chloroquine. Biochemistry 2023;62:1093-1110. [PMID: 36800498 PMCID: PMC10950298 DOI: 10.1021/acs.biochem.2c00669] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Revised: 02/02/2023] [Indexed: 02/19/2023]
46
Azizogli AR, Pai V, Coppola F, Jafari R, Dodd-o JB, Harish R, Balasubramanian B, Kashyap J, Acevedo-Jake AM, Král P, Kumar VA. Scalable Inhibitors of the Nsp3-Nsp4 Coupling in SARS-CoV-2. ACS OMEGA 2023;8:5349-5360. [PMID: 36798146 PMCID: PMC9923439 DOI: 10.1021/acsomega.2c06384] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/29/2022] [Indexed: 06/18/2023]
47
Sun J, Kulandaisamy A, Liu J, Hu K, Gromiha MM, Zhang Y. Machine learning in computational modelling of membrane protein sequences and structures: From methodologies to applications. Comput Struct Biotechnol J 2023;21:1205-1226. [PMID: 36817959 PMCID: PMC9932300 DOI: 10.1016/j.csbj.2023.01.036] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/16/2023] [Accepted: 01/25/2023] [Indexed: 01/29/2023]  Open
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Yang Y, Hu Y, Yao F, Yang J, Ge L, Wang P, Xu X. Virtual screening and activity evaluation of human uric acid transporter 1 (hURAT1) inhibitors. RSC Adv 2023;13:3474-3486. [PMID: 36756549 PMCID: PMC9871872 DOI: 10.1039/d2ra07193b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Accepted: 12/13/2022] [Indexed: 01/25/2023]  Open
49
Taylor KM. The LIV-1 Subfamily of Zinc Transporters: From Origins to Present Day Discoveries. Int J Mol Sci 2023;24:ijms24021255. [PMID: 36674777 PMCID: PMC9861476 DOI: 10.3390/ijms24021255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 01/03/2023] [Accepted: 01/06/2023] [Indexed: 01/11/2023]  Open
50
Ma Y, Zhang M, Yang J, Zhu L, Dai J, Wu X. Characterization of the renal tubular transport of creatinine by activity-based protein profiling and transport kinetics. Eur J Pharm Sci 2023;180:106342. [PMID: 36435354 DOI: 10.1016/j.ejps.2022.106342] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/14/2022] [Accepted: 11/23/2022] [Indexed: 11/25/2022]
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