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For: Studer G, Biasini M, Schwede T. Assessing the local structural quality of transmembrane protein models using statistical potentials (QMEANBrane). ACTA ACUST UNITED AC 2015;30:i505-11. [PMID: 25161240 PMCID: PMC4147910 DOI: 10.1093/bioinformatics/btu457] [Citation(s) in RCA: 112] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Number Cited by Other Article(s)
1
Ruiz-Castelan JE, Villa-Díaz F, Castro ME, Melendez FJ, Scior T. The α/β3 complex of human voltage-gated sodium channel hNav1.7 to study mechanistic differences in presence and absence of auxiliary subunit β3. J Mol Model 2025;31:168. [PMID: 40397258 PMCID: PMC12095431 DOI: 10.1007/s00894-025-06378-9] [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: 12/03/2024] [Accepted: 04/25/2025] [Indexed: 05/22/2025]
2
Torres Juárez JA, Hernández Puga AG, Sánchez Tusie AA. Differential molecular interactions between iberiotoxin and human SLO3 and SLO1 potassium channels. J Mol Model 2025;31:155. [PMID: 40358624 DOI: 10.1007/s00894-025-06379-8] [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: 09/26/2024] [Accepted: 04/28/2025] [Indexed: 05/15/2025]
3
Bing RG, Buhrman GK, Ford KC, Straub CT, Laemthong T, Rose RB, Adams MWW, Kelly RM. Structural and kinetic characterization of an acetoacetyl-Coenzyme A: acetate Coenzyme A transferase from the extreme thermophile Thermosipho melanesiensis. Biochem J 2025;482:225-240. [PMID: 39869497 DOI: 10.1042/bcj20240747] [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: 11/20/2024] [Revised: 01/22/2025] [Accepted: 01/27/2025] [Indexed: 01/29/2025]
4
Minere M, Mortensen M, Dorovykh V, Warnes G, Nizetic D, Smart TG, Hannan SB. Presynaptic hyperexcitability reversed by positive allosteric modulation of a GABABR epilepsy variant. Brain 2025;148:533-548. [PMID: 39028675 PMCID: PMC11788220 DOI: 10.1093/brain/awae232] [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: 10/27/2023] [Revised: 04/05/2024] [Accepted: 06/23/2024] [Indexed: 07/21/2024]  Open
5
Niu Y, Qin P, Lin P. Advances of deep Neural Networks (DNNs) in the development of peptide drugs. Future Med Chem 2025;17:485-499. [PMID: 39935356 PMCID: PMC11834456 DOI: 10.1080/17568919.2025.2463319] [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: 11/24/2024] [Accepted: 01/27/2025] [Indexed: 02/13/2025]  Open
6
Wicaksono IA, Destiarani W, Romadhon SF, Nugraha BAP, Yusuf M, Milanda T, Amalia R. Transmembrane Prostate Androgen-Induced Protein 1 Molecular Modeling and Refinement Using Coarse-Grained Molecular Dynamics. ACS OMEGA 2025;10:2712-2724. [PMID: 39895701 PMCID: PMC11780462 DOI: 10.1021/acsomega.4c08451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/14/2024] [Revised: 12/20/2024] [Accepted: 12/26/2024] [Indexed: 02/04/2025]
7
Yegnaswamy S, C SK, Aldaais E. Conformational dynamics of the membrane protein of MERS-CoV in comparison with SARS-CoV-2 in ERGIC complex. J Biomol Struct Dyn 2025:1-15. [PMID: 39755960 DOI: 10.1080/07391102.2024.2437529] [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: 01/28/2024] [Accepted: 05/21/2024] [Indexed: 01/07/2025]
8
de La Bourdonnaye G, Ghazalova T, Fojtik P, Kutalkova K, Bednar D, Damborsky J, Rotrekl V, Stepankova V, Chaloupkova R. Computer-aided engineering of stabilized fibroblast growth factor 21. Comput Struct Biotechnol J 2024;23:942-951. [PMID: 38379823 PMCID: PMC10877085 DOI: 10.1016/j.csbj.2024.02.001] [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: 10/09/2023] [Revised: 02/03/2024] [Accepted: 02/03/2024] [Indexed: 02/22/2024]  Open
9
Labossiere EH, Gonzalez-Diaz S, Enns S, Lopez P, Yang X, Kidane B, Vazquez-Grande G, Siddik AB, Kung SKP, Sandstrom P, Ravandi A, Ball TB, Su RC. Detectability of cytokine and chemokine using ELISA, following sample-inactivation using Triton X-100 or heat. Sci Rep 2024;14:26777. [PMID: 39500912 PMCID: PMC11538312 DOI: 10.1038/s41598-024-74739-0] [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: 05/02/2024] [Accepted: 09/30/2024] [Indexed: 11/08/2024]  Open
10
Gallino SL, Agüero L, Boffi JC, Schottlender G, Buonfiglio P, Dalamon V, Marcovich I, Carpaneto A, Craig PO, Plazas PV, Elgoyhen AB. Key role of the TM2-TM3 loop in calcium potentiation of the α9α10 nicotinic acetylcholine receptor. Cell Mol Life Sci 2024;81:337. [PMID: 39120784 PMCID: PMC11335262 DOI: 10.1007/s00018-024-05381-2] [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: 01/19/2024] [Revised: 07/09/2024] [Accepted: 07/23/2024] [Indexed: 08/10/2024]
11
Waterhouse AM, Studer G, Robin X, Bienert S, Tauriello G, Schwede T. The structure assessment web server: for proteins, complexes and more. Nucleic Acids Res 2024;52:W318-W323. [PMID: 38634802 PMCID: PMC11223858 DOI: 10.1093/nar/gkae270] [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: 02/02/2024] [Revised: 03/21/2024] [Accepted: 04/02/2024] [Indexed: 04/19/2024]  Open
12
Rao P, Ninama J, Dudhat M, Goswami D, Rawal RM. Curcumin interferes with chitin synthesis in Aedes aegypti: a computational and experimental investigation. Mol Divers 2024;28:1505-1529. [PMID: 37358753 DOI: 10.1007/s11030-023-10672-0] [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] [Received: 05/09/2023] [Accepted: 06/10/2023] [Indexed: 06/27/2023]
13
Ma B, Shi S, Guo W, Zhang H, Zhao Z, An H. Liensinine, a Novel and Food-Derived Compound, Exerts Potent Antihepatoma Efficacy via Inhibiting the Kv10.1 Channel. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024;72:4689-4702. [PMID: 38382537 DOI: 10.1021/acs.jafc.3c06142] [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: 02/23/2024]
14
Nogueira KMV, Mendes V, Kamath KS, Cheruku A, Oshiquiri LH, de Paula RG, Carraro C, Pedersoli WR, Pereira LMS, Vieira LC, Steindorff AS, Amirkhani A, McKay MJ, Nevalainen H, Molloy MP, Silva RN. Proteome profiling of enriched membrane-associated proteins unraveled a novel sophorose and cello-oligosaccharide transporter in Trichoderma reesei. Microb Cell Fact 2024;23:22. [PMID: 38229067 DOI: 10.1186/s12934-023-02279-9] [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: 07/25/2023] [Accepted: 12/18/2023] [Indexed: 01/18/2024]  Open
15
Ma B, Shi S, Ren S, Qu C, Zhao Z, An H. Corydaline binds to a druggable pocket of hEAG1 channel and inhibits hepatic carcinoma cell viability. Eur J Pharmacol 2024;962:176240. [PMID: 38048981 DOI: 10.1016/j.ejphar.2023.176240] [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: 08/11/2023] [Revised: 11/22/2023] [Accepted: 11/28/2023] [Indexed: 12/06/2023]
16
Biswas S, Hossen MR, Akter S, Ali MA, Halim MA, Ullah MO. Structural dynamics and functional analysis of Saprolegnia parasitica chitin synthases 5 in a phospholipid bilayer. J Biomol Struct Dyn 2024;42:461-474. [PMID: 36995127 DOI: 10.1080/07391102.2023.2193993] [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: 08/13/2022] [Accepted: 03/15/2023] [Indexed: 03/31/2023]
17
Bains A, Fischer K, Guan W, LiWang PJ. The Antiviral Activity of the Lectin Griffithsin against SARS-CoV-2 Is Enhanced by the Presence of Structural Proteins. Viruses 2023;15:2452. [PMID: 38140693 PMCID: PMC10747160 DOI: 10.3390/v15122452] [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: 10/14/2023] [Revised: 12/07/2023] [Accepted: 12/14/2023] [Indexed: 12/24/2023]  Open
18
Zhao Y, Zheng Z, Zhang Z, Xu Y, Hillpot E, Lin YS, Zakusilo FT, Lu JY, Ablaeva J, Biashad SA, Miller RA, Nevo E, Seluanov A, Gorbunova V. Evolution of high-molecular-mass hyaluronic acid is associated with subterranean lifestyle. Nat Commun 2023;14:8054. [PMID: 38052795 PMCID: PMC10698142 DOI: 10.1038/s41467-023-43623-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Accepted: 11/15/2023] [Indexed: 12/07/2023]  Open
19
Zhao Y, Zheng Z, Zhang Z, Hillpot E, Lin YS, Zakusilo FT, Lu JY, Ablaeva J, Miller RA, Nevo E, Seluanov A, Gorbunova V. Evolution of High-Molecular-Mass Hyaluronic Acid is Associated with Subterranean Lifestyle. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.08.539764. [PMID: 37215017 PMCID: PMC10197608 DOI: 10.1101/2023.05.08.539764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
20
Jamali Langeroudi A, Sabet MS, Jalali-Javaran M, Zamani K, Lohrasebi T, Malboobi MA. Functional assessment of AtPAP17; encoding a purple acid phosphatase involved in phosphate metabolism in Arabidopsis thaliana. Biotechnol Lett 2023;45:719-739. [PMID: 37074554 DOI: 10.1007/s10529-023-03375-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 03/05/2023] [Accepted: 04/03/2023] [Indexed: 04/20/2023]
21
Yang T, Wang Y, Jiang J, Wang P, Zhong Y, Zhou Q, Wang X, Cai J, Huang M, Jiang D, Dai T, Cao W. Influence of High-Molecular-Weight Glutenin Subunit on Components and Multiscale Structure of Gluten and Dough Quality in Soft Wheat. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023;71:4943-4956. [PMID: 36924464 DOI: 10.1021/acs.jafc.2c07958] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
22
Leiva S, Bugnon Valdano M, Gardiol D. Unravelling the epidemiological diversity of Zika virus by analyzing key protein variations. Arch Virol 2023;168:115. [PMID: 36943525 DOI: 10.1007/s00705-023-05726-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Accepted: 01/19/2023] [Indexed: 03/23/2023]
23
Jaciuk M, Scherf D, Kaszuba K, Gaik M, Rau A, Kościelniak A, Krutyhołowa R, Rawski M, Indyka P, Graziadei A, Chramiec-Głąbik A, Biela A, Dobosz D, Lin TY, Abbassi NEH, Hammermeister A, Rappsilber J, Kosinski J, Schaffrath R, Glatt S. Cryo-EM structure of the fully assembled Elongator complex. Nucleic Acids Res 2023;51:2011-2032. [PMID: 36617428 PMCID: PMC10018365 DOI: 10.1093/nar/gkac1232] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 11/22/2022] [Accepted: 12/09/2022] [Indexed: 01/10/2023]  Open
24
Siddiqui AJ, Kumar V, Jahan S, Alshahrani MM, Al Awadh AA, Siddiqui MA, Hamadou WS, Abdelgadir A, Saxena J, Badraoui R, Snoussi M, Adnan M. Computational insight into structural basis of human ELOVL1 inhibition. Comput Biol Med 2023;157:106786. [PMID: 36924735 DOI: 10.1016/j.compbiomed.2023.106786] [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: 11/09/2022] [Revised: 02/17/2023] [Accepted: 03/10/2023] [Indexed: 03/13/2023]
25
Afshinpour M, Mahdiuni H. Arginine transportation mechanism through cationic amino acid transporter 1: insights from molecular dynamics studies. J Biomol Struct Dyn 2023;41:13580-13594. [PMID: 36762692 DOI: 10.1080/07391102.2023.2175374] [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: 07/21/2022] [Accepted: 01/28/2023] [Indexed: 02/11/2023]
26
L-proline transporter inhibitor (LQFM215) promotes neuroprotection in ischemic stroke. Pharmacol Rep 2023;75:276-292. [PMID: 36719635 DOI: 10.1007/s43440-023-00451-x] [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] [Received: 10/01/2022] [Revised: 01/12/2023] [Accepted: 01/13/2023] [Indexed: 02/01/2023]
27
Folacci M, Estaran S, Ménard C, Bertaud A, Rousset M, Roussel J, Thibaud JB, Vignes M, Chavanieu A, Charnet P, Cens T. Functional Characterization of Four Known Cav2.1 Variants Associated with Neurodevelopmental Disorders. MEMBRANES 2023;13:96. [PMID: 36676903 PMCID: PMC9864995 DOI: 10.3390/membranes13010096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 01/06/2023] [Accepted: 01/09/2023] [Indexed: 06/17/2023]
28
Matamoros-Recio A, Mínguez-Toral M, Martín-Santamaría S. Modeling of Transmembrane Domain and Full-Length TLRs in Membrane Models. Methods Mol Biol 2023;2700:3-38. [PMID: 37603172 DOI: 10.1007/978-1-0716-3366-3_1] [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: 08/22/2023]
29
Bartuzi D, Kaczor AA, Matosiuk D. Illuminating the "Twilight Zone": Advances in Difficult Protein Modeling. Methods Mol Biol 2023;2627:25-40. [PMID: 36959440 DOI: 10.1007/978-1-0716-2974-1_2] [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]
30
Evadgian A, Bharatha A, Cohall D. Use of Cheminformatics to Determine Potential Drug Interactions between Popular Barbadian Botanical Medicines and Antihypertensive Drugs. ACS OMEGA 2022;7:44603-44619. [PMID: 36530331 PMCID: PMC9753521 DOI: 10.1021/acsomega.2c02446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 10/21/2022] [Indexed: 06/17/2023]
31
Farhana R, Lei R, Pham K, Derrien V, Cedeño J, Rodriquez V, Bernad S, Lima FF, Miksovska J. Globin X: A highly stable intrinsically hexacoordinate globin. J Inorg Biochem 2022;236:111976. [PMID: 36058051 DOI: 10.1016/j.jinorgbio.2022.111976] [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: 06/29/2022] [Revised: 08/10/2022] [Accepted: 08/18/2022] [Indexed: 12/15/2022]
32
Shamkh IM, Al-Majidi M, Shntaif AH, Deng Kai PT, Nh-Pham N, Rahman I, Hamza D, Khan MS, Elsharayidi MS, Salah ET, Haikal A, Omoniyi MA, Abdalrahman MA, Karpinski TM. Nontoxic and Naturally Occurring Active Compounds as Potential Inhibitors of Biological Targets in Liriomyza trifolii. Int J Mol Sci 2022;23:12791. [PMID: 36361586 PMCID: PMC9657120 DOI: 10.3390/ijms232112791] [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: 08/19/2022] [Revised: 10/15/2022] [Accepted: 10/17/2022] [Indexed: 12/07/2023]  Open
33
Holmes AOM, Goldman A, Kalli AC. mPPases create a conserved anionic membrane fingerprint as identified via multi-scale simulations. PLoS Comput Biol 2022;18:e1010578. [PMID: 36191052 PMCID: PMC9560603 DOI: 10.1371/journal.pcbi.1010578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Revised: 10/13/2022] [Accepted: 09/16/2022] [Indexed: 11/06/2022]  Open
34
In Silico Evaluation of Hexamethylene Amiloride Derivatives as Potential Luminal Inhibitors of SARS-CoV-2 E Protein. Int J Mol Sci 2022;23:ijms231810647. [PMID: 36142556 PMCID: PMC9503309 DOI: 10.3390/ijms231810647] [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: 07/25/2022] [Revised: 09/01/2022] [Accepted: 09/01/2022] [Indexed: 11/24/2022]  Open
35
Liang YY, Yan LQ, Tan MH, Li GH, Fang JH, Peng JY, Li KT. Isolation, characterization, and genome sequencing of a novel chitin deacetylase producing Bacillus aryabhattai TCI-16. Front Microbiol 2022;13:999639. [PMID: 36171752 PMCID: PMC9511218 DOI: 10.3389/fmicb.2022.999639] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/23/2022] [Indexed: 11/23/2022]  Open
36
Bitton M, Keasar C. Estimation of model accuracy by a unique set of features and tree-based regressor. Sci Rep 2022;12:14074. [PMID: 35982086 PMCID: PMC9388490 DOI: 10.1038/s41598-022-17097-z] [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: 02/24/2022] [Accepted: 07/20/2022] [Indexed: 11/26/2022]  Open
37
Pervaiz I, Zahra FT, Mikelis C, Al-Ahmad AJ. An in vitro model of glucose transporter 1 deficiency syndrome at the blood-brain barrier using induced pluripotent stem cells. J Neurochem 2022;162:483-500. [PMID: 35943296 DOI: 10.1111/jnc.15684] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 07/08/2022] [Accepted: 08/03/2022] [Indexed: 11/28/2022]
38
Mahtarin R, Islam S, Islam MJ, Ullah MO, Ali MA, Halim MA. Structure and dynamics of membrane protein in SARS-CoV-2. J Biomol Struct Dyn 2022;40:4725-4738. [PMID: 33353499 PMCID: PMC7784837 DOI: 10.1080/07391102.2020.1861983] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 12/05/2020] [Indexed: 12/15/2022]
39
López-Rivera JJ, Rodríguez-Salazar L, Soto-Ospina A, Estrada-Serrato C, Serrano D, Chaparro-Solano HM, Londoño O, Rueda PA, Ardila G, Villegas-Lanau A, Godoy-Corredor M, Cuartas M, Vélez JI, Vidal OM, Isaza-Ruget MA, Arcos-Burgos M. Structural Protein Effects Underpinning Cognitive Developmental Delay of the PURA p.Phe233del Mutation Modelled by Artificial Intelligence and the Hybrid Quantum Mechanics–Molecular Mechanics Framework. Brain Sci 2022;12:brainsci12070871. [PMID: 35884678 PMCID: PMC9313109 DOI: 10.3390/brainsci12070871] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/21/2022] [Accepted: 06/24/2022] [Indexed: 02/06/2023]  Open
40
Llanos MA, Enrique N, Sbaraglini ML, Garofalo FM, Talevi A, Gavernet L, Martín P. Structure-Based Virtual Screening Identifies Novobiocin, Montelukast, and Cinnarizine as TRPV1 Modulators with Anticonvulsant Activity In Vivo. J Chem Inf Model 2022;62:3008-3022. [PMID: 35696534 DOI: 10.1021/acs.jcim.2c00312] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
41
Gain and loss of TASK3 channel function and its regulation by novel variation cause KCNK9 imprinting syndrome. Genome Med 2022;14:62. [PMID: 35698242 PMCID: PMC9195326 DOI: 10.1186/s13073-022-01064-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 05/19/2022] [Indexed: 11/10/2022]  Open
42
Incampo G, Giangregorio N, Gambacorta N, Nicolotti O, Pacifico C, Palmieri L, Tonazzi A. Praseodymium trivalent ion is an effective inhibitor of mitochondrial basic amino acids and carnitine/acylcarnitine carriers. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022;1863:148557. [PMID: 35367451 DOI: 10.1016/j.bbabio.2022.148557] [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: 01/13/2022] [Revised: 03/18/2022] [Accepted: 03/25/2022] [Indexed: 06/14/2023]
43
Ben Ayed R, Chirmade T, Hanana M, Khamassi K, Ercisli S, Choudhary R, Kadoo N, Karunakaran R. Comparative Analysis and Structural Modeling of Elaeis oleifera FAD2, a Fatty Acid Desaturase Involved in Unsaturated Fatty Acid Composition of American Oil Palm. BIOLOGY 2022;11:529. [PMID: 35453727 PMCID: PMC9032008 DOI: 10.3390/biology11040529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 03/13/2022] [Accepted: 03/23/2022] [Indexed: 11/17/2022]
44
Zimmermann MT. Molecular Modeling is an Enabling Approach to Complement and Enhance Channelopathy Research. Compr Physiol 2022;12:3141-3166. [PMID: 35578963 DOI: 10.1002/cphy.c190047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
45
Prabu R, Mohanty A, Balakrishnan SS, Jayalakshmi G, Sundar K. Molecular docking and simulation of IcaC protein as O-succinyltransferase function in staphylococcus epidermidis biofilm formation. Curr Res Struct Biol 2022;4:78-86. [PMID: 35399651 PMCID: PMC8987812 DOI: 10.1016/j.crstbi.2022.03.002] [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: 12/28/2021] [Revised: 02/19/2022] [Accepted: 03/13/2022] [Indexed: 12/04/2022]  Open
46
Shi S, Pang C, Ren S, Sun F, Ma B, Guo S, Li J, Chen Y, An H. Molecular dynamics simulation of TMEM16A channel: Linking structure with gating. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022;1864:183777. [PMID: 34537214 DOI: 10.1016/j.bbamem.2021.183777] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Revised: 08/23/2021] [Accepted: 09/12/2021] [Indexed: 10/20/2022]
47
Bengtsson RJ, Simpkin AJ, Pulford CV, Low R, Rasko DA, Rigden DJ, Hall N, Barry EM, Tennant SM, Baker KS. Pathogenomic analyses of Shigella isolates inform factors limiting shigellosis prevention and control across LMICs. Nat Microbiol 2022;7:251-261. [PMID: 35102306 PMCID: PMC8813619 DOI: 10.1038/s41564-021-01054-z] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 12/17/2021] [Indexed: 12/17/2022]
48
Felsztyna I, Villarreal MA, García DA, Miguel V. Insect RDL Receptor Models for Virtual Screening: Impact of the Template Conformational State in Pentameric Ligand-Gated Ion Channels. ACS OMEGA 2022;7:1988-2001. [PMID: 35071887 PMCID: PMC8771969 DOI: 10.1021/acsomega.1c05465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Accepted: 12/28/2021] [Indexed: 06/14/2023]
49
Topin J, Bouysset C, Pacalon J, Kim Y, Rhyu MR, Fiorucci S, Golebiowski J. Functional molecular switches of mammalian G protein-coupled bitter-taste receptors. Cell Mol Life Sci 2021;78:7605-7615. [PMID: 34687318 PMCID: PMC11073308 DOI: 10.1007/s00018-021-03968-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 09/20/2021] [Accepted: 09/26/2021] [Indexed: 10/20/2022]
50
Soto-Ospina A, Araque Marín P, Bedoya GDJ, Villegas Lanau A. Structural Predictive Model of Presenilin-2 Protein and Analysis of Structural Effects of Familial Alzheimer's Disease Mutations. Biochem Res Int 2021;2021:9542038. [PMID: 34881055 PMCID: PMC8648483 DOI: 10.1155/2021/9542038] [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: 06/18/2021] [Accepted: 10/21/2021] [Indexed: 12/12/2022]  Open
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