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For: Velankar S, Burley SK, Kurisu G, Hoch JC, Markley JL. The Protein Data Bank Archive. Methods Mol Biol 2021;2305:3-21. [PMID: 33950382 DOI: 10.1007/978-1-0716-1406-8_1] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Number Cited by Other Article(s)
1
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]
2
Chu J, Song J, Fan Z, Zhang R, Wang Q, Yi K, Gong Q, Liu B. Investigating the Effect and Mechanism of 3-Methyladenine Against Diabetic Encephalopathy by Network Pharmacology, Molecular Docking, and Experimental Validation. Pharmaceuticals (Basel) 2025;18:605. [PMID: 40430426 PMCID: PMC12115123 DOI: 10.3390/ph18050605] [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: 03/20/2025] [Revised: 04/15/2025] [Accepted: 04/18/2025] [Indexed: 05/29/2025]  Open
3
Sil S, Datta I, Basu S. Use of AI-methods over MD simulations in the sampling of conformational ensembles in IDPs. Front Mol Biosci 2025;12:1542267. [PMID: 40264953 PMCID: PMC12011600 DOI: 10.3389/fmolb.2025.1542267] [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: 12/09/2024] [Accepted: 03/17/2025] [Indexed: 04/24/2025]  Open
4
Wang J, Wang H, Kang X, Wang X, Li X, Guo J, Jing X, Chu X, Han X. Integrated network pharmacology, molecular docking, and animal experiments to reveal the potential mechanism of hesperetin on COPD. Sci Rep 2025;15:11024. [PMID: 40164657 PMCID: PMC11958725 DOI: 10.1038/s41598-025-95810-4] [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: 01/21/2025] [Accepted: 03/24/2025] [Indexed: 04/02/2025]  Open
5
Citriniti EL, Rocca R, Costa G, Sciacca C, Cardullo N, Muccilli V, Karioti A, Carta F, Supuran CT, Alcaro S, Ortuso F. Discover the Power of Lithospermic Acid as Human Carbonic Anhydrase VA and Pancreatic Lipase Inhibitor Through In Silico and In Vitro Studies. Arch Pharm (Weinheim) 2025;358:e3128. [PMID: 40257393 PMCID: PMC12010950 DOI: 10.1002/ardp.202500046] [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: 01/15/2025] [Revised: 02/24/2025] [Accepted: 03/21/2025] [Indexed: 04/22/2025]
6
da Conceição PJP, Ayusso GM, Carvalho T, Duarte Lima ML, Marinho MDS, Moraes FR, Galán-Jurado PE, González-Santamaría J, Bittar C, Zhang B, Jardim ACG, Rahal P, Calmon MF. In Vitro Evaluation of the Antiviral Activity of Polyphenol (-)-Epigallocatechin-3-Gallate (EGCG) Against Mayaro Virus. Viruses 2025;17:258. [PMID: 40007013 PMCID: PMC11860591 DOI: 10.3390/v17020258] [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: 12/17/2024] [Revised: 02/11/2025] [Accepted: 02/12/2025] [Indexed: 02/27/2025]  Open
7
Cao R, Liu Y, Wei K, Jin N, Liang Y, Ao R, Pan W, Wang X, Wang X, Zhang L, Xie J. Genes related to neural tube defects and glioblastoma. Sci Rep 2025;15:3777. [PMID: 39885289 PMCID: PMC11782569 DOI: 10.1038/s41598-025-86891-2] [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: 06/20/2024] [Accepted: 01/14/2025] [Indexed: 02/01/2025]  Open
8
Zhuo C, Zeng C, Liu H, Wang H, Peng Y, Zhao Y. Advances and Mechanisms of RNA-Ligand Interaction Predictions. Life (Basel) 2025;15:104. [PMID: 39860045 PMCID: PMC11767038 DOI: 10.3390/life15010104] [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: 12/10/2024] [Revised: 01/13/2025] [Accepted: 01/15/2025] [Indexed: 01/27/2025]  Open
9
Qin B, Lv Z, Yang H, Xiao T, Su J. TRIM103 activates the RLRs pathway to enhance antiviral response by targeting VP5 and VP7. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2024;161:105254. [PMID: 39214323 DOI: 10.1016/j.dci.2024.105254] [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: 05/15/2024] [Revised: 08/26/2024] [Accepted: 08/26/2024] [Indexed: 09/04/2024]
10
Zhuo C, Gao J, Li A, Liu X, Zhao Y. A Machine Learning Method for RNA-Small Molecule Binding Preference Prediction. J Chem Inf Model 2024;64:7386-7397. [PMID: 39265103 DOI: 10.1021/acs.jcim.4c01324] [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: 09/14/2024]
11
Jabbar M, Baboo I, Majeed H, Farooq Z, Palangi V, Lackner M. Preparation and Characterization of Cumin Essential Oil Nanoemulsion (CEONE) as an Antibacterial Agent and Growth Promoter in Broilers: A Study on Efficacy, Safety, and Health Impact. Animals (Basel) 2024;14:2860. [PMID: 39409810 PMCID: PMC11475229 DOI: 10.3390/ani14192860] [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: 07/03/2024] [Revised: 09/25/2024] [Accepted: 10/02/2024] [Indexed: 10/20/2024]  Open
12
Wang QX, Cai J, Chen ZJ, Liu JC, Wang JJ, Zhou H, Li QQ, Wang ZX, Wang YB, Tong ZJ, Yang J, Wei TH, Zhang MY, Zhou Y, Dai WC, Ding N, Leng XJ, Yin XY, Sun SL, Yu YC, Li NG, Shi ZH. Exploring drug repositioning possibilities of kinase inhibitors via molecular simulation. Mol Inform 2024;43:e202300336. [PMID: 39031899 DOI: 10.1002/minf.202300336] [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: 12/06/2023] [Revised: 04/09/2024] [Accepted: 04/28/2024] [Indexed: 07/22/2024]
13
Gu X, Myung Y, Rodrigues CHM, Ascher DB. EFG-CS: Predicting chemical shifts from amino acid sequences with protein structure prediction using machine learning and deep learning models. Protein Sci 2024;33:e5096. [PMID: 38979954 PMCID: PMC11232051 DOI: 10.1002/pro.5096] [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: 12/17/2023] [Revised: 05/06/2024] [Accepted: 06/15/2024] [Indexed: 07/10/2024]
14
Ceasar SA, Prabhu S, Ebeed HT. Protein research in millets: current status and way forward. PLANTA 2024;260:43. [PMID: 38958760 DOI: 10.1007/s00425-024-04478-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 06/27/2024] [Indexed: 07/04/2024]
15
Çapan İ, Hawash M, Qaoud MT, Gülüm L, Tunoglu ENY, Çifci KU, Çevrimli BS, Sert Y, Servi S, Koca İ, Tutar Y. Synthesis of novel carbazole hydrazine-carbothioamide scaffold as potent antioxidant, anticancer and antimicrobial agents. BMC Chem 2024;18:102. [PMID: 38773663 PMCID: PMC11110238 DOI: 10.1186/s13065-024-01207-1] [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: 01/18/2024] [Accepted: 05/13/2024] [Indexed: 05/24/2024]  Open
16
Curcio A, Rocca R, Alcaro S, Artese A. The Histone Deacetylase Family: Structural Features and Application of Combined Computational Methods. Pharmaceuticals (Basel) 2024;17:620. [PMID: 38794190 PMCID: PMC11124352 DOI: 10.3390/ph17050620] [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: 04/18/2024] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024]  Open
17
Burley SK, Piehl DW, Vallat B, Zardecki C. RCSB Protein Data Bank: supporting research and education worldwide through explorations of experimentally determined and computationally predicted atomic level 3D biostructures. IUCRJ 2024;11:279-286. [PMID: 38597878 PMCID: PMC11067742 DOI: 10.1107/s2052252524002604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 03/19/2024] [Indexed: 04/11/2024]
18
Canales CSC, Pavan AR, Dos Santos JL, Pavan FR. In silico drug design strategies for discovering novel tuberculosis therapeutics. Expert Opin Drug Discov 2024;19:471-491. [PMID: 38374606 DOI: 10.1080/17460441.2024.2319042] [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: 02/12/2024] [Indexed: 02/21/2024]
19
Sun F, Deng Y, Ma X, Liu Y, Zhao L, Yu S, Zhang L. Structure-based prediction of protein-protein interaction network in rice. Genet Mol Biol 2024;47:e20230068. [PMID: 38314883 PMCID: PMC10849033 DOI: 10.1590/1678-4685-gmb-2023-0068] [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: 03/03/2023] [Accepted: 10/02/2023] [Indexed: 02/07/2024]  Open
20
Yu Y, Zu L, Jiang J, Wu Y, Wang Y, Xu M, Liu Q. Structure-aware deep model for MHC-II peptide binding affinity prediction. BMC Genomics 2024;25:127. [PMID: 38291350 PMCID: PMC10826266 DOI: 10.1186/s12864-023-09900-6] [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: 08/30/2023] [Accepted: 12/12/2023] [Indexed: 02/01/2024]  Open
21
Zhang J, Han M, Wang S, Wu R, Zhao Q, Chen M, Yang Y, Zhang J, Meng X, Zhang Y, Wang Z. Study on the anti-mitochondrial apoptosis mechanism of Erigeron breviscapus injection based on UPLC-Q-TOF-MS metabolomics and molecular docking in rats with cerebral ischemia-reperfusion injury. JOURNAL OF ETHNOPHARMACOLOGY 2024;319:117310. [PMID: 37827296 DOI: 10.1016/j.jep.2023.117310] [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: 07/12/2023] [Revised: 10/08/2023] [Accepted: 10/10/2023] [Indexed: 10/14/2023]
22
Varadi M, Bertoni D, Magana P, Paramval U, Pidruchna I, Radhakrishnan M, Tsenkov M, Nair S, Mirdita M, Yeo J, Kovalevskiy O, Tunyasuvunakool K, Laydon A, Žídek A, Tomlinson H, Hariharan D, Abrahamson J, Green T, Jumper J, Birney E, Steinegger M, Hassabis D, Velankar S. AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences. Nucleic Acids Res 2024;52:D368-D375. [PMID: 37933859 PMCID: PMC10767828 DOI: 10.1093/nar/gkad1011] [Citation(s) in RCA: 508] [Impact Index Per Article: 508.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/13/2023] [Accepted: 10/18/2023] [Indexed: 11/08/2023]  Open
23
Wang T, Zhang W, Fang C, Wang N, Zhuang Y, Gao S. Research on the Regulatory Mechanism of Ginseng on the Tumor Microenvironment of Colorectal Cancer based on Network Pharmacology and Bioinformatics Validation. Curr Comput Aided Drug Des 2024;20:486-500. [PMID: 37287284 DOI: 10.2174/1573409919666230607103721] [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: 11/20/2022] [Revised: 04/24/2023] [Accepted: 05/12/2023] [Indexed: 06/09/2023]
24
Tsuchiya Y, Yonezawa T, Yamamori Y, Inoura H, Osawa M, Ikeda K, Tomii K. PoSSuM v.3: A Major Expansion of the PoSSuM Database for Finding Similar Binding Sites of Proteins. J Chem Inf Model 2023;63:7578-7587. [PMID: 38016694 PMCID: PMC10716853 DOI: 10.1021/acs.jcim.3c01405] [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: 09/01/2023] [Revised: 10/28/2023] [Accepted: 11/01/2023] [Indexed: 11/30/2023]
25
Jacob P, Lindelöf H, Rustad CF, Sutton VR, Moosa S, Udupa P, Hammarsjö A, Bhavani GS, Batkovskyte D, Tveten K, Dalal A, Horemuzova E, Nordgren A, Tham E, Shah H, Merckoll E, Orellana L, Nishimura G, Girisha KM, Grigelioniene G. Clinical, genetic and structural delineation of RPL13-related spondyloepimetaphyseal dysplasia suggest extra-ribosomal functions of eL13. NPJ Genom Med 2023;8:39. [PMID: 37993442 PMCID: PMC10665555 DOI: 10.1038/s41525-023-00380-x] [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: 04/06/2023] [Accepted: 10/10/2023] [Indexed: 11/24/2023]  Open
26
Muthusamy SK, Pushpitha P, Makeshkumar T, Sheela MN. Genome-wide identification and expression analysis of Hsp70 family genes in Cassava (Manihot esculenta Crantz). 3 Biotech 2023;13:341. [PMID: 37705861 PMCID: PMC10495308 DOI: 10.1007/s13205-023-03760-3] [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: 02/24/2023] [Accepted: 08/30/2023] [Indexed: 09/15/2023]  Open
27
Ribeiro AJM, Riziotis IG, Tyzack JD, Borkakoti N, Thornton JM. EzMechanism: an automated tool to propose catalytic mechanisms of enzyme reactions. Nat Methods 2023;20:1516-1522. [PMID: 37735566 PMCID: PMC10555830 DOI: 10.1038/s41592-023-02006-7] [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: 09/05/2022] [Accepted: 08/15/2023] [Indexed: 09/23/2023]
28
Santos MFA, Pessoa JC. Interaction of Vanadium Complexes with Proteins: Revisiting the Reported Structures in the Protein Data Bank (PDB) since 2015. Molecules 2023;28:6538. [PMID: 37764313 PMCID: PMC10536487 DOI: 10.3390/molecules28186538] [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: 07/27/2023] [Revised: 09/04/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023]  Open
29
Oda M. Analysis of the Structural Dynamics of Proteins in the Ligand-Unbound and -Bound States by Diffracted X-ray Tracking. Int J Mol Sci 2023;24:13717. [PMID: 37762021 PMCID: PMC10531450 DOI: 10.3390/ijms241813717] [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: 09/03/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023]  Open
30
Varadi M, Velankar S. The impact of AlphaFold Protein Structure Database on the fields of life sciences. Proteomics 2023;23:e2200128. [PMID: 36382391 DOI: 10.1002/pmic.202200128] [Citation(s) in RCA: 48] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/07/2022] [Accepted: 11/08/2022] [Indexed: 09/06/2023]
31
Wodak SJ, Vajda S, Lensink MF, Kozakov D, Bates PA. Critical Assessment of Methods for Predicting the 3D Structure of Proteins and Protein Complexes. Annu Rev Biophys 2023;52:183-206. [PMID: 36626764 PMCID: PMC10885158 DOI: 10.1146/annurev-biophys-102622-084607] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
32
Cao T, Wu H, Ji T. Bioinformatics-based construction of prognosis-related methylation prediction model for pancreatic cancer patients and its application value. Front Pharmacol 2023;14:1086309. [PMID: 36969862 PMCID: PMC10034005 DOI: 10.3389/fphar.2023.1086309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 02/06/2023] [Indexed: 03/12/2023]  Open
33
Role of N-Terminal Extensional Long α-Helix in the Arylesterase from Lacticaseibacillus rhamnosus GG on Catalysis and Stability. Catalysts 2023. [DOI: 10.3390/catal13020441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]  Open
34
Hashemi-Shahraki F, Shareghi B, Farhadian S. Investigation of the interaction behavior between quercetin and pepsin by spectroscopy and MD simulation methods. Int J Biol Macromol 2023;227:1151-1161. [PMID: 36464189 DOI: 10.1016/j.ijbiomac.2022.11.296] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 10/23/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022]
35
Chen L, Lang K, Zhang B, Shi J, Ye X, Stanley DW, Fang Q, Ye G. iVenomDB: A manually curated database for insect venom proteins. INSECT SCIENCE 2023;30:264-266. [PMID: 35633312 DOI: 10.1111/1744-7917.13054] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 04/11/2022] [Indexed: 06/15/2023]
36
Patiyal S, Dhall A, Bajaj K, Sahu H, Raghava GPS. Prediction of RNA-interacting residues in a protein using CNN and evolutionary profile. Brief Bioinform 2023;24:6901899. [PMID: 36516298 DOI: 10.1093/bib/bbac538] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 09/28/2022] [Accepted: 11/08/2022] [Indexed: 12/15/2022]  Open
37
Coudert E, Gehant S, de Castro E, Pozzato M, Baratin D, Neto T, Sigrist CJA, Redaschi N, Bridge A, The UniProt Consortium BridgeAlan JAimoLucilaArgoud-PuyGhislaineAuchinclossAndrea HAxelsenKristian BBansalParitBaratinDelphineNetoTeresa M BatistaBlatterMarie-ClaudeBollemanJerven TBoutetEmmanuelBreuzaLionelGilBlanca CabreraCasals-CasasCristinaEchioukhKamal ChikhCoudertElisabethCucheBeatricede CastroEdouardEstreicherAnneFamigliettiMaria LFeuermannMarcGasteigerElisabethGaudetPascaleGehantSebastienGerritsenVivienneGosArnaudGruazNadineHuloChantalHyka-NouspikelNevilaJungoFlorenceKerhornouArnaudLe MercierPhilippeLieberherrDamienMassonPatrickMorgatAnneMuthukrishnanVenkateshPaesanoSalvoPedruzziIvoPilboutSandrinePourcelLucillePouxSylvainPozzatoMonicaPruessManuelaRedaschiNicoleRivoireCatherineSigristChristian J ASonessonKarinSundaramShyamalaBatemanAlexMartinMaria-JesusOrchardSandraMagraneMicheleAhmadShadabAlpiEmanueleBowler-BarnettEmily HBrittoRamonaA-JeeHema Bye-CukuraAustraDennyPaulDoganTuncaEbenezerThankGodFanJunGarmiriPenelopeda Costa GonzalesLeonardo JoseHatton-EllisEmmaHusseinAbdulrahmanIgnatchenkoAlexandrInsanaGiuseppeIshtiaqRizwanJoshiVishalJyothiDushyanthKandasaamySwaathiLockAntoniaLucianiAurelienLugaricMarijaLuoJieLussiYvonneMacDougallAlistairMadeiraFabioMahmoudyMahdiMishraAlokMoulangKatieNightingaleAndrewPundirSangyaQiGuoyingRajShriyaRaposoPedroRiceDaniel LSaidiRabieSantosRafaelSperettaElenaStephensonJamesTotooPrabhatTurnerEdwardTyagiNidhiVasudevPreethiWarnerKateWatkinsXavierZaruRossanaZellnerHermannWuCathy HArighiCecilia NArminskiLeslieChenChumingChenYongxingHuangHongzhanLaihoKatiMcGarveyPeterNataleDarren ARossKarenVinayakaC RWangQinghuaWangYuqiSwiss-Prot Group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, 1211 Geneva 4, SwitzerlandEuropean Molecular Biology Laboratory—European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire CB10 1SD, UKProtein Information Resource, University of Delaware, Newark, DE 19711, USAProtein Information Resource, Georgetown University Medical Center, Washington, DC 20007, USA. Annotation of biologically relevant ligands in UniProtKB using ChEBI. Bioinformatics 2023;39:6885442. [PMID: 36484697 PMCID: PMC9825770 DOI: 10.1093/bioinformatics/btac793] [Citation(s) in RCA: 130] [Impact Index Per Article: 65.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 11/09/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022]  Open
38
Cuperlovic-Culf M, Nguyen-Tran T, Bennett SAL. Machine Learning and Hybrid Methods for Metabolic Pathway Modeling. Methods Mol Biol 2023;2553:417-439. [PMID: 36227553 DOI: 10.1007/978-1-0716-2617-7_18] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
39
Galyan SM, Ewald CY, Jalencas X, Masrani S, Meral S, Mestres J. Fragment-based virtual screening identifies a first-in-class preclinical drug candidate for Huntington's disease. Sci Rep 2022;12:19642. [PMID: 36385140 PMCID: PMC9668931 DOI: 10.1038/s41598-022-21900-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 10/05/2022] [Indexed: 11/17/2022]  Open
40
Pepe G, Appierdo R, Carrino C, Ballesio F, Helmer-Citterich M, Gherardini PF. Artificial intelligence methods enhance the discovery of RNA interactions. Front Mol Biosci 2022;9:1000205. [PMID: 36275611 PMCID: PMC9585310 DOI: 10.3389/fmolb.2022.1000205] [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: 07/21/2022] [Accepted: 09/20/2022] [Indexed: 11/13/2022]  Open
41
Azmi MB, Naeem U, Saleem A, Jawed A, Usman H, Qureshi SA, Azim MK. In silico identification of the rare-coding pathogenic mutations and structural modeling of human NNAT gene associated with anorexia nervosa. Eat Weight Disord 2022;27:2725-2744. [PMID: 35655118 DOI: 10.1007/s40519-022-01422-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 05/10/2022] [Indexed: 10/18/2022]  Open
42
Chakraborty C, Bhattacharya M, Sharma AR, Dhama K, Agoramoorthy G. A comprehensive analysis of the mutational landscape of the newly emerging Omicron (B.1.1.529) variant and comparison of mutations with VOCs and VOIs. GeroScience 2022;44:2393-2425. [PMID: 35989365 PMCID: PMC9393103 DOI: 10.1007/s11357-022-00631-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 07/20/2022] [Indexed: 01/18/2023]  Open
43
Grillone K, Riillo C, Rocca R, Ascrizzi S, Spanò V, Scionti F, Polerà N, Maruca A, Barreca M, Juli G, Arbitrio M, Di Martino MT, Caracciolo D, Tagliaferri P, Alcaro S, Montalbano A, Barraja P, Tassone P. The New Microtubule-Targeting Agent SIX2G Induces Immunogenic Cell Death in Multiple Myeloma. Int J Mol Sci 2022;23:ijms231810222. [PMID: 36142133 PMCID: PMC9499408 DOI: 10.3390/ijms231810222] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 08/30/2022] [Accepted: 09/01/2022] [Indexed: 12/31/2022]  Open
44
Pan J, Yang H, Zhu L, Lou Y, Jin B. Qingfei Jiedu decoction inhibits PD-L1 expression in lung adenocarcinoma based on network pharmacology analysis, molecular docking and experimental verification. Front Pharmacol 2022;13:897966. [PMID: 36091822 PMCID: PMC9454399 DOI: 10.3389/fphar.2022.897966] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 07/25/2022] [Indexed: 11/25/2022]  Open
45
Kumar S, Kumar GS, Maitra SS, Malý P, Bharadwaj S, Sharma P, Dwivedi VD. Viral informatics: bioinformatics-based solution for managing viral infections. Brief Bioinform 2022;23:6659740. [PMID: 35947964 DOI: 10.1093/bib/bbac326] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Revised: 06/26/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022]  Open
46
Heacock ML, Lopez AR, Amolegbe SM, Carlin DJ, Henry HF, Trottier BA, Velasco ML, Suk WA. Enhancing Data Integration, Interoperability, and Reuse to Address Complex and Emerging Environmental Health Problems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2022;56:7544-7552. [PMID: 35549252 PMCID: PMC9227711 DOI: 10.1021/acs.est.1c08383] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Indexed: 05/21/2023]
47
Qin Q, Qin L, Xie R, Peng S, Guo C, Yang B. Insight Into Biological Targets and Molecular Mechanisms in the Treatment of Arsenic-Related Dermatitis With Vitamin A via Integrated in silico Approach. Front Nutr 2022;9:847320. [PMID: 35685889 PMCID: PMC9171494 DOI: 10.3389/fnut.2022.847320] [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: 01/02/2022] [Accepted: 04/22/2022] [Indexed: 11/13/2022]  Open
48
Computational Resources for Molecular Biology 2022. J Mol Biol 2022;434:167625. [PMID: 35569508 DOI: 10.1016/j.jmb.2022.167625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
49
Krieger JM, Sorzano COS, Carazo JM, Bahar I. Protein dynamics developments for the large scale and cryoEM: case study of ProDy 2.0. Acta Crystallogr D Struct Biol 2022;78:399-409. [PMID: 35362464 PMCID: PMC8972803 DOI: 10.1107/s2059798322001966] [Citation(s) in RCA: 9] [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: 11/30/2021] [Accepted: 02/18/2022] [Indexed: 11/24/2022]  Open
50
Bhattacharya M, Sharma AR, Dhama K, Agoramoorthy G, Chakraborty C. Omicron variant (B.1.1.529) of SARS-CoV-2: understanding mutations in the genome, S-glycoprotein, and antibody-binding regions. GeroScience 2022;44:619-637. [PMID: 35258772 PMCID: PMC8902853 DOI: 10.1007/s11357-022-00532-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 02/16/2022] [Indexed: 01/18/2023]  Open
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