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For: Armon A, Graur D, Ben-Tal N. ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. J Mol Biol 2001;307:447-63. [PMID: 11243830 DOI: 10.1006/jmbi.2000.4474] [Citation(s) in RCA: 362] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Number Cited by Other Article(s)
1
Gorges DM, Filippin-Monteiro FB. Genetic variants in the LRP5 gene associated with gain and loss of bone mineral density. In Silico Pharmacol 2025;13:61. [PMID: 40255261 PMCID: PMC12003225 DOI: 10.1007/s40203-025-00341-5] [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: 10/10/2024] [Accepted: 03/17/2025] [Indexed: 04/22/2025]  Open
2
Washington EJ. Developing the trehalose biosynthesis pathway as an antifungal drug target. NPJ ANTIMICROBIALS AND RESISTANCE 2025;3:30. [PMID: 40229515 PMCID: PMC11997177 DOI: 10.1038/s44259-025-00095-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2024] [Accepted: 03/18/2025] [Indexed: 04/16/2025]
3
Hanna MG, Rodriguez Cruz HO, Fujise K, Wu Y, Xu CS, Pang S, Li Z, Monetti M, De Camilli P. BLTP3A is associated with membranes of the late endocytic pathway and is an effector of CASM. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2024.09.28.615015. [PMID: 39386594 PMCID: PMC11463362 DOI: 10.1101/2024.09.28.615015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/12/2024]
4
Sugawara R, Hamada K, Ito H, Scala M, Ueda H, Tabata H, Ogata K, Nagata KI. A p.N92K variant of the GTPase RAC3 disrupts cortical neuron migration and axon elongation. J Biol Chem 2025;301:108346. [PMID: 40015633 PMCID: PMC11968283 DOI: 10.1016/j.jbc.2025.108346] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2024] [Revised: 02/05/2025] [Accepted: 02/19/2025] [Indexed: 03/01/2025]  Open
5
Gerulskis R, Minteer SD. Terminator: A Software Package for Fast and Local Optimization of His-Tag Placement for Protein Affinity Purification. ACS BIO & MED CHEM AU 2025;5:55-65. [PMID: 39990946 PMCID: PMC11843336 DOI: 10.1021/acsbiomedchemau.4c00055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/05/2024] [Revised: 12/16/2024] [Accepted: 12/17/2024] [Indexed: 02/25/2025]
6
Vincenzi M, Mercurio FA, Autiero I, Leone M. Sam-Sam Association Between EphA2 and SASH1: In Silico Studies of Cancer-Linked Mutations. Molecules 2025;30:718. [PMID: 39942820 PMCID: PMC11820823 DOI: 10.3390/molecules30030718] [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: 12/23/2024] [Revised: 01/21/2025] [Accepted: 01/30/2025] [Indexed: 02/16/2025]  Open
7
Sacher S, Ray A. In Silico Strategies for Characterizing Inner Cavities of Lipid-Binding Proteins. Methods Mol Biol 2025;2888:305-320. [PMID: 39699739 DOI: 10.1007/978-1-0716-4318-1_20] [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: 12/20/2024]
8
Nael MA, Ghoneim MM, Almuqbil M, Al-Serwi RH, El-Sherbiny M, Mostafa AE, Elokely KM. An evaluation of the precision of computational methods used in drug development initiatives. J Biomol Struct Dyn 2024:1-15. [PMID: 39659185 DOI: 10.1080/07391102.2024.2435633] [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: 01/04/2024] [Accepted: 03/29/2024] [Indexed: 12/12/2024]
9
Utgés JS, Barton GJ. Comparative evaluation of methods for the prediction of protein-ligand binding sites. J Cheminform 2024;16:126. [PMID: 39529176 PMCID: PMC11552181 DOI: 10.1186/s13321-024-00923-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2024] [Accepted: 10/28/2024] [Indexed: 11/16/2024]  Open
10
Lariviere PJ, Ashraf AHMZ, Gifford I, Tanguma SL, Barrick JE, Moran NA. Virulence-linked adhesin drives mutualist colonization of the bee gut via biofilm formation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.14.618124. [PMID: 39464101 PMCID: PMC11507737 DOI: 10.1101/2024.10.14.618124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/29/2024]
11
Ivica J, Kejzar N, Ho H, Stockwell I, Kuchtiak V, Scrutton AM, Nakagawa T, Greger IH. Proton-triggered rearrangement of the AMPA receptor N-terminal domains impacts receptor kinetics and synaptic localization. Nat Struct Mol Biol 2024;31:1601-1613. [PMID: 39138332 PMCID: PMC11479944 DOI: 10.1038/s41594-024-01369-5] [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: 03/29/2024] [Accepted: 07/08/2024] [Indexed: 08/15/2024]
12
Wang B, Li W. Advances in the Application of Protein Language Modeling for Nucleic Acid Protein Binding Site Prediction. Genes (Basel) 2024;15:1090. [PMID: 39202449 PMCID: PMC11353971 DOI: 10.3390/genes15081090] [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: 07/22/2024] [Revised: 08/13/2024] [Accepted: 08/14/2024] [Indexed: 09/03/2024]  Open
13
O'Neil PT, Swint‐Kruse L, Fenton AW. Rheostatic contributions to protein stability can obscure a position's functional role. Protein Sci 2024;33:e5075. [PMID: 38895978 PMCID: PMC11187868 DOI: 10.1002/pro.5075] [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: 02/14/2024] [Revised: 05/24/2024] [Accepted: 05/27/2024] [Indexed: 06/21/2024]
14
Chadani Y, Yamanouchi S, Uemura E, Yamasaki K, Niwa T, Ikeda T, Kurihara M, Iwasaki W, Taguchi H. The ABCF proteins in Escherichia coli individually cope with 'hard-to-translate' nascent peptide sequences. Nucleic Acids Res 2024;52:5825-5840. [PMID: 38661232 PMCID: PMC11162784 DOI: 10.1093/nar/gkae309] [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: 10/29/2023] [Revised: 03/18/2024] [Accepted: 04/10/2024] [Indexed: 04/26/2024]  Open
15
Yuan H, Liu RD, Gao ZY, Zhong LT, Zhou YC, Tan JH, Huang ZS, Li Z, Chen SB. Targeting ATP-binding site of WRN Helicase: Identification of novel inhibitors through pocket analysis and Molecular Dynamics-Enhanced virtual screening. Bioorg Med Chem Lett 2024;104:129711. [PMID: 38521175 DOI: 10.1016/j.bmcl.2024.129711] [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: 08/16/2023] [Revised: 03/14/2024] [Accepted: 03/20/2024] [Indexed: 03/25/2024]
16
Chikunova A, Manley MP, Heijjer CN, Drenth CS, Cramer-Blok AJ, Ahmad MUD, Perrakis A, Ubbink M. Conserved proline residues prevent dimerization and aggregation in the β-lactamase BlaC. Protein Sci 2024;33:e4972. [PMID: 38533527 DOI: 10.1002/pro.4972] [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: 12/08/2023] [Revised: 03/07/2024] [Accepted: 03/11/2024] [Indexed: 03/28/2024]
17
Singh L, Karthikeyan S, Thakur KG. Biochemical and structural characterization reveals Rv3400 codes for β-phosphoglucomutase in Mycobacterium tuberculosis. Protein Sci 2024;33:e4943. [PMID: 38501428 PMCID: PMC10949319 DOI: 10.1002/pro.4943] [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: 08/25/2023] [Revised: 01/22/2024] [Accepted: 02/11/2024] [Indexed: 03/20/2024]
18
Radko-Juettner S, Yue H, Myers JA, Carter RD, Robertson AN, Mittal P, Zhu Z, Hansen BS, Donovan KA, Hunkeler M, Rosikiewicz W, Wu Z, McReynolds MG, Roy Burman SS, Schmoker AM, Mageed N, Brown SA, Mobley RJ, Partridge JF, Stewart EA, Pruett-Miller SM, Nabet B, Peng J, Gray NS, Fischer ES, Roberts CWM. Targeting DCAF5 suppresses SMARCB1-mutant cancer by stabilizing SWI/SNF. Nature 2024;628:442-449. [PMID: 38538798 PMCID: PMC11184678 DOI: 10.1038/s41586-024-07250-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 02/28/2024] [Indexed: 04/06/2024]
19
Roche R, Moussad B, Shuvo MH, Tarafder S, Bhattacharya D. EquiPNAS: improved protein-nucleic acid binding site prediction using protein-language-model-informed equivariant deep graph neural networks. Nucleic Acids Res 2024;52:e27. [PMID: 38281252 PMCID: PMC10954458 DOI: 10.1093/nar/gkae039] [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: 09/13/2023] [Revised: 12/22/2023] [Accepted: 01/11/2024] [Indexed: 01/30/2024]  Open
20
Wang X, Li A, Li X, Cui H. Empowering Protein Engineering through Recombination of Beneficial Substitutions. Chemistry 2024;30:e202303889. [PMID: 38288640 DOI: 10.1002/chem.202303889] [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] [Indexed: 02/24/2024]
21
Levillayer L, Brighelli C, Demeret C, Sakuntabhai A, Bureau JF. Role of two modules controlling the interaction between SKAP1 and SRC kinases comparison with SKAP2 architecture and consequences for evolution. PLoS One 2024;19:e0296230. [PMID: 38483858 PMCID: PMC10939263 DOI: 10.1371/journal.pone.0296230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 02/28/2024] [Indexed: 03/17/2024]  Open
22
Çapan ÖY, Türkdoğan D, Atalay S, Çağlayan HS. Developmental and epileptic encephalopathy 82 (DEE82) with novel compound heterozygous mutations of GOT2 gene. Seizure 2024;116:126-132. [PMID: 37977948 DOI: 10.1016/j.seizure.2023.11.003] [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: 08/09/2023] [Revised: 10/28/2023] [Accepted: 11/08/2023] [Indexed: 11/19/2023]  Open
23
Waheed S, Ramzan K, Ahmad S, Khan MS, Wajid M, Ullah H, Umar A, Iqbal R, Ullah R, Bari A. Identification and In-Silico study of non-synonymous functional SNPs in the human SCN9A gene. PLoS One 2024;19:e0297367. [PMID: 38394191 PMCID: PMC10889873 DOI: 10.1371/journal.pone.0297367] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 12/29/2023] [Indexed: 02/25/2024]  Open
24
Wang B, Vartak R, Zaltsman Y, Naing ZZC, Hennick KM, Polacco BJ, Bashir A, Eckhardt M, Bouhaddou M, Xu J, Sun N, Lasser MC, Zhou Y, McKetney J, Guiley KZ, Chan U, Kaye JA, Chadha N, Cakir M, Gordon M, Khare P, Drake S, Drury V, Burke DF, Gonzalez S, Alkhairy S, Thomas R, Lam S, Morris M, Bader E, Seyler M, Baum T, Krasnoff R, Wang S, Pham P, Arbalaez J, Pratt D, Chag S, Mahmood N, Rolland T, Bourgeron T, Finkbeiner S, Swaney DL, Bandyopadhay S, Ideker T, Beltrao P, Willsey HR, Obernier K, Nowakowski TJ, Hüttenhain R, State MW, Willsey AJ, Krogan NJ. A foundational atlas of autism protein interactions reveals molecular convergence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.12.03.569805. [PMID: 38076945 PMCID: PMC10705567 DOI: 10.1101/2023.12.03.569805] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2023]
25
Kim SY, Yoon SI. Structural analysis of the YqeY proteins from Campylobacter jejuni and Vibrio parahaemolyticus. Biochem Biophys Res Commun 2024;695:149485. [PMID: 38211535 DOI: 10.1016/j.bbrc.2024.149485] [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: 12/29/2023] [Accepted: 01/04/2024] [Indexed: 01/13/2024]
26
Gahlawat A, Singh A, Sandhu H, Garg P. CRAFT: a web-integrated cavity prediction tool based on flow transfer algorithm. J Cheminform 2024;16:12. [PMID: 38291536 PMCID: PMC10829215 DOI: 10.1186/s13321-024-00803-6] [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: 09/04/2023] [Accepted: 01/13/2024] [Indexed: 02/01/2024]  Open
27
Thore S, Raoelijaona F, Talenton V, Fribourg S, Mackereth CD. Molecular details of the CPSF73-CPSF100 C-terminal heterodimer and interaction with Symplekin. Open Biol 2023;13:230221. [PMID: 37989222 PMCID: PMC10688271 DOI: 10.1098/rsob.230221] [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: 07/11/2023] [Accepted: 09/27/2023] [Indexed: 11/23/2023]  Open
28
Igbaria-Jaber Y, Hofmann L, Gevorkyan-Airapetov L, Shenberger Y, Ruthstein S. Revealing the DNA Binding Modes of CsoR by EPR Spectroscopy. ACS OMEGA 2023;8:39886-39895. [PMID: 37901548 PMCID: PMC10601412 DOI: 10.1021/acsomega.3c06336] [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: 08/25/2023] [Accepted: 09/28/2023] [Indexed: 10/31/2023]
29
Yang Z, Zhou N, Jiang X, Wang L. Loop Evolutionary Patterns Shape Catalytic Efficiency of TRI101/201 for Trichothecenes: Insights into Protein-Substrate Interactions. J Chem Inf Model 2023;63:6316-6331. [PMID: 37821422 DOI: 10.1021/acs.jcim.3c00787] [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: 10/13/2023]
30
Roche R, Moussad B, Shuvo MH, Tarafder S, Bhattacharya D. EquiPNAS: improved protein-nucleic acid binding site prediction using protein-language-model-informed equivariant deep graph neural networks. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.14.557719. [PMID: 37745556 PMCID: PMC10515942 DOI: 10.1101/2023.09.14.557719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
31
Elangeeb ME, Elfaki I, Elkhalifa MA, Adam KM, Alameen AO, Elfadl AK, Albalawi IA, Almasoudi KS, Almotairi R, Alsaedi BSO, Alhelali MH, Mir MM, Amle D, Mir R. In Silico Investigation of AKT2 Gene and Protein Abnormalities Reveals Potential Association with Insulin Resistance and Type 2 Diabetes. Curr Issues Mol Biol 2023;45:7449-7475. [PMID: 37754255 PMCID: PMC10528407 DOI: 10.3390/cimb45090471] [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: 07/18/2023] [Revised: 08/12/2023] [Accepted: 08/24/2023] [Indexed: 09/28/2023]  Open
32
Hasan MM, Nabi AN, Yasmin T. Comprehensive analysis predicting effects of deleterious SNPs of human progesterone receptor gene on its structure and functions: a computational approach. J Biomol Struct Dyn 2023;41:8002-8017. [PMID: 36166622 DOI: 10.1080/07391102.2022.2127908] [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: 07/22/2022] [Accepted: 09/17/2022] [Indexed: 10/14/2022]
33
Ibrahim MI, Ramadan AM, Amer M, Khan TK, Mohamed NG, Said OA. Deciphering the enigma of RNA editing in the ATP1_alpha subunit of ATP synthase in Triticum aestivum. Saudi J Biol Sci 2023;30:103703. [PMID: 37389198 PMCID: PMC10300253 DOI: 10.1016/j.sjbs.2023.103703] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/25/2023] [Accepted: 06/02/2023] [Indexed: 07/01/2023]  Open
34
Mashraqi MM, Alzamami A, Alturki NA, Alshamrani S, Alshahrani MM, Almasoudi HH, Basharat Z. Molecular Mimicry Mapping in Streptococcus pneumoniae: Cues for Autoimmune Disorders and Implications for Immune Defense Activation. Pathogens 2023;12:857. [PMID: 37513704 PMCID: PMC10383125 DOI: 10.3390/pathogens12070857] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/08/2023] [Accepted: 06/20/2023] [Indexed: 07/30/2023]  Open
35
Carter AA, Ramsey KM, Hatem CL, Sherry KP, Majumdar A, Barrick D. Structural features of the Notch ankyrin domain-Deltex WWE2 domain heterodimer determined by NMR spectroscopy and functional implications. Structure 2023;31:584-594.e5. [PMID: 36977409 PMCID: PMC10338078 DOI: 10.1016/j.str.2023.03.003] [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: 02/21/2020] [Revised: 11/14/2022] [Accepted: 03/02/2023] [Indexed: 03/29/2023]
36
Kim SY, Cho HY, Yoon SI. Unique dimeric structure of the DUF2891 family protein CJ0554 from Campylobacter jejuni. Biochem Biophys Res Commun 2023;655:11-17. [PMID: 36913761 DOI: 10.1016/j.bbrc.2023.03.010] [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: 02/22/2023] [Accepted: 03/05/2023] [Indexed: 03/08/2023]
37
Yariv B, Yariv E, Kessel A, Masrati G, Chorin AB, Martz E, Mayrose I, Pupko T, Ben‐Tal N. Using evolutionary data to make sense of macromolecules with a "face-lifted" ConSurf. Protein Sci 2023;32:e4582. [PMID: 36718848 PMCID: PMC9942591 DOI: 10.1002/pro.4582] [Citation(s) in RCA: 162] [Impact Index Per Article: 81.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 01/21/2023] [Accepted: 01/27/2023] [Indexed: 02/01/2023]
38
Singer MR, Dinh T, Levintov L, Annamalai AS, Rey JS, Briganti L, Cook NJ, Pye VE, Taylor IA, Kim K, Engelman AN, Kim B, Perilla JR, Kvaratskhelia M, Cherepanov P. The Drug-Induced Interface That Drives HIV-1 Integrase Hypermultimerization and Loss of Function. mBio 2023;14:e0356022. [PMID: 36744954 PMCID: PMC9973045 DOI: 10.1128/mbio.03560-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 01/03/2023] [Indexed: 02/07/2023]  Open
39
Yu Y, Xu S, He R, Liang G. Application of Molecular Simulation Methods in Food Science: Status and Prospects. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023;71:2684-2703. [PMID: 36719790 DOI: 10.1021/acs.jafc.2c06789] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
40
Foo ACY, Nesbit JB, Gipson SAY, DeRose EF, Cheng H, Hurlburt BK, Kulis MD, Kim EH, Dreskin SC, Mustafa S, Maleki SJ, Mueller GA. Structure and IgE Cross-Reactivity among Cashew, Pistachio, Walnut, and Peanut Vicilin-Buried Peptides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023;71:2990-2998. [PMID: 36728846 PMCID: PMC10402694 DOI: 10.1021/acs.jafc.2c07061] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
41
Dorgan B, Liu Y, Wang S, Aduse-Opoku J, Whittaker SBM, Roberts MAJ, Lorenz CD, Curtis MA, Garnett JA. Structural Model of a Porphyromonas gingivalis type IX Secretion System Shuttle Complex. J Mol Biol 2022;434:167871. [PMID: 36404438 DOI: 10.1016/j.jmb.2022.167871] [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: 05/28/2022] [Revised: 10/14/2022] [Accepted: 10/21/2022] [Indexed: 11/06/2022]
42
G. V, Hasan QA, Kumar R, Eranki A. Analysis of single-nucleotide polymorphisms in genes associated with triple-negative breast cancer. Front Genet 2022;13:1071352. [PMID: 36561320 PMCID: PMC9763624 DOI: 10.3389/fgene.2022.1071352] [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: 10/16/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022]  Open
43
Structural analysis of the pseudaminic acid synthase PseI from Campylobacter jejuni. Biochem Biophys Res Commun 2022;635:252-258. [DOI: 10.1016/j.bbrc.2022.10.050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 10/13/2022] [Indexed: 11/20/2022]
44
Scott O, Gu J, Chan AE. Classification of Protein-Binding Sites Using a Spherical Convolutional Neural Network. J Chem Inf Model 2022;62:5383-5396. [PMID: 36341715 PMCID: PMC9709917 DOI: 10.1021/acs.jcim.2c00832] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
45
Lázár T, Tantos A, Tompa P, Schad E. Intrinsic protein disorder uncouples affinity from binding specificity. Protein Sci 2022;31:e4455. [PMID: 36305763 PMCID: PMC9601785 DOI: 10.1002/pro.4455] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 12/29/2022]
46
Katsonis P, Wilhelm K, Williams A, Lichtarge O. Genome interpretation using in silico predictors of variant impact. Hum Genet 2022;141:1549-1577. [PMID: 35488922 PMCID: PMC9055222 DOI: 10.1007/s00439-022-02457-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 04/17/2022] [Indexed: 02/06/2023]
47
Identification and Mutation Analysis of Nonconserved Residues on the TIM-Barrel Surface of GH5_5 Cellulases for Catalytic Efficiency and Stability Improvement. Appl Environ Microbiol 2022;88:e0104622. [PMID: 36000858 PMCID: PMC9469711 DOI: 10.1128/aem.01046-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]  Open
48
Yasmin T. In silico comprehensive analysis of coding and non-coding SNPs in human mTOR protein. PLoS One 2022;17:e0270919. [PMID: 35788771 PMCID: PMC9255762 DOI: 10.1371/journal.pone.0270919] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2022] [Accepted: 06/17/2022] [Indexed: 11/21/2022]  Open
49
Ahmad HI, Ijaz N, Afzal G, Asif AR, ur Rehman A, Rahman A, Ahmed I, Yousaf M, Elokil A, Muhammad SA, Albogami SM, Alotaibi SS. Computational Insights into the Structural and Functional Impacts of nsSNPs of Bone Morphogenetic Proteins. BIOMED RESEARCH INTERNATIONAL 2022;2022:4013729. [PMID: 35832847 PMCID: PMC9273450 DOI: 10.1155/2022/4013729] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 06/15/2022] [Indexed: 12/12/2022]
50
Tortorici MA, Walls AC, Joshi A, Park YJ, Eguia RT, Miranda MC, Kepl E, Dosey A, Stevens-Ayers T, Boeckh MJ, Telenti A, Lanzavecchia A, King NP, Corti D, Bloom JD, Veesler D. Structure, receptor recognition, and antigenicity of the human coronavirus CCoV-HuPn-2018 spike glycoprotein. Cell 2022;185:2279-2291.e17. [PMID: 35700730 PMCID: PMC9135795 DOI: 10.1016/j.cell.2022.05.019] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 04/24/2022] [Accepted: 05/23/2022] [Indexed: 02/01/2023]
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