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For: Passos Ó, Fernandes PA, Ramos MJ. Theoretical insights into the catalytic mechanism of β-hexosaminidase. Theor Chem Acc 2011;129:119-29. [DOI: 10.1007/s00214-011-0904-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Number Cited by Other Article(s)
1
Perez S, Makshakova O. Multifaceted Computational Modeling in Glycoscience. Chem Rev 2022;122:15914-15970. [PMID: 35786859 DOI: 10.1021/acs.chemrev.2c00060] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
2
Sousa SF, Ribeiro AJM, Neves RPP, Brás NF, Cerqueira NMFSA, Fernandes PA, Ramos MJ. Application of quantum mechanics/molecular mechanics methods in the study of enzymatic reaction mechanisms. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1281] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
3
Tankrathok A, Iglesias-Fernández J, Williams RJ, Pengthaisong S, Baiya S, Hakki Z, Robinson RC, Hrmova M, Rovira C, Williams SJ, Ketudat Cairns JR. A Single Glycosidase Harnesses Different Pyranoside Ring Transition State Conformations for Hydrolysis of Mannosides and Glucosides. ACS Catal 2015. [DOI: 10.1021/acscatal.5b01547] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
4
Pérez S, Tvaroška I. Carbohydrate-protein interactions: molecular modeling insights. Adv Carbohydr Chem Biochem 2015;71:9-136. [PMID: 25480504 DOI: 10.1016/b978-0-12-800128-8.00001-7] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
5
Jitonnom J, Sattayanon C, Kungwan N, Hannongbua S. A DFT study of the unusual substrate-assisted mechanism of Serratia marcescens chitinase B reveals the role of solvent and mutational effect on catalysis. J Mol Graph Model 2015;56:53-9. [DOI: 10.1016/j.jmgm.2014.12.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 12/05/2014] [Accepted: 12/08/2014] [Indexed: 11/29/2022]
6
Bobovská A, Tvaroška I, Kóňa J. Theoretical study of enzymatic catalysis explains why the trapped covalent intermediate in the E303C mutant of glycosyltransferase GTB was not detected in the wild-type enzyme. Glycobiology 2014;25:3-7. [DOI: 10.1093/glycob/cwu085] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]  Open
7
Jitonnom J, Limb MAL, Mulholland AJ. QM/MM free-energy simulations of reaction in Serratia marcescens Chitinase B reveal the protonation state of Asp142 and the critical role of Tyr214. J Phys Chem B 2014;118:4771-83. [PMID: 24730355 DOI: 10.1021/jp500652x] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
8
Pan XL, Liu W, Liu JY. Mechanism of the Glycosylation Step Catalyzed by Human α-Galactosidase: A QM/MM Metadynamics Study. J Phys Chem B 2013;117:484-9. [DOI: 10.1021/jp308747c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
9
Dependence of the optical absorption and Na+ binding energies of coumarin-crown ethers on the size and attachment position of ether ring: density functional investigation. J Mol Model 2012;19:173-8. [PMID: 22842819 DOI: 10.1007/s00894-012-1500-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2012] [Accepted: 06/07/2012] [Indexed: 10/28/2022]
10
Sousa SF, Fernandes PA, Ramos MJ. Computational enzymatic catalysis – clarifying enzymatic mechanisms with the help of computers. Phys Chem Chem Phys 2012;14:12431-41. [DOI: 10.1039/c2cp41180f] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
11
Passos Ó, Fernandes PA, Ramos MJ. QM/MM Study of the Catalytic Mechanism of GalNAc Removal from GM2 Ganglioside Catalyzed by Human β-HexosaminidaseA. J Phys Chem B 2011;115:14751-9. [DOI: 10.1021/jp205826n] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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