Suárez D - Search Results

1

Assessing the Interactions between Snake Venom Metalloproteinases and Hydroxamate Inhibitors Using Kinetic and ITC Assays, Molecular Dynamics Simulations and MM/PBSA-Based Scoring Functions.

de Souza RA, Díaz N, G Fuentes L, Pimenta A, Nagem RAP, Chávez-Olórtegui C, Schneider FS, Molina F, Sanchez EF, Suárez D, Ferreira RS. de Souza RA, et al. Among authors: suarez d. ACS Omega. 2024 Dec 10;9(51):50599-50621. doi: 10.1021/acsomega.4c08439. eCollection 2024 Dec 24. ACS Omega. 2024. PMID: 39741831 Free PMC article.

2

Molecular dynamics simulations of matrix metalloproteinase 2: role of the structural metal ions.

Díaz N, Suarez D. Díaz N, et al. Among authors: suarez d. Biochemistry. 2007 Aug 7;46(31):8943-52. doi: 10.1021/bi700541p. Epub 2007 Jul 7. Biochemistry. 2007. PMID: 17616173

3

Molecular dynamics simulations of the active matrix metalloproteinase-2: positioning of the N-terminal fragment and binding of a small peptide substrate.

Díaz N, Suárez D. Díaz N, et al. Among authors: suarez d. Proteins. 2008 Jul;72(1):50-61. doi: 10.1002/prot.21894. Proteins. 2008. PMID: 18186480

4

Alternative interdomain configurations of the full-length MMP-2 enzyme explored by molecular dynamics simulations.

Díaz N, Suárez D. Díaz N, et al. Among authors: suarez d. J Phys Chem B. 2012 Mar 8;116(9):2677-86. doi: 10.1021/jp211088d. Epub 2012 Feb 24. J Phys Chem B. 2012. PMID: 22324833

5

Extensive simulations of the full-length matrix metalloproteinase-2 enzyme in a prereactive complex with a collagen triple-helical peptide.

Díaz N, Suárez D. Díaz N, et al. Among authors: suarez d. Biochemistry. 2015 Feb 10;54(5):1243-58. doi: 10.1021/bi501014w. Epub 2015 Jan 28. Biochemistry. 2015. PMID: 25600631

6

Sampling Assessment for Molecular Simulations Using Conformational Entropy Calculations.

Suárez D, Díaz N. Suárez D, et al. J Chem Theory Comput. 2014 Oct 14;10(10):4718-29. doi: 10.1021/ct500700d. Epub 2014 Oct 2. J Chem Theory Comput. 2014. PMID: 26588161

7

Unraveling the distinctive features of hemorrhagic and non-hemorrhagic snake venom metalloproteinases using molecular simulations.

de Souza RA, Díaz N, Nagem RA, Ferreira RS, Suárez D. de Souza RA, et al. Among authors: suarez d. J Comput Aided Mol Des. 2016 Jan;30(1):69-83. doi: 10.1007/s10822-015-9889-5. Epub 2015 Dec 16. J Comput Aided Mol Des. 2016. PMID: 26676823

8

Role of the Protonation State on the Structure and Dynamics of Albumin.

Díaz N, Suárez D. Díaz N, et al. Among authors: suarez d. J Chem Theory Comput. 2016 Apr 12;12(4):1972-88. doi: 10.1021/acs.jctc.5b01001. Epub 2016 Apr 4. J Chem Theory Comput. 2016. PMID: 27014836

9

Conformational and entropy analyses of extended molecular dynamics simulations of α-, β- and γ-cyclodextrins and of the β-cyclodextrin/nabumetone complex.

Suárez D, Díaz N. Suárez D, et al. Phys Chem Chem Phys. 2017 Jan 4;19(2):1431-1440. doi: 10.1039/c6cp06107a. Phys Chem Chem Phys. 2017. PMID: 27982145

10

Molecular Dynamics Studies of Matrix Metalloproteases.

Díaz N, Suárez D. Díaz N, et al. Among authors: suarez d. Methods Mol Biol. 2017;1579:111-134. doi: 10.1007/978-1-4939-6863-3_7. Methods Mol Biol. 2017. PMID: 28299735

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