Ribeiro AJ - Search Results

1

Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for copper complexes.

Sousa SF, Pinto GR, Ribeiro AJ, Coimbra JT, Fernandes PA, Ramos MJ. Sousa SF, et al. Among authors: ribeiro aj. J Comput Chem. 2013 Sep 15;34(24):2079-90. doi: 10.1002/jcc.23349. Epub 2013 Jun 25. J Comput Chem. 2013. PMID: 23798313

2

Protein-ligand docking in the new millennium--a retrospective of 10 years in the field.

Sousa SF, Ribeiro AJ, Coimbra JT, Neves RP, Martins SA, Moorthy NS, Fernandes PA, Ramos MJ. Sousa SF, et al. Among authors: ribeiro aj. Curr Med Chem. 2013;20(18):2296-314. doi: 10.2174/0929867311320180002. Curr Med Chem. 2013. PMID: 23531220 Review.

3

The catalytic mechanism of HIV-1 integrase for DNA 3'-end processing established by QM/MM calculations.

Ribeiro AJ, Ramos MJ, Fernandes PA. Ribeiro AJ, et al. J Am Chem Soc. 2012 Aug 15;134(32):13436-47. doi: 10.1021/ja304601k. Epub 2012 Aug 7. J Am Chem Soc. 2012. PMID: 22793648

4

The catalytic mechanism of protein phosphatase 5 established by DFT calculations.

Ribeiro AJ, Alberto ME, Ramos MJ, Fernandes PA, Russo N. Ribeiro AJ, et al. Chemistry. 2013 Oct 11;19(42):14081-9. doi: 10.1002/chem.201301565. Epub 2013 Sep 6. Chemistry. 2013. PMID: 24014428

5

Analyses of cobalt-ligand and potassium-ligand bond lengths in metalloproteins: trends and patterns.

Brás NF, Ribeiro AJ, Oliveira M, Paixão NM, Tamames JA, Fernandes PA, Ramos MJ. Brás NF, et al. Among authors: ribeiro aj. J Mol Model. 2014 Jun;20(6):2271. doi: 10.1007/s00894-014-2271-z. Epub 2014 May 22. J Mol Model. 2014. PMID: 24850495

6

Benchmarking of DFT Functionals for the Hydrolysis of Phosphodiester Bonds.

Ribeiro AJ, Ramos MJ, Fernandes PA. Ribeiro AJ, et al. J Chem Theory Comput. 2010 Aug 10;6(8):2281-92. doi: 10.1021/ct900649e. Epub 2010 Jul 8. J Chem Theory Comput. 2010. PMID: 26613486

7

Improving the Biodesulfurization of Crude Oil and Derivatives: A QM/MM Investigation of the Catalytic Mechanism of NADH-FMN Oxidoreductase (DszD).

Sousa SF, Sousa JF, Barbosa AC, Ferreira CE, Neves RP, Ribeiro AJ, Fernandes PA, Ramos MJ. Sousa SF, et al. Among authors: ribeiro aj. J Phys Chem A. 2016 Jul 14;120(27):5300-6. doi: 10.1021/acs.jpca.6b01536. Epub 2016 May 9. J Phys Chem A. 2016. PMID: 27128525

8

Binding free energy calculations on E-selectin complexes with sLe^x oligosaccharide analogs.

Barra PA, Ribeiro AJ, Ramos MJ, Jiménez VA, Alderete JB, Fernandes PA. Barra PA, et al. Among authors: ribeiro aj. Chem Biol Drug Des. 2017 Jan;89(1):114-123. doi: 10.1111/cbdd.12837. Epub 2016 Sep 21. Chem Biol Drug Des. 2017. PMID: 27515911

9

Divalent metal ion-based catalytic mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli.

Hong MK, Ribeiro AJ, Kim JK, Ngo HP, Kim J, Lee CH, Ahn YJ, Fernandes PA, Li Q, Ramos MJ, Kang LW. Hong MK, et al. Among authors: ribeiro aj. Acta Crystallogr D Biol Crystallogr. 2014 May;70(Pt 5):1297-310. doi: 10.1107/S1399004714002570. Epub 2014 Apr 29. Acta Crystallogr D Biol Crystallogr. 2014. PMID: 24816099

10

New insights in the catalytic mechanism of tyrosine ammonia-lyase given by QM/MM and QM cluster models.

Pinto GP, Ribeiro AJ, Ramos MJ, Fernandes PA, Toscano M, Russo N. Pinto GP, et al. Among authors: ribeiro aj. Arch Biochem Biophys. 2015 Sep 15;582:107-15. doi: 10.1016/j.abb.2015.03.002. Epub 2015 Mar 12. Arch Biochem Biophys. 2015. PMID: 25772386

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