Publications


My publications (23):

  1. Articles (14)
  2. Book Chapters (2)
  3. Thesis (3)
  4. Conference Papers (4)

1. Articles

14 ➤ Santos-Pereira C, Rocha JF, Fernandes HS, Rodrigues LR, Côrte-Real M, and Sousa SF
“The milk-derived lactoferrin inhibits V-ATPase activity by targeting its V1 domain”
International Journal of Biological Macromolecules
(2021)
https://doi.org/10.1016/j.ijbiomac.2021.06.200
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Impact Factor: 6.953


13 ➤ Fernandes HS, Sousa SF, and Cerqueira NMFSA
“New insights into the catalytic mechanism of the SARS-CoV-2 main protease: an ONIOM QM/MM approach”
Molecular Diversity
(2021)
https://doi.org/10.1007/s11030-021-10259-7
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Impact Factor: 2.943


12 ➤ Fernandes HS, Cerqueira NMFSA, and Sousa SF
“Developing and Using BioSIM-AR, an Augmented Reality Program to Visualize and Learn about Chemical Structures in a Virtual Environment on Any Internet-Connected Device”
Journal of Chemical Education
(2021)
https://doi.org/10.1021/acs.jchemed.0c01317
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Impact Factor: 2.979


11 ➤ Lapaillerie D, Charlier C, Fernandes HS, Sousa SF, Lesbats P, Weigel P, Favereaux A, Guyonnet-Dupérat V, and Parissi V
In silico, in vitro and in cellulo models for monitoring SARS-CoV-2 spike/human ACE2 complex, viral entry and cell fusion”
Viruses
(2021)
https://doi.org/10.3390/v13030365
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Impact Factor: 5.048


10 ➤ Gonçalves IG, Fernandes HS, Melo A, Sousa SF, Simões LC, and Simões M
“LegionellaDB – A Database on Legionella Outbreaks”
Cell: Trends in Microbiology
(2021)
https://doi.org/10.1016/j.tim.2021.01.015
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Impact Factor: 17.079


9 ➤ Ribeiro PMG, Fernandes HS, Maia LB, Sousa SF, Moura JG, Cerqueira NMFSA
“The complete catalytic mechanism of Xanthine Oxidase: a computational study”
Inorganic Chemistry Frontiers
(2021)
https://doi.org/10.1039/D0QI01029D
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Impact factor: 6.569


8 ➤ Magalhães RP, Vieira TF, Fernandes HS, Melo A, Simões M, and Sousa SF
“The Biofilms Structural Database”
Cell: Trends in Biotechnology
(2020)
https://doi.org/10.1016/j.tibtech.2020.04.002
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Impact factor: 13.747


7 ➤ Magalhães RP, Fernandes HS, and Sousa SF
“Modelling Enzymatic Mechanisms with QM/MM Approaches: Current Status and Future Challenges”
Israel Journal of Chemistry
(2020)
https://doi.org/10.1002/ijch.202000014
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Impact factor: 2.220


6 ➤ Fernandes HS, Sousa SF, and Cerqueira NMFSA
“VMD Store – a VMD Plugin to Browse, Discover, and Install VMD Extensions”
Journal of Chemical Information and Modeling
(2019)
https://doi.org/10.1021/acs.jcim.9b00739
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Impact factor: 3.966


5 ➤ Fernandes HS, Teixeira CSS, Sousa SF, and Cerqueira NMFSA
“Formation of Unstable and very Reactive Chemical Species Catalyzed by Metalloenzymes: A Mechanistic Overview”
Molecules, 24(13)
pp 2462 (2019) [Cover]
https://doi.org/10.3390/molecules24132462
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Impact factor: 3.060


4 ➤ Fernandes HS, Ramos MJ, and Cerqueira NMFSA
The catalytic mechanism of the Serine Hydroxymethyltransferase – a computational ONIOM QM/MM study
ACS Catalysis,  8 (11)
pp 10096–10110 (2018)
http://dx.doi.org/10.1021/acscatal.8b02321
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Impact factor: 11.384


3 ➤ [2018] Fernandes HS, Ramos MJ, and Cerqueira NMFSA
molUP: a VMD plugin to handle QM and ONIOM calculations using the Gaussian software
Journal of Computational Chemistry, 39(19) pp. 1344–1353 (2018[Cover]
http://dx.doi.org/10.1002/jcc.25189
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Impact factor: 3.229


2 ➤ [2017] Henrique S. Fernandes, M. J. Ramos, and Nuno M. F. S. A. Cerqueira “The catalytic mechanism of the PLP-dependent enzyme, histidine decarboxylase: a computational study.
Chemistry – a European Journal, 23 pp. 9162 –9173 (2017)[Hot Paper]
http://dx.doi.org/10.1002/chem.201701375
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Impact factor: 5.771


1 ➤ [2017] Fernandes, H. S., C. S. Silva Teixeira, P. A. Fernandes, M. J. Ramos, and N. M. F. S. A. Cerqueira. “Amino Acid Deprivation Using Enzymes as a Targeted Therapy for Cancer and Viral Infections.
Expert Opinion on Therapeutic Patents 27, no. 3 (2017/03/04 2017): 283-97. http://dx.doi.org/10.1080/13543776.2017.1254194
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Impact factor: 4.626


2. Book Chapters

2 ➤ [2019] CHAPTER 8 “Enzymatic Amino Acid Deprivation Therapies Targeting Cancer”
Carla S. S. Teixeira, Henrique S. Fernandes, Sérgio F. Sousa, and Nuno M. F. S. A. Cerqueira
DOI: 10.1201/9780429295034-8
Book: Pharamaceutical Biocatalysis: Fundamentals, Enzyme Inhibitors, and Enzymes in Health and Diseases
Pages: 311-347
Editor: Peter Grunwald – Pan Stanford Publishing Pte. Ltd.
Buy on Pan Stanford | Buy on Amazon


1 ➤ [2017] CHAPTER 24 “Cancer therapies based on Enzymatic Amino-Acid Depletion”
Carla Teixeira*, Henrique Fernandes*, P. A. Fernandes, M. J. Ramos and Nuno M. F. S. A. Cerqueira (* contributed equally to this work)
DOI: 10.1016/B978-0-323-46144-3.00024-6
Book: Nanostructures for Cancer Therapy
Pages: 920 (30 Chapters)
Publish Date: April 14th, 2017
eBook ISBN: 9780323461504
Hardcover ISBN: 9780323461443
Editor(s)Alexandru Grumezescu and Anton Ficai – Elsevier
Buy on Elsevier | Buy on Amazon | Available on iTunes | Preview | See more


3. Thesis

3 ➤ [2021] “Computational studies addressed to PLP-dependent enzymes” | PhD Thesis | UCIBIO@REQUIMTE – Departamento de Biomedicina da Faculdade de Medicina da Universidade do Porto
Available on “Repositório Aberto da Universidade do Porto” (ID: 135396)

2 ➤ [2016] “Computational studies addressed to Histidine decarboxylase” | Master’s Thesis | UCIBIO-REQUIMTE – Departamento de Química e Bioquímica da Faculdade de Ciências da Universidade do Porto
Available on “Repositório Aberto da Universidade do Porto” (ID: 135603)

1 ➤ [2014] “Influência das proteases aspárticas de Candida albicans na respostas imunitária mediada por linfócitos T reguladores num modelo de peritonite” (“Candida albicans secreted aspartic proteases expression facilitates murine peritoneal infection in a Treg/IL-10-dependent manner”) | Bachelor’s Thesis | Laboratório Mário Arala Chaves do Instituto de Ciências Biomédicas Abel Salazar da Universidade do Porto

 4. Conference Papers

1 ➤ [2017] Fernandes, H. S., Ramos, M. J., Cerqueira, N. M. F. S. A., “Development of computational tools to enhance the study of catalytic mechanisms”,  MOL2NET 2017, International Conference on Multidisciplinary Sciences, 3rd edition, 2017 December.
DOI: 10.3390/mol2net-03-05073

2 ➤ [2018] Fernandes, H. S., Sousa, S. F., and Cerqueira, N. M. F. S. A., “Is the 5,10-methylenetetrahydrofolate cofactor synthesized through a non-enzymatic or enzymatic mechanism?” MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition, 2018 December
DOI: 10.3390/mol2net-04-06004

3 ➤ [2018] Magalhães, R., Vieira, T., Fernandes, H.S., Cerqueira, N. M. F. S. A., Melo, A., Simões, M., Sousa, S., “Creation of a Structural Database for Inhibition of Biofilm Formation” MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition, 2018 December
DOI: 10.3390/mol2net-04-06079

4 ➤ [2019] Fernandes, H.S., Sousa, S.F., Cerqueira, N.M.F.S.A. (2019, July). Enhancing the catalytic power of serine hydroxymethyltransferase to produce commercially valuable compounds. In FEBS OPEN BIO (Vol. 9, pp. 411-412). 111 RIVER ST, HOBOKEN 07030-5774, NJ USA: WILEY.
DOI: 10.1002/2211-5463.12675