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Papers authored by Fernandes PA

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

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Sousa SF, Carvalho ES, Ferreira DM, Tavares IS, Fernandes PA, Ramos MJ, and Gomes JA

Journal of computational chemistry 30(16):2752-63, 2009 Dec - Who cited this? | PubMed ID: 19399915 | Fulltext

The Zinc proteome: a tale of stability and functionality.

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Sousa SF, Lopes AB, Fernandes PA, and Ramos MJ

Dalton transactions (Cambridge, England : 2003)(38):7946-56, 2009 Oct 14 - Who cited this? | PubMed ID: 19771357 | Fulltext

ABAD: A Potential Therapeutic Target for Abeta-Induced Mitochondrial Dysfunction in Alzheimer's Disease.

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Marques AT, Fernandes PA, and Ramos MJ

Mini reviews in medicinal chemistry 9(8):1002-8, 2009 Jul - Who cited this? | PubMed ID: 19601895 | Fulltext

Molecular dynamics simulations on the critical states of the farnesyltransferase enzyme.

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Sousa SF, Fernandes PA, and Ramos MJ

Bioorganic & medicinal chemistry 17(9):3369-78, 2009 May 1 - Who cited this? | PubMed ID: 19369081 | Fulltext

Local corticosterone infusion enhances nocturnal pineal melatonin production in vivo.

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Fernandes PA, Bothorel B, Clesse D, Monteiro AW, Calgari C, Raison S, Simonneaux V, and Markus RP

Journal of neuroendocrinology 21(2):90-7, 2009 Feb - Who cited this? | PubMed ID: 19076264 | Fulltext

[Prescription of phosphorus binders and calcitriol for chronic hemodialysis patients.].

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Martins MT, Silva LF, Martins MT, Matos CM, Melo NA, Azevedo MF, Travessa IE, Amoedo MK, Fernandes PA, Nogueira FC, Lopes GB, and Lopes AA

Revista da Associacao Medica Brasileira (1992) 55(1):70-4, 2009 - Who cited this? | PubMed ID: 19360282 | Fulltext

The search for the mechanism of the reaction catalyzed by farnesyltransferase.

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Sousa SF, Fernandes PA, and Ramos MJ

Chemistry (Weinheim an der Bergstrasse, Germany) 15(17):4243-7, 2009 - Who cited this? | PubMed ID: 19301336 | Fulltext

Modelling beta-1,3-exoglucanase-saccharide interactions: structure of the enzyme-substrate complex and enzyme binding to the cell wall.

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Moura-Tamames SA, Ramos MJ, and Fernandes PA

Journal of molecular graphics & modelling 27(8):908-20, 2009 - Who cited this? | PubMed ID: 19394255 | Fulltext

Detection of human papillomavirus infection in penile samples through liquid-based cytology and polymerase chain reaction.

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de Lima Rocha MG, Faria FL, Souza Mdo C, Vago AR, Fernandes AP, and Fernandes PA

Cancer 114(6):489-93, 2008 Dec 25 - Who cited this? | PubMed ID: 18973183 | Fulltext

Quantitative analysis of scanning transmission X-ray microscopy images of gas-filled PVA-based microballoons.

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Fernandes PA, Tzvetkov G, Fink RH, Paradossi G, and Fery A

Langmuir : the ACS journal of surfaces and colloids 24(23):13677-82, 2008 Dec 2 - Who cited this? | PubMed ID: 18980347 | Fulltext

Mechanistic studies on the formation of glycosidase-substrate and glycosidase-inhibitor covalent intermediates.

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Brás NF, Moura-Tamames SA, Fernandes PA, and Ramos MJ

Journal of computational chemistry 29(15):2565-74, 2008 Nov 30 - Who cited this? | PubMed ID: 18470964 | Fulltext

Molecular dynamics simulations of the amyloid-beta binding alcohol dehydrogenase (ABAD) enzyme.

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Marques AT, Fernandes PA, and Ramos MJ

Bioorganic & medicinal chemistry, 2008 Sep 19 - Who cited this? | PubMed ID: 18835182 | Fulltext

Glutathione Transferase: New Model for Glutathione Activation.

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Dourado DF, Fernandes PA, Mannervik B, and Ramos MJ

Chemistry (Weinheim an der Bergstrasse, Germany), 2008 Sep 12 - Who cited this? | PubMed ID: 18792041 | Fulltext

Role of the variable active site residues in the function of thioredoxin family oxidoreductases.

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Carvalho AT, Fernandes PA, Swart M, Van Stralen JN, Bickelhaupt FM, and Ramos MJ

Journal of computational chemistry, 2008 Sep 8 - Who cited this? | PubMed ID: 18780356 | Fulltext

Mammalian cytosolic glutathione transferases.

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Dourado DF, Fernandes PA, and Ramos MJ

Current protein & peptide science 9(4):325, 2008 Aug - Who cited this? | PubMed ID: 18691123 | Fulltext

Enzyme flexibility and the catalytic mechanism of farnesyltransferase: targeting the relation.

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Sousa SF, Fernandes PA, and Ramos MJ

The journal of physical chemistry. B 112(29):8681-91, 2008 Jul 24 - Who cited this? | PubMed ID: 18572907 | Fulltext

MADAMM: A multistaged docking with an automated molecular modeling protocol.

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Cerqueira NM, Bras NF, Fernandes PA, and Ramos MJ

Proteins, 2008 Jul 10 - Who cited this? | PubMed ID: 18618708 | Fulltext

Molecular determinants of ligand specificity in family 11 carbohydrate binding modules: an NMR, X-ray crystallography and computational chemistry approach.

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Viegas A, Brás NF, Cerqueira NM, Fernandes PA, Prates JA, Fontes CM, Bruix M, Romão MJ, Carvalho AL, Ramos MJ, Macedo AL, and Cabrita EJ

The FEBS journal 275(10):2524, 2008 May - Who cited this? | PubMed ID: 18422658 | Fulltext

Mechanism of thioredoxin-catalyzed disulfide reduction. Activation of the buried thiol and role of the variable active-site residues.

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Carvalho AT, Swart M, Stralen JN, Fernandes PA, Ramos MJ, and Bickelhaupt FM

The journal of physical chemistry. B 112(8):2511-23, 2008 Feb 28 - Who cited this? | PubMed ID: 18237164 | Fulltext

Farnesyltransferase inhibitors: a detailed chemical view on an elusive biological problem.

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Sousa SF, Fernandes PA, and Ramos MJ

Current medicinal chemistry 15(15):1478, 2008 - Who cited this? | PubMed ID: 18537624 | Fulltext

The Current Status of the NNRTI Family of Antiretrovirals Used in the HAART Regime Against HIV Infection.

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Martins S, Ramos MJ, and Fernandes PA

Current medicinal chemistry 15(11):1083-95, 2008 - Who cited this? | PubMed ID: 18473804 | Fulltext

Analysis of zinc-ligand bond lengths in metalloproteins: trends and patterns.

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Tamames B, Sousa SF, Tamames J, Fernandes PA, and Ramos MJ

Proteins 69(3):466-75, 2007 Nov 15 - Who cited this? | PubMed ID: 17623850 | Fulltext

General performance of density functionals.

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Sousa SF, Fernandes PA, and Ramos MJ

The journal of physical chemistry. A 111(42):10439-52, 2007 Oct 25 - Who cited this? | PubMed ID: 17718548 | Fulltext

The excision mechanism in reverse transcriptase: pyrophosphate leaving and fingers opening are uncoupled events with the analogues AZT and d4T.

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Carvalho AT, Fernandes PA, and Ramos MJ

The journal of physical chemistry. B 111(41):12032-9, 2007 Oct 18 - Who cited this? | PubMed ID: 17887788 | Fulltext

Drug design: new inhibitors for HIV-1 protease based on Nelfinavir as lead.

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Perez MA, Fernandes PA, and Ramos MJ

Journal of molecular graphics & modelling 26(3):634-42, 2007 Oct - Who cited this? | PubMed ID: 17459746 | Fulltext

Hot spots--a review of the protein-protein interface determinant amino-acid residues.

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Moreira IS, Fernandes PA, and Ramos MJ

Proteins 68(4):803-12, 2007 Sep 1 - Who cited this? | PubMed ID: 17546660 | Fulltext

Comparative assessment of theoretical methods for the determination of geometrical properties in biological zinc complexes.

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Sousa SF, Fernandes PA, and Ramos MJ

The journal of physical chemistry. B 111(30):9146-52, 2007 Aug 2 - Who cited this? | PubMed ID: 17602523 | Fulltext

Theoretical studies on farnesyl transferase: evidence for thioether product coordination to the active-site zinc sphere.

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Sousa SF, Fernandes PA, and Ramos MJ

Journal of computational chemistry 28(7):1160-8, 2007 May - Who cited this? | PubMed ID: 17342704 | Fulltext

Molecular detection of Chlamydia trachomatis and HPV infections in cervical samples with normal and abnormal cytopathological findings.

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de Paula FD, Fernandes AP, Carmo BB, Vieira DC, Dutra MS, Santos CG, Souza Mdo C, Andrade TC, Vago AR, and Fernandes PA

Diagnostic cytopathology 35(4):198-202, 2007 Apr - Who cited this? | PubMed ID: 17351932 | Fulltext

Hot spot occlusion from bulk water: a comprehensive study of the complex between the lysozyme HEL and the antibody FVD1.3.

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Moreira IS, Fernandes PA, and Ramos MJ

The journal of physical chemistry. B 111(10):2697-706, 2007 Mar 15 - Who cited this? | PubMed ID: 17315919 | Fulltext

Vascular endothelial growth factor (VEGF) inhibition--a critical review.

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Moreira IS, Fernandes PA, and Ramos MJ

Anti-cancer agents in medicinal chemistry 7(2):223-45, 2007 Mar - Who cited this? | PubMed ID: 17348829 | Fulltext

The carboxylate shift in zinc enzymes: a computational study.

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Sousa SF, Fernandes PA, and Ramos MJ

Journal of the American Chemical Society 129(5):1378-85, 2007 Feb 7 - Who cited this? | PubMed ID: 17263422 | Fulltext

Computational alanine scanning mutagenesis--an improved methodological approach.

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Moreira IS, Fernandes PA, and Ramos MJ

Journal of computational chemistry 28(3):644-54, 2007 Feb - Who cited this? | PubMed ID: 17195156 | Fulltext

Theoretical studies on farnesyltransferase: the distances paradox explained.

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Sousa SF, Fernandes PA, and Ramos MJ

Proteins 66(1):205-18, 2007 Jan 1 - Who cited this? | PubMed ID: 17068802 | Fulltext

Understanding ribonucleotide reductase inactivation by gemcitabine.

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Cerqueira NM, Fernandes PA, and Ramos MJ

Chemistry (Weinheim an der Bergstrasse, Germany) 13(30):8507-15, 2007 - Who cited this? | PubMed ID: 17636467 | Fulltext

The Immune-Pineal Axis: A Shuttle between Endocrine and Paracrine Melatonin Sources.

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Markus RP, Ferreira ZS, Fernandes PA, and Cecon E

Neuroimmunomodulation 14(3-4):126-33, 2007 - Who cited this? | PubMed ID: 18073503 | Fulltext

Molecular detection of HPV 16 and 18 in cervical samples of patients from Belo Horizonte, Minas Gerais, Brazil.

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Freitas TP, Carmo BB, Paula FD, Rodrigues LF, Fernandes AP, and Fernandes PA

Revista do Instituto de Medicina Tropical de Sao Paulo 49(5):297-301, 2007 - Who cited this? | PubMed ID: 18026636 | Fulltext

Ribonucleotide reductase: a critical enzyme for cancer chemotherapy and antiviral agents.

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Cerqueira NM, Fernandes PA, and Ramos MJ

Recent patents on anti-cancer drug discovery 2(1):11-29, 2007 Jan - Who cited this? | PubMed ID: 18221051 | Fulltext

Insights on resistance to reverse transcriptase: the different patterns of interaction of the nucleoside reverse transcriptase inhibitors in the deoxyribonucleotide triphosphate binding site relative to the normal substrate.

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Carvalho AT, Fernandes PA, and Ramos MJ

Journal of medicinal chemistry 49(26):7675-82, 2006 Dec 28 - Who cited this? | PubMed ID: 17181150 | Fulltext

Effect of TNF-alpha on the melatonin synthetic pathway in the rat pineal gland: basis for a 'feedback' of the immune response on circadian timing.

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Fernandes PA, Cecon E, Markus RP, and Ferreira ZS

Journal of pineal research 41(4):344-50, 2006 Nov - Who cited this? | PubMed ID: 17014691 | Fulltext

Enzyme ribonucleotide reductase: unraveling an enigmatic paradigm of enzyme inhibition by furanone derivatives.

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Cerqueira NM, Fernandes PA, and Ramos MJ

The journal of physical chemistry. B 110(42):21272-81, 2006 Oct 26 - Who cited this? | PubMed ID: 17048956 | Fulltext

Protein-ligand docking: current status and future challenges.

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Sousa SF, Fernandes PA, and Ramos MJ

Proteins 65(1):15-26, 2006 Oct 1 - Who cited this? | PubMed ID: 16862531 | Fulltext

Molecular dynamics model of unliganded HIV-1 reverse transcriptase.

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Carvalho AT, Fernandes PA, and Ramos MJ

Medicinal chemistry (Shariqah (United Arab Emirates)) 2(5):491-8, 2006 Sep - Who cited this? | PubMed ID: 17017988 | Fulltext

Molecular dynamics simulations of the enzyme Cu, Zn superoxide dismutase.

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Branco RJ, Fernandes PA, and Ramos MJ

The journal of physical chemistry. B 110(33):16754-62, 2006 Aug 24 - Who cited this? | PubMed ID: 16913815 | Fulltext

Similarities and differences in the thioredoxin superfamily.

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Carvalho AP, Fernandes PA, and Ramos MJ

Progress in biophysics and molecular biology 91(3):229-48, 2006 Jul - Who cited this? | PubMed ID: 16098567 | Fulltext

Unraveling the importance of protein-protein interaction: application of a computational alanine-scanning mutagenesis to the study of the IgG1 streptococcal protein G (C2 fragment) complex.

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Moreira IS, Fernandes PA, and Ramos MJ

The journal of physical chemistry. B 110(22):10962-9, 2006 Jun 8 - Who cited this? | PubMed ID: 16771349 | Fulltext

Determination of the DeltapKa between the active site cysteines of thioredoxin and DsbA.

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Carvalho AT, Fernandes PA, and Ramos MJ

Journal of computational chemistry 27(8):966-75, 2006 Jun - Who cited this? | PubMed ID: 16586531 | Fulltext

Detailed microscopic study of the full zipA:FtsZ interface.

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Moreira IS, Fernandes PA, and Ramos MJ

Proteins 63(4):811-21, 2006 Jun 1 - Who cited this? | PubMed ID: 16538616 | Fulltext

Molecular insights into the mechanisms of HIV-1 reverse transcriptase resistance to nucleoside analogs.

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Carvalho AP, Fernandes PA, and Ramos MJ

Mini reviews in medicinal chemistry 6(5):549-55, 2006 May - Who cited this? | PubMed ID: 16719829 | Fulltext

Theoretical study of the unusual protonation properties of the active site cysteines in thioredoxin.

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Carvalho AT, Fernandes PA, and Ramos MJ

The journal of physical chemistry. B 110(11):5758-61, 2006 Mar 23 - Who cited this? | PubMed ID: 16539521 | Fulltext

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