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Papers authored by Ramos MJ

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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

Synthesis and structural characterization of two diasteroisomers of vinylcatechin dimers.

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Cruz L, Brás NF, Teixeira N, Fernandes A, Mateus N, Ramos MJ, Rodríguez-Borges J, and de Freitas V

Journal of agricultural and food chemistry 57(21):10341-8, 2009 Nov 11 - Who cited this? | PubMed ID: 19817383 | 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

Influence of fatty acid composition of raw materials on biodiesel properties.

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Ramos MJ, Fernández CM, Casas A, Rodríguez L, and Pérez A

Bioresource technology 100(1):261-8, 2009 Jan - Who cited this? | PubMed ID: 18693011 | 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

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

Anchoring effects in a wide binding pocket: The molecular basis of regioselectivity in engineered cytochrome P450 monooxygenase from B. megaterium.

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Branco RJ, Seifert A, Budde M, Urlacher VB, Ramos MJ, and Pleiss J

Proteins 73(3):597-607, 2008 Nov 15 - Who cited this? | PubMed ID: 18473391 | Fulltext

Structural Insight on the Activity of Type 1 Angiotensin II Peptide Antagonists Using MD Simulations.

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Preto MA, Melo A, Rodrigues LM, Maia HL, and Ramos MJ

The journal of physical chemistry. B 112(43):13620-8, 2008 Oct 30 - Who cited this? | PubMed ID: 18834172 | Fulltext

The Use of Rifampicin-Miconazole-Impregnated Catheters Reduces the Incidence of Femoral and Jugular Catheter-Related Bacteremia.

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Lorente L, Lecuona M, Ramos MJ, Jiménez A, Mora ML, and Sierra A

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 2008 Sep 22 - Who cited this? | PubMed ID: 18808356 | 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

The protein kinase inhibitor balanol: structure-activity relationships and structure-based computational studies.

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Pande V, Ramos MJ, and Gago F

Anti-cancer agents in medicinal chemistry 8(6):638, 2008 Aug - Who cited this? | PubMed ID: 18690827 | 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

Carotid bifurcation atherosclerosis in the over-65s: a prevalence study.

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Vallina-Victorero M, Vaquero F, Alvarez A, Ramos MJ, Vicente M, and Alvarez J

The Journal of cardiovascular surgery 49(2):207-11, 2008 Apr - Who cited this? | PubMed ID: 18431341 | Fulltext

A comparative density-functional study of the reaction mechanism of the O(2)-dependent coproporphyrinogen III oxidase.

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Silva PJ and Ramos MJ

Bioorganic & medicinal chemistry 16(6):2726-33, 2008 Mar 15 - Who cited this? | PubMed ID: 18226911 | Fulltext

Comparative Density Functional Study of Models for the Reaction Mechanism of Uroporphyrinogen III Synthase.

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Silva PJ and Ramos MJ

The journal of physical chemistry. B 112(10):3144-8, 2008 Mar 13 - Who cited this? | PubMed ID: 18281969 | 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 adaptive evolution of the mammalian mitochondrial genome.

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da Fonseca RR, Johnson WE, O'Brien SJ, Ramos MJ, and Antunes A

BMC genomics 9:119, 2008 - Who cited this? | PubMed ID: 18318906 | Fulltext

Study of doubly charged alkaline earth metal and 3-azidopropionitrile complexes by electrospray ionization mass spectrometry.

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Couto N, Ramos MJ, Fernandez MT, Rodrigues P, Barros MT, Costa ML, Cabral BJ, and Duarte MF

Rapid communications in mass spectrometry : RCM 22(4):582-90, 2008 - Who cited this? | PubMed ID: 18220327 | 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

Reaction mechanism of the vitamin K-dependent glutamate carboxylase: a computational study.

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Silva PJ and Ramos MJ

The journal of physical chemistry. B 111(44):12883-7, 2007 Nov 8 - Who cited this? | PubMed ID: 17935315 | 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

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

Structural divergence and adaptive evolution in mammalian cytochromes P450 2C.

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da Fonseca RR, Antunes A, Melo A, and Ramos MJ

Gene 387(1-2):58-66, 2007 Jan 31 - Who cited this? | PubMed ID: 17045425 | Fulltext

Mitochondrial introgressions into the nuclear genome of the domestic cat.

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Antunes A, Pontius J, Ramos MJ, O'Brien SJ, and Johnson WE

The Journal of heredity 98(5):414, 2007 - Who cited this? | PubMed ID: 17660503 | Fulltext

Structural and functional implications of positive selection at the primate angiogenin gene.

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Osorio DS, Antunes A, and Ramos MJ

BMC evolutionary biology 7:167, 2007 - Who cited this? | PubMed ID: 17883850 | 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

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

Gathering computational genomics and proteomics to unravel adaptive evolution.

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Antunes A and Ramos MJ

Evolutionary bioinformatics online 3:207-9, 2007 - Who cited this? | PubMed ID: 19461985 | 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

QM/QM study of the coverage effects on the adsorption of amino-cyclopentene at the Si(100) surface.

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Santos HR, Ujaque G, Ramos MJ, and Gomes JA

Journal of computational chemistry 27(15):1892-7, 2006 Nov 30 - Who cited this? | PubMed ID: 16983672 | 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

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