Selected Publications
Below is a selection of my publications, listed by date and updated on the 31/December/2019.
2019-2020| 2017-2018| 2015-2016| 2013-2014| 2011-2012| 2009-2010| 2007-2008| 2005-2006| 2003-2004| 2000-2002|Publications 2011-2012
Nave, Frederico; Bras, Natercia F.; Cruz, Luis; Teixeira, Natercia; Mateus, Nuno; Ramos, Maria J., Di Meo, Florent, Trouillas, Patrick, Dangles, Olivier, De Freitas, Victor, Influence of a Flavan-3-ol Substituent on the Affinity of Anthocyanins (Pigments) toward Vinylcatechin Dimers and Proanthocyanidins (Copigments), JOURNAL OF PHYSICAL CHEMISTRY B, 116, 14089-14099 (2012)
Moorthy, Narayana Subbiah Hari Narayana; Sousa, Sergio F.; Ramos, Maria J.; Fernandes, Pedro A., In silico Based Structural Analysis of Some Piperidine Analogs as Farnesyltransferase Inhibitors, MEDICINAL CHEMISTRY, 8, 853-864 (2012)
Sousa, Sergio Filipe; Fernandes, Pedro Alexandrino; Ramos, Maria J., Computational enzymatic catalysis - clarifying enzymatic mechanisms with the help of computers, PHYSICAL CHEMISTRY CHEMICAL PHYSICS , 14, 12431-12441 (2012)
Ribeiro, António J.M.; Ramos Maria J.; Fernandes Pedro A., The Catalytic Mechanism of HIV-1 Integrase for DNA 3’-End Processing Established by QM/MM Calculations, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 134, 13436–13447 (2012)
De Rienzo, Francesca; Barbosa, Armenio J. Moura; Perez, Marta A. S., Pedro Alexandrino; Ramos, Maria J., The extracellular subunit interface of the 5-HT3 receptors: a computational alanine scanning mutagenesis study, JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 30, 280-298 (2012)
Bras, Natercia F.; Ramos, Maria J.; Fernandes, Pedro A., The catalytic mechanism of mouse renin studied with QM/MM calculations, PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 14, 12605-12613 (2012)
Moorthy, N. S. H. N.; Ramos, M. J.; Fernandes, P. A., Analysis of van der Waals surface area properties for human ether-a-go-go-related gene blocking activity: computational study on structurally diverse compounds, SAR AND QSAR IN ENVIRONMENTAL RESEARCH, 23, 521-536 (2012)
Zhang, Wei; Dourado, Daniel F. A. R.; Fernandes, Pedro A.; Ramos, M.J.; Mannervik, B., Multidimensional epistasis and fitness landscapes in enzyme evolution, BIOCHEMICAL JOURNAL, 445, 39-46 (2012)
Ribeiro, Joao V.; Cerqueira, Nuno M. F. S. A.; Moreira, Irina S.; Fernandes P. A.; Ramos M. J., CompASM: an Amber-VMD alanine scanning mutagenesis plug-in, THEORETICAL CHEMISTRY ACCOUNTS, 131 (2012)
Gesto D. S.; Cerqueira N. M. F. S. A.; Fernandes P. A.; Ramos M. J., Gemcitabine: A Critical Nucleoside for Cancer Therapy, CURRENT MEDICINAL CHEMISTRY, 19, 7, 1076-1087 (2012)
Silva Pedro J.; Perez Marta A. S.; Bras Natercia F.; Fernandes Pedro A., Ramos Maria J., Improving the study of proton transfers between amino acid side chains in solution: choosing appropriate DFT functionals and avoiding hidden pitfalls, THEORETICAL CHEMISTRY ACCOUNTS, 131, 3, 1179 (2012)
Moreira, I S; Martins, J M; Ramos, R M; Fernandes Pedro A., Ramos Maria J., Understanding the importance of the aromatic amino-acid residues as hot-spots, BIOCHIMICA ET BIOPHYSICA ACTA, 1834, 1, 404-14 DOI: 10.1016/j.bbapap.2012.07.005
Moorthy, N. S. H. N.; Bras, Natercia F.; Ramos, Maria J.; Fernandes P. A., Virtual screening and QSAR study of some pyrrolidine derivatives as alpha-mannosidase inhibitors for binding feature analysis, BIOORGANIC & MEDICINAL CHEMISTRY, 20, 24, 6945-6959 (2012)
Teixeira, N.; Mateus, N.; Ramos, M.J.; Di Meo, F.; Trouillas, P.; Dangles, O.; De Freitas, V., Influence of a Flavan-3-ol Substituent on the Affinity of Anthocyanins (Pigments) toward Vinylcatechin Dimers and Proanthocyanidins (Copigments), JOURNAL OF PHYSICAL CHEMISTRY B, 116, 48, 14089-14099 (2012)
Coelho, Catarina; Mahro, Martin; Trincao, Jose; Carvalho, ATP; Ramos, MJ; Terao, M; Garattini, E.; Leimkuhler, S.; Romao, MJ, The First Mammalian Aldehyde Oxidase Crystal Structure Insights into substrate specificity, JOURNAL OF BIOLOGICAL CHEMISTRY, 287, 48, 40690-40702 (2012)
Marcial, Bruna L.; Sousa, Sergio F.; Barbosa, Ingrid L.; Chemically Modified Tetracyclines as Inhibitors of MMP-2 Matrix Metalloproteinase: A Molecular and Structural Study, JOURNAL OF PHYSICAL CHEMISTRY B, 116, 46, 13644-13654 (2012)
Moorthy N. S. Hari N.; Ramos Maria J.; Fernandes Pedro A., hERG binding feature analysis of structurally diverse compounds by QSAR and fragmental analysis, RSC ADVANCES, 1, 1126-1136 (2011)
Oliveira Eduardo F.; Cerqueira Nuno M. F. S. A.; Fernandes Pedro A.; Ramos Maria J., Mechanism of Formation of the Internal Aldimine in Pyridoxal 5 '-Phosphate-Dependent Enzymes, JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 133, 15496-15505 (2011)
Passos Oscar; Fernandes Pedro A.; Ramos Maria J., QM/MM Study of the Catalytic Mechanism of GalNAc Removal from GM2 Ganglioside Catalyzed by Human beta-HexosaminidaseA , JOURNAL OF PHYSICAL CHEMISTRY B, 115, 14751-14759 (2011)
Moorthy N. S. Hari Narayana; Ramos Maria J.; Fernandes Pedro A., Topological, hydrophobicity, and other descriptors on alpha-glucosidase inhibition: a QSAR study on xanthone derivatives , JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY, 26, 755-766 (2011)
Moorthy N. S. Hari Narayana; Sousa Sergio F.; Ramos Maria J.; Structural feature study of benzofuran derivatives as farnesyltransferase inhibitors , JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY, 26, 777-791 (2011)
Neves Ana R.; Fernandes Pedro A.; Ramos Maria J., The Accuracy of Density Functional Theory in the Description of Cation-pi and pi-Hydrogen Bond Interactions, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7, 2059-2067 ( 2011)
Sousa Sergio F.; Tamames B.; Fernandes Pedro A.; Ramos Maria J., Detailed Atomistic Analysis of the HIV-1 Protease Interface, JOURNAL OF PHYSICAL CHEMISTRY B, 115, 7045-7057 (2011)
Silva Pedro J.; Ramos Maria J., Successes and failures of DFT functionals in acid/base and redox reactions of organic and biochemical interest, COMPUTATIONAL AND THEORETICAL CHEMISTRY, 966, 120-126 (2011)
Silva Pedro J.; Ramos Maria J., Computational Insights Into the Photochemical Step of the Reaction Catalyzed by Protochlorophylide Oxidoreductase, INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 111, 1472-1479 (2011)
Bras Natercia F.; Cruz Luis; Fernandes Pedro A.; Ramos Maria J.; De Freitas Victor, Conformational Study of Two Diasteroisomers of Vinylcatechin Dimers in a Methanol Solution, INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 111, 1498-1510 (2011)
Cerqueira N. M. F. S. A.; Fernandes P. A.; Ramos M. J., Computational Mechanistic Studies Addressed to the Transimination Reaction Present in All Pyridoxal 5 '-Phosphate-Requiring Enzymes, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 1356-1368 (2011)
Passos Oscar; Fernandes Pedro A.; Ramos Maria J., Theoretical insights into the catalytic mechanism of beta-hexosaminidase , THEORETICAL CHEMISTRY ACCOUNTS, 129, 119-129 (2011)
Cerqueira Nuno M. F. S. A.; Ribeiro J.; Fernandes Pedro A.; Ramos Maria J., vsLab-An Implementation for Virtual High-Throughput Screening Using AutoDock and VMD, INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 111, 1208-1212 (2011)
Carvalho Alexandra T. P.; Fernandes Pedro A.; Ramos Maria J., The Catalytic Mechanism of RNA Polymerase II, JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 7, 1177-1188 (2011)
Silva Pedro J.; Ramos Maria J., Computational Characterization of the Substrate-Binding Mode in Coproporphyrinogen III Oxidase, JOURNAL OF PHYSICAL CHEMISTRY B, 115, 1903-1910 (2011)
Tamames Juan A. C.; Ramos Maria J., Metals in proteins: cluster analysis studies JOURNAL OF MOLECULAR MODELING, 17, 429-442 (2011)
Moorthy N. S. Hari N.; Ramos Maria J.; Fernandes Pedro A., Prediction of the relationship between the structural features of andrographolide derivatives and alpha-glucosidase inhibitory activity: A quantitative structure-activity relationship (QSAR) Study, JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY, 2, 78-87 (2011)
Moorthy N. S. Hari N.; Ramos Maria J.; Fernandes Pedro A., QSAR Analysis of Isosteviol Derivatives as alpha-Glucosidase Inhibitors with Element Count and Other Descriptors , LETTERS IN DRUG DESIGN & DISCOVERY, 8, 14-25 (2011)
Perez Marta A. S.; Sousa Sergio F.; Oliveira Eduardo F. T.; Fernandes Pedro A.; Ramos Maria J., Detection of Farnesyltransferase Interface Hot Spots through Computational Alanine Scanning Mutagenesis, JOURNAL OF PHYSICAL CHEMISTRY B, 115, 15339-15354 (2011)
Oliveira, J.; Petrov, V.; Parola, A. J.; Pina, F.; Azevedo, J.; Teixeira, N.; Brás, N. F.; Fernandes, P. A.; Mateus, N.; Ramos, M. J.; De Freitas, V. Chemical Behavior of Methylpyranomalvidin-3-O-glucoside in Aqueous Solution Studied by NMR and UV-visible Spectroscopy, JOURNAL OF PHYSICAL CHEMISTRY B, 115, 1538-1545 (2011)