Maria João Ramos

Computational Biochemistry, University of Porto


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 2005-2006

Carvalho, ATP; Fernandes, PA; Ramos MJ

Insights on resistance to RT: The different patterns of interaction of NRTIS in the dNTP binding site relative to the normal substrate

JOURNAL OF MEDICINAL CHEMISTRY, 49 (26): 7675-7682 DEC 28 2006

 

Cerqueira, NM; Fernandes, PA; Ramos MJ

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

JOURNAL OF PHYSICAL CHEMISTRY B, 110(42):21272-81 OCT 26 2006

 

Marques, AT; Antunes, A; Fernandes, PA; Ramos, MJ

Comparative evolutionary genomics of the HADH2 gene encoding A beta-binding alcohol dehydrogenase/17 beta-hydroxysteroid dehydrogenase type 10 (ABAD/HSD10)

BMC GENOMICS, 7: Art. No. 202 AUG 9 2006

 

Sousa, SF; Fernandes, PA; Ramos, MJ

Protein-ligand docking: Current status and future challenges

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 65 (1): 15-26 OCT 1 2006 (Review Article)

 

Carvalho, AT; Fernandes, PA; Ramos, MJ

Molecular dynamics model of unliganded HIV-1 reverse transcriptase

MEDICINAL CHEMISTRY, 2(5):491-8 SEP 2006

 

Tamames, B; Fernandes, PA; Ramos, MJ

Catalysis and inhibition of HIV-1 Protease

CURRENT BIOACTIVE COMPOUNDS 12,357 2006 (Invited Review Article)

 

Santos HR; Ujaque G;Ramos MJ; Gomes JA

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

JOURNAL OF COMPUTATIONAL CHEMISTRY, 27(15):1892-7 NOV 30 2006

 

Ramos, MJ; Fernandes, PA

Atomic-Level Rational Drug Design

CURRENT COMPUTER-AIDED DRUG DESIGN 2, 57 2006 (Invited Review Article)

 

Branco, RJF; Fernandes, PA; Ramos, MJ

Molecular dynamics simulations of the enzyme Cu, Zn superoxide dismutase

JOURNAL OF PHYSICAL CHEMISTRY B, 110 (33): 16754-16762 AUG 24 2006

 

Fernandes, PA; Araujo, MLAC; Barbosa, AJM; Alves, CN; Ferreira, ZQ; Gonzalez, CRN; Lima, CFRAC; Loureiro, SIE; Magalhaes, JMT; Maia, FC; Moura, SA; Peredo, EMM; Perez, MAS; Rodrigues, TAQ; Pessoa, AM; da Silva, CAM; da Silva, JPA; Ramos, MJ

Lead optimisation: Improving the affinity of the antiretrovirals Nelfinavir and Amprenavir for HIV-1 protease

LETTERS IN DRUG DESIGN & DISCOVERY, 3 (6): 383-389 AUG 2006 (Invited Article)

 

Sharma, RK; Chopra, S; Sharma, SD; Pande, V; Ramos, MJ; Meguro, K; Inoue, JI; Otsuka, M

Biological evaluation, chelation, and molecular modeling studies of novel metal-chelating inhibitors of NF-kappa B-DNA binding: Structure activity relationships

JOURNAL OF MEDICINAL CHEMISTRY, 49 (12): 3595-3601 JUN 15 2006

 

Carvalho, AP; Fernandes, PA; Ramos, MJ

Similarities and differences in the thioredoxin superfamily

PROGRESS IN BIOPHYSICS & MOLECULAR BIOLOGY, 91 (3): 229-248 JUL 2006 (Review Article)

 

Moreira, IS; Fernandes, PA; Ramos, MJ

Detailed microscopic study of the full ZipA : FtsZ interface

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 63 (4): 811-821 JUN 1 2006

 

Moreira, IS; Fernandes, PA; Ramos, MJ

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

JOURNAL OF PHYSICAL CHEMISTRY B, 110 (22): 10962-10969 JUN 8 2006

 

Lucas, MF; Ramos, MJ

Mechanism of a soluble fumarate reductase from Shewanella frigidimarina: A theoretical study

JOURNAL OF PHYSICAL CHEMISTRY B, 110 (21): 10550-10556 JUN 1 2006

 

Henriques, ES; Nascimento, MAC; Ramos, MJ

Computational study of some benzamidine-based inhibitors of thrombin-like snake venom proteinases

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 106 (9): 2107-2121 AUG 5 2006

 

Carvalho, AP; Fernandes, PA; Ramos, MJ

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

MINI-REVIEWS IN MEDICINAL CHEMISTRY, 6 (5): 549-555 MAY 2006 (Invited Review Article)

 

Carvalho, ATP; Fernandes, PA; Ramos, MJ

Determination of the Delta pKa between the active site cysteines of thioredoxin and DsbA

JOURNAL OF COMPUTATIONAL CHEMISTRY, 27 (8): 966-975 JUN 2006

 

Carvalho, ATP; Fernandes, PA; Ramos, MJ

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

JOURNAL OF PHYSICAL CHEMISTRY B, 110 (11): 5758-5761 MAR 23 2006

 

da Fonseca R, Melo A, Iori F, Menziani MC, Ramos MJ

Molecular interactions between human cytochrome P450 1A2 and flavone derivatives

MEDICINAL CHEMISTRY, 2 : 401-406 2006 (Invited Article)

 

Cerqueira, NMFSA; Fernandes, PA; Eriksson, LA; Ramos, MJ

Dehydration of ribonucleotides catalyzed by ribonucleotide reductase: The role of the enzyme

BIOPHYSICAL JOURNAL, 90 (6): 2109-2119 MAR 2006

 

Branco, RJF; Fernandes, PA; Ramos, MJ

Cu, Zn Superoxide dismutase: distorted active site binds substrate without significant energetic cost

THEORETICAL CHEMISTRY ACCOUNTS, 115 (1): 27-31 FEB 2006

 

Pereira, S; Cerqueira, NMFSA; Fernandes, PA; Ramos, MJ

Computational studies on class I ribonucleotide reductase: Understanding the mechanisms of action and inhibition of a cornerstone enzyme for the treatment of cancer

EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 35 (2): 125-135 JAN 2006 (Review Article)

2005

 

Da Fonseca, R; Marini, M; Melo, A; Menziani, MC; Ramos, MJ

Computational Insight into Anti-mutagenic Properties of CYP1A Flavonoid Ligands

MEDICINAL CHEMISTRY, 1: 355-360 2005 (Invited Article)

 

Antunes, A; Ramos, MJ

Discovery of a large number of previously unrecognized mitochondrial pseudogenes in fish genomes

GENOMICS, 86 (6): 708-717 DEC 2005

 

Pande, V; Ramos, MJ

Structural basis for the GSK-3 beta binding affinity and selectivity against CDK-2 of 1-(4-aminofurazan-3yl)-5-dialkylaminomethyl-1-H-[1,2,3] triazole-4-carboxylic acid derivatives

BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 15 (23): 5129-5135 DEC 1 2005

 

Santos, HRR; Ramos, MJ; Gomes, JANF

A new strategy to model the Si(100) surface

COMPTES RENDUS CHIMIE, 8 (9-10): 1461-1468 SEP-OCT 2005

 

Ramos, MJ; Magalhaes, AL; Melo, AS; Fernandes, PA

Special issue: A collection of papers presented at the 30th international congress of theoretical chemists of Latin Expression, Porto, Portugal, 8-12 September 2004 - Foreword

JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 729 (1-2): VII-VII SEP 16 2005

 

Moreira, IS; Fernandes, PA; Ramos, MJ

Accuracy of the numerical solution of the Poisson-Boltzmann equation

JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 729 (1-2): 11-18 SEP 16 2005

 

Sousa, SF; Fernandes, PA; Ramos, MJ

Farnesyltransferase: Theoretical studies on peptide substrate entrance thiol or thiolate coordination?

JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 729 (1-2): 125-129 SEP 16 2005

 

Branco, RJF; Fernandes, PA; Ramos, MJ

Density-functional calculations of the Cu, Zn superoxide dismutase redox potential: The influence of active site distortion

JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 729 (1-2): 141-146 SEP 16 2005

 

Silva, PJ; Ramos, MJ

Density-functional study of mechanisms for the cofactor-free decarboxylation performed by uroporphyrinogen III decarboxylase

JOURNAL OF PHYSICAL CHEMISTRY B, 109 (38): 18195-18200 SEP 29 2005

 

Preto, MAC; Melo, A; Maia, HLS; Mavromoustakos, T; Ramos, MJ

Molecular dynamics simulations of angiotensin II in aqueous and dimethyl sulfoxide environments

JOURNAL OF PHYSICAL CHEMISTRY B, 109 (37): 17743-17751 SEP 22 2005

 

Santos, HRR; Ramos, MJ; Gomes, JANF

Adsorption of protected and unprotected amino-cyclopentene at the Si(100) surface modeled with a hybrid quantum mechanical cluster technique

PHYSICAL REVIEW B, 72 (7): Art. No. 075445 AUG 2005

 

Pande, V; Ramos, MJ

Molecular recognition of 15-deoxy-Delta(12,14)-prostaglandin J(2) by nuclear factor-kappa B and other cellular proteins

BIOORGANIC & MEDICINAL CHEMISTRY LETTERS, 15 (18): 4057-4063 SEP 15 2005

 

Iori, F; da Fonseca, R; Ramos, MJ; Menziani, MC

Theoretical quantitative structure-activity relationships of flavone ligands interacting with cytochrome P450 1A1 and 1A2 isozymes

BIOORGANIC & MEDICINAL CHEMISTRY, 13 (14): 4366-4374 JUL 15 2005

 

Ramos, MJ; Fernandes, PA

Computer modeling and research in the classroom

JOURNAL OF CHEMICAL EDUCATION, 82 (7): 1021-1025 JUL 2005

 

Fernandes, PA; Maia, ARR; Almeida, AAS; Silva, BFB; Ribeiro, CMS; Ribeiro, CFB; Ribeiro, DSM; Fonseca, DAP; Henriques, ES; Cunha, EMS; Maia, FRNC; Pereira, JAA; Pacheco, JPG; Ferreira, JAAD; Matos, LRC; Pinto, MABP; Borges, MCS; Magalhaes, PJCR; Teixeira, PFRD; Veloso, PNBC; Ferreira, RJF; Gomes, SS; Barros, TF; Selao, TSJT; Pande, V; Fernandes, VMMC; Ramos, MJ

New designs for inhibitors of the NF-kappa B: DNA binding

THEORETICAL CHEMISTRY ACCOUNTS, 113 (4): 197-204 MAY 2005

 

Lucas, MD; Ramos, MJ

Theoretical study of the suicide inhibition mechanism of the enzyme pyruvate formate lyase by methacrylate

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 127 (18): 6902-6909 MAY 11 2005

 

Cerqueira, NMFSA; Pereira, S; Fernandes, PA; Ramos, MJ

Overview of ribonucleotide reductase inhibitors: An appealing target in anti-tumour therapy

CURRENT MEDICINAL CHEMISTRY, 12 (11): 1283-1294 2005 (Review Article)

 

Pereira, S; Fernandes, PA; Ramos, MJ

Theoretical study on the inhibition of ribonucleotide reductase by 2 '-mercapto-2 '-deoxyribonucleoside-5 '-diphosphates

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 127 (14): 5174-5179 APR 13 2005

 

Sharma, RK; Pande, V; Ramos, MJ; Rajor, HK; Chopra, S; Meguro, K; Inoue, J; Otsuka, M

Inhibitory activity of polyhydroxycarboxylate chelators against recombinant NF-kappa B p50 protein-DNA binding

BIOORGANIC CHEMISTRY, 33 (2): 67-81 APR 2005

 

Pande, V; Ramos, MJ

NF-kappa B in human disease: current inhibitors and prospects for de novo structure based design of inhibitors

CURRENT MEDICINAL CHEMISTRY, 12 (3): 357-374 2005 (Review Article)

 

Sousa, SF; Fernandes, PA; Ramos, MJ

Unraveling the mechanism of the farnesyltransferase enzyme

JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY, 10 (1): 3-10 JAN 2005

 

Sousa, SF; Fernandes, PA; Ramos, MJ

Farnesyltransferase - New insights into the zinc-coordination sphere paradigm: Evidence for a carboxylate-shift mechanism

BIOPHYSICAL JOURNAL, 88 (1): 483-494 JAN 2005