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