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 2007-2008
Dourado,
DFAR; Fernandes, PA; ; Mannervik, B; Ramos, MJ
Glutathione Transferase: New model
for GSH activation
CHEMISTRY-A EUROPEAN JOURNAL, 14
(31):9591-9598 2008
Marques, AT; Fernandes, PA; Ramos,
MJ
Molecular dynamics simulations of
the amyloid-beta binding alcohol dehydrogenase (ABAD) enzyme
BIOORGANIC
& MEDICINAL CHEMISTRY, 16 (21):9511-9518 2008
Brás, NF;
Cerqueira, NMFSA; Fernandes, PA; Ramos, MJ
Carbohydrate-binding modules from
family 11: Understanding the binding mode of polysaccharides
INTERNATIONAL JOURNAL OF QUANTUM
CHEMISTRY 108, 2030-2040, 2008
Sousa, SF;
Fernandes, PA; Ramos, MJ
Enzyme Flexibility and the Catalytic
Mechanism of Farnesyltransferase: Targeting the Relation
JOURNAL OF PHYSICAL CHEMISTRY B, 112
(29):8681-8691 2008
Moreira, IS;
Fernandes, PA; Ramos, MJ
Protein-protein recognition: a
computational mutagenesis study of the MDM2-P53 complex
THEORETICAL CHEMISTRY ACCOUNTS 120
(4-6):533-542 2008
Preto, MAC; Melo, A; Rodrigues, LM;
Maia, HLS; Ramos, MJ
Structural insight on the activity
of Type 1 Angiotensin II peptide antagonists using MD simulations
JOURNAL OF PHYSICAL CHEMISTRY B, 112
(43):13620-13628 2008
Sousa, SF;
Fernandes, PA; Ramos, MJ
Farnesyltransferase Inhibitors: a
Detailed Chemical View on an Elusive Biological Problem
CURRENT MEDICINAL CHEMISTRY, 15
(15):1478-1492, 2008 (Review Article)
Pande V;
Ramos MJ; Gago F
The Protein Kinase Inhibitor
Balanol: Structure Activity Relationships and Structural and Computational
Studies
ANTI-CANCER AGENTS IN MEDICINAL
CHEMISTRY, 8 (6):638-645 2008 (Review Article)
Russo, N;
Ramos, MJ; Ugalde, JM; Eriksson, LA
Special issue: Proceedings of the
3rd Theoretical Biophysics Symposium - Centraro, Italy, June 16-20, 2007 –
Introduction
INTERNATIONAL JOURNAL OF QUANTUM
CHEMISTRY, 108 (11): 2008
Dourado,
DFAR; Fernandes, PA; Ramos, MJ
Mammalian Cytosolic Glutathione
S-Transferases
CURRENT PROTEIN & PEPTIDE
SCIENCE, 9 (4):325-337 2008
Sousa, SF;
Fernandes, PA; Ramos, MJ
Molecular Dynamics Analysis of
Farnesyltransferase: A Closer Look into the Amino Acid Behaviour
INTERNATIONAL JOURNAL OF QUANTUM
CHEMISTRY, 108 (11):1939-1950 2008
Martins S,
Ramos MJ; Fernandes PA
The current status of the NNRTI
family of antiretrovirals used in the HAART regime against HIV infection
CURRENT
MEDICINAL CHEMISTRY, 15 (11):1083-1095 2008
Brás, NF;
Moura-Tamames, SA; Fernandes, PA; Ramos, MJ
Mechanistic studies on the formation
of Glycosidase-substrate and Glycosidase-inhibitor covalent intermediates
JOURNAL OF COMPUTATIONAL CHEMISTRY,
29 (15):2565-2574 2008
Marques, AT; Antunes, A; Fernandes,
PA; Ramos, MJ,
Computational optimisation of
AG18051 inhibitor for amyloid-beta binding alcohol dehydrogenase (ABAD) enzyme
INTERNATIONAL JOURNAL OF QUANTUM
CHEMISTRY, 108 (11):1982-1991 2008
Ramos MJ;
Fernandes PA
Computational
Enzymatic Catalysis
ACCOUNTS OF CHEMICAL RESEARCH, 41
(6):689-698 2008
Branco, RJF; Seifert, A; Budde, M;
Urlacher, VB; Ramos, MJ; Pleiss, J
Anchoring Effects in a Wide Binding
Pocket: The Molecular Basis of Regioselectivity in Engineered Cytochrome P450
Monooxygenase from B. megaterium
PROTEINS-STRUCTURE FUNCTION AND
BIOINFORMATICS 73 (3):597-607 2008
Viegas A;
Brás NF; Cerqueira NMFSA; Fernandes PA; Prates JAM; Fontes CMGA; Bruix M; Romao
MJ; Carvalho AL; Ramos MJ; Macedo AL; Cabrita EJ
Molecular Determinants of Ligand
Specificity in Family 11 Carbohydrate Binding Modules (CBM11): an NMR, X-Ray
Crystallography and Computational Chemistry Approach
FEBS JOURNAL, 275 (10):2524-2535
2008
Da Fonseca, R; Johnson, WE; O’Brien,
SJ; Ramos, MJ, Antunes, A
he adaptive evolution of the
mammalian mitochondrial genome
BMC
GENOMICS, 9, 119, 2008
Silva PJ;
Ramos MJ
A comparative density-functional
study of the reaction mechanism of the O2-dependent coproporphyrinogen III
oxidase
BIOORGANIC MEDICINAL CHEMISTRY, 16
(6):2726-2733 2008
Silva, PJ; Ramos, MJ
Comparative density functional study
of models for the reaction mechanism of uroporphyrinogen III synthase
JOURNAL OF PHYSICAL CHEMISTRY B,
112, 3144-3148, 2008
Carvalho,
ATP; Swart, M; van Stralen, JNP; Fernandes, PA; Ramos MJ; Bickelhaupt FM
Mechanism of thioredoxin-catalyzed
disulfide reaction. Activation of the buried thiol and role of the variable
active-site residues
JOURNAL OF PHYSICAL CHEMISTRY B, 112
(8):2511-2523 2008
2007
Cerqueira,
NMFSA; Fernandes, PA; Ramos, MJ
Understanding ribonucleotide
reductase inactivation by gemcitabine
CHEMISTRY-A EUROPEAN JOURNAL 13:
8507-8515, 2007
Osorio, DS; Antunes, A; Ramos, MJ
Structural and functional
implications of positive selection at the primate angiogenin gene
BMC EVOLUTIONARY BIOLOGY, 7, Article
Number: 167, 2007
Santos, HRR;
Ramos, MJ; Gomes, JANF
Microscopic detail provided for the
adsorption of protected amino-cyclopentene on Si(100)
CHEMICAL PHYSICS LETTERS, 448,
111-114, 2007
Sousa, SF; Fernandes, PA; Ramos, MJ
General performance of density
functionals
JOURNAL OF PHYSICAL CHEMISTRY A; 111
(42): 10439-10452, 2007 (Review Article)
Silva PJ; Ramos MJ
Reaction mechanism of the vitamin
K-dependent glutamate carboxylase: A computational study
JOURNAL OF PHYSICAL CHEMISTRY B 111:
12883-12887, NOV 8 2007
Tamames, B;
Sousa, SF; Tamames, J; Fernandes, PA; Ramos, MJ
Analysis of zinc-ligand bond lengths
in metalloproteins: Trends and patterns
PROTEINS-STRUCTURE FUNCTION AND
BIOINFORMATICS 69 (3): 466-475 NOV 15 2007
Carvalho
ATP, Fernandes PA, Ramos MJ
The excision mechanism in reverse
transcriptase: Pyrophosphate leaving and fingers opening are uncoupled events
with the analogues AZT and d4T
JOURNAL OF PHYSICAL CHEMISTRY B 111
(41): 12032-12039 OCT 18 2007
Antunes A, Pontius J, Ramos MJ,
O'Brien SJ, Johnson WE
Mitochondrial introgressions into
the nuclear genome of the domestic cat
JOURNAL OF HEREDITY 98 (5): 414-420
Sp. Iss. SI 2007
Moreira IS,
Fernandes PA, Ramos MJ
Hot spots-A review of the
protein-protein interface determinant amino-acid residues
PROTEINS-STRUCTURE FUNCTION AND
BIOINFORMATICS 68 (4): 803-812 SEP 2007
Sousa, SF;
Fernandes, PA; Ramos, MJ
Comparative assessment of
theoretical methods for the determination of geometrical properties in
biological zinc complexes
JOURNAL OF PHYSICAL CHEMISTRY B 111 (30):
9146-9152 AUG 2 2007
Moreira, IS;
Fernandes, PA; Ramos, MJ
Vascular Endothelial Growth Factor
(VEGF) inhibition - a critical review
ANTI-CANCER AGENTS IN MEDICINAL
CHEMISTRY; 7: 223-245, 2007 (Invited Review Article)
Perez, MAS;
Fernandes, PA; Ramos, MJ
Drug design: New inhibitors for
HIV-1 protease based on Nelfinavir as lead
JOURNAL OF MOLECULAR GRAPHICS AND
MODELLING, 26(3): 634-642 OCT 2007 (Invited Article)
Moreira, IS;
Fernandes, PA; Ramos, MJ
Backbone importance for
protein-protein binding
JOURNAL OF CHEMICAL THEORY AND
COMPUTATION 3(3): 885–893 MAY-JUN 2007 (Invited article)
Sousa, SF;
Fernandes, PA; Ramos, MJ
Theoretical studies on
farnesyltransferase: Evidence for thioether product coordination to the active-site
zinc sphere
JOURNAL OF COMPUTATIONAL CHEMISTRY,
28 (7): 1160-1168 MAY 2007
Luo SJ, Cai QX, David VA, Zhang L,
Martelli P, Lim NTL, Ferrand N, Chin SC, Gaubert P, Ramos MJ, O'Brien SJ,
Antunes A, Johnson WE
Isolation and characterization of
microsatellite markers in pangolins (Mammalia, Pholidota, Manis spp.)
MOLECULAR
ECOLOGY NOTES 7 (2): 269-272 MAR 2007
Moreira, IS;
Fernandes, PA; Ramos, MJ
Hot spot occlusion from bulk water:
A comprehensive study of the complex between the lysozyme HEL and the antibody
FVD1.3
JOURNAL OF PHYSICAL CHEMISTRY B, 111
(10): 2697-2706 MAR 15 2007
Santos, HRR;
Ujaque, G; Ramos, MJ; Gomes, JANF
Effect of the tert-butiloxycarbonyl
protecting group on the adsorption of protected amino-cyclopentene on the
Si(100) surface
PHYSICAL REVIEW B, 75 (12): Art. No.
125413 MAR 2007
Carvalho
ATP, Fernandes PA, Ramos MJ
Parameterization of AZT - A widely
used nucleoside inhibitor of HIV-1 reverse transcriptase
INTERNATIONAL JOURNAL OF QUANTUM
CHEMISTRY 107 (2): 292-298 FEB 2007
Moreira, IS;
Fernandes, PA; Ramos MJ
Computational alanine scanning
mutagenesis - An improved methodological approach
JOURNAL OF COMPUTATIONAL CHEMISTRY,
28 (3): 644-654 FEB 2007
Sousa, SF;
Fernandes, PA; Ramos, MJ
The Carboxylate Shift in Zinc
Enzymes: A Computational Study
JOURNAL OF THE AMERICAN CHEMICAL
SOCIETY, 129 (5): 1378-1385 FEB 7 2007
Moreira, IS;
Fernandes, PA; Ramos MJ
Hot spot computational
identification: Application to the complex formed between the hen egg white
lysozyme (HEL) and the antibody HyHEL-10
INTERNATIONAL JOURNAL OF QUANTUM
CHEMISTRY 107 (2): 299-310 FEB 2007
da Fonseca
RR, Antunes A, Melo A, Ramos MJ
Structural divergence and adaptive
evolution in mammalian cytochromes P4502C
GENE 387
(1-2): 58-66 JAN 31 2007
Cerqueira,
NMFS Fernandes, PA Ramos, MJ
Ribonucleotide Reductase: A critical
enzyme for cancer chemotherapy and antiviral agents
RECENT PATENTS IN ANTICANCER DRUG
DISCOVERY, 2:11-29. JAN 2007
Sousa, SF;
Fernandes, PA; Ramos, MJ
Effective tailor-made force field
parameterization of the several Zn coordination environments in the puzzling
FTase enzyme: opening the door to the full understanding of its elusive
catalytic mechanism
THEORETICAL CHEMISTRY ACCOUNTS 117
(1): 171-181 JAN 2007
Moreira, IS; Fernandes, PA; Ramos MJ
Unravelling Hot Spots: a
comprehensive mutagenesis study
THEORETICAL CHEMISTRY ACCOUNTS 117
(1): 99-113 JAN 2007
Sousa, SF; Fernandes, PA; Ramos, MJ
Theoretical studies on
farnesyltransferase: The distances paradox explained
PROTEINS-STRUCTURE FUNCTION AND
BIOINFORMATICS 66 (1): 205-218 JAN 2007