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 2013-2014

Coimbra, JTS; Moniz, T; Bras, NF; Iyanova, G;Fernandes, PA; Ramos, MJ; Rangel, M

Relevant Interactions of Antimicrobial Iron Chelators and Membrane Models Revealed by Nuclear Magnetic Resonance and Molecular Dynamics Simulations

JOURNAL OF PHYSICAL CHEMISTRY B, 118 (50): 14590-14601, 2014

DOI: 10.1021/jp509491p

 

Araujo,AR; Ribeiro, AJM; Fernandes, PA; Ramos, MJ

Catalytic Mechanism of Retroviral Integrase for the Strand Transfer Reaction Explored by QM/MM Calculations

JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10 (12): 5458-5466, 2014

DOI: 10.1021/ct500570g

 

Coimbra, JTS; Neves, RPP; Passos, O; Jarukanont, D; Fernandes, PA; Patel, S; Garcia, ME; Ramos, MJ

Influence of the environment on protein bond energies

CHEMICAL PHYSICS LETTERS, 615: 75-82, 2014

DOI: 10.1016/j.cplett.2014.09.066

 

Calixto, AR; Bras, NF; Fernandes, PA; Ramos, MJ

Reaction Mechanism of Human Renin Studied by Quantum Mechanics/Molecular Mechanics (QM/MM) Calculations

ACS CATALYSIS, 4 (11): 3869-3876, 2014

DOI: 10.1021/cs500497f

 

Neves, RPP; Fernandes, PA; Varandas, AJC; Ramos, MJ

Benchmarking of Density Functionals for the Accurate Description of Thiol-Disulfide Exchange

JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10 (11): 4842-4856, 2014

DOI: 10.1021/ct500840f

 

Jarukanont, D; Coimbra, JTS; Bauerhenne, B; Fernandes, PA; Patel, S; Ramos, MJ; Garcia, ME

Biomolecular structure manipulation using tailored electromagnetic radiation: a proof of concept on a simplified model of the active site of bacterial DNA topoisomerase

PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 16 (39): 21768-21777, 2014

DOI: 10.1039/c4cp02289k

 

Sousa, SF; Cerqueira, NMFSA; Bras, NF; Fernandes, PA; Ramos, MJ

Enzymatic "Tricks": Carboxylate Shift and Sulfur Shift

INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 114 (19): 1253-1256, 2014 (Review Article)

DOI: 10.1002/qua.24689

 

Aranda, J; Cerqueira, NMFSA; Fernandes, PA; Roca, M; Tunon, I; Ramos, MJ

The Catalytic Mechanism of Carboxylesterases: A Computational Study

BIOCHEMISTRY, 53 (36): 5820-5829, 2014

DOI: 10.1021/bi500934j

 

Dourado, DFAR; Fernandes, PA; Mannervik, B; Ramos, MJ

Isomerization of Delta(5)-Androstene-3,17-dione into Delta(4)-Androstene-3, 17-dione Catalyzed by Human Glutathione Transferase A3-3: A Computational Study Identifies a Dual Role for Glutathione

JOURNAL OF PHYSICAL CHEMISTRY A, 118 (31): 5790-5800, 2014

DOI: 10.1021/jp410810q

 

Santos-Martins, D; Forli, S; Ramos, MJ; Olson, AJ

AutoDock4(Zn): An Improved Auto Dock Force Field for Small-Molecule Docking to Zinc Metalloproteins

JOURNAL OF CHEMICAL INFORMATION AND MODELING, 54 (8): 2371-2379, 2014

DOI: 10.1021/ci500209e

 

Bras, NF; Cerqueira, NMFSA; Ramos, MJ; Fernandes, PA

Glycosidase inhibitors: a patent review (2008-2013)

EXPERT OPINION ON THERAPEUTIC PATENTS, 24 (8): 857-874, 2014 (Review Article)

DOI: 10.1517/13543776.2014.916280

 

Martins, SA; Sousa, SF; Ramos, MJ; Fernandes, PA

Prediction of Solvation Free Energies with Thermodynamic Integration Using the General Amber Force Field

JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 10 (8): 3570-3577, 2014

DOI: 10.1021/ct500346y

 

Bras, NF; Fernandes, PA; Ramos, MJ

QM/MM Study and MD Simulations on the Hypertension Regulator Angiotensin-Converting Enzyme

ACS CATALYSIS, 4 (8): 2587-2587, 2014

DOI: 10.1021/cs500093h

 

Silva, AMN; Sousa, PRH; Coimbra, JTS; Bras, NF; Vitorino, R; Fernandes, PA; Ramos, MJ; Rangel, M; Domingues, P

The glycation site specificity of human serum transferrin is a determinant for transferrin's functional impairment under elevated glycaemic conditions

BIOCHEMICAL JOURNAL, 461: 33-42, 2014

DOI: 10.1042/BJ20140133


Ribeiro, JV; Cerqueira, NMFSA; Fernandes, PA; Ramos, MJ

chem-path-tracker: An Automated Tool to Analyze Chemical Motifs in Molecular Structures

CHEMICAL BIOLOGY & DRUG DESIGN, 84 (1): 44-53, 2014

DOI: 10.1111/cbdd.12349

 

Bras, NF; Ribeiro, AJM; Oliveira, M; Paixao, NM; Tamames, JA; Fernandes, PA; Ramos, MJ

Analyses of cobalt-ligand and potassium-ligand bond lengths in metalloproteins: trends and patterns

JOURNAL OF MOLECULAR MODELING, 20 (6), 2014

DOI: 10.1007/s00894-014-2271-z

 

Moorthy, NSHN; Ramos, MJ; Fernandes, PA

Predictive QSAR models development and validation for human ether-a-go-go related gene (hERG) blockers using newer tools

JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY, 29 (3): 317-324, 2014

DOI: 10.3109/14756366.2013.779264

 

Hong, MK; Ribeiro, AJM; Kim, JK; Ngo, HPT; Kim, J; Lee, CH; Ahn, YJ; Fernandes, PA; Li, Q; Ramos, MJ; Kang, LW

Divalent metal ion-based catalytic mechanism of the Nudix hydrolase Orf153 (YmfB) from Escherichia coli

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 70: 1297-1310, 2014

DOI: 10.1107/S1399004714002570

 

Gesto, DS; Cerqueira, NMFSA; Ramos, MJ; Fernandes, PA

Discovery of new druggable sites in the anti-cholesterol target HMG-CoA reductase by computational alanine scanning mutagenesis

JOURNAL OF MOLECULAR MODELING, 20 (4), 2014

DOI: 10.1007/s00894-014-2178-8

 

Bras, NF; Fernandes, PA; Ramos, MJ

Discovery of New Sites for Drug Binding to the Hypertension-Related Renin-Angiotensinogen Complex

CHEMICAL BIOLOGY & DRUG DESIGN, 83 (4): 427-439, 2014

DOI: 10.1111/cbdd.12258

 

Bras, NF; Fernandes, PA; Ramos, MJ

Molecular dynamics studies on both bound and unbound renin protease

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 32 (3): 351-363, 2014

DOI: 10.1080/07391102.2013.768553


Fernandes, A; Ivanova, G; Bras, NF; Mateus, N; Ramos, MJ; Rangel, M; de Freitas, V

Structural characterization of inclusion complexes between cyanidin-3-0-glucoside and beta-cyclodextrin

CARBOHYDRATE POLYMERS, 102: 269-277, 2014

DOI: 10.1016/j.carbpol.2013.11.037

 

Ngo, HPT; Cerqueira, NMFSA; Kim, JK; Hong, MK; Fernandes, PA; Ramos, MJ; Kang, LW

PLP undergoes conformational changes during the course of an enzymatic reaction

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 70: 596-606, 2014

DOI: 10.1107/S1399004713031283

 

Moreira, IS; Ramos, RM; Martins, JM; Fernandes, PA; Ramos, MJ

Are hot-spots occluded from water?

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 32 (2): 186-197, 2014

DOI: 10.1080/07391102.2012.758598

 

Coimbra, JTS; Sousa, SF; Fernandes, PA; Rangel, M; Ramos, MJ

Biomembrane simulations of 12 lipid types using the general amber force field in a tensionless ensemble

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 32 (1): 88-103, 2014

DOI: 10.1080/07391102.2012.750250

 

Moorthy, NSHN; Martins, SA; Sousa, SF; Ramos, MJ; Fernandes, PA

Classification study of solvation free energies of organic molecules using machine learning techniques

RSC ADVANCES, 4 (106): 61624-61630, 2014

DOI: 10.1039/c4ra07961b

 

Marcial, BL; Sousa, SF; Dos Santos, HF; Ramos, MJ

Structural and dynamics analysis of matrix metalloproteinases MMP-2 complexed with chemically modified tetracyclines (CMTs)

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 32 (12): 1907-1918, 2014

DOI: 10.1080/07391102.2013.842186

 

Moorthy, NSHN; Pratheepa, V; Ramos, MJ; Vasconcelos, V; Fernandes, PA

Fused Aryl-Phenazines: Scaffold for the Development of Bioactive Molecules

CURRENT DRUG TARGETS, 15 (7): 681-688, 2014

 

Moorthy, NSHN; Bras, NF; Ramos, MJ; Fernandes, PA

Binding mode prediction and identification of new lead compounds from natural products as renin and angiotensin converting enzyme inhibitors

RSC ADVANCES, 4 (38): 19550-19568, 2014

DOI: 10.1039/c4ra00856a


Moorthy, NSHN; Sousa, SF; Ramos, MJ; Fernandes, PA

Farnesyltransferase Inhibitors: A Comprehensive Review Based on Quantitative Structural Analysis
CURRENT MEDICINAL CHEMISTRY, 20 (38): 4888- 4923, 2013


Ribeiro, JV; Tamames, JAC; Cerqueira, NMFSA; Fernandes, PA; Ramos, MJ

Volarea - A Bioinformatics Tool to Calculate the Surface Area and the Volume of Molecular Systems
CHEMICAL BIOLOGY & DRUG DESIGN, 82 (6): 743-755, 2013
DOI: 10.1111/cbdd.12197

Oliveira, J; da Silva, MA; Parola, AJ; Mateus, N; Bras, NF; Ramos, MJ; de Freitas, V

Structural characterization of a A-type linked trimeric anthocyanin derived pigment occurring in a young Port wine
FOOD CHEMISTRY, 141 (3): 1987-1996, 2013
DOI: 10.1016/j.foodchem.2013.04.091


Dourado, DFAR; Fernandes, PA; Ramos, MJ; Mannervik, B

Mechanism of Glutathione Transferase P1-1-Catalyzed Activation of the Prodrug Canfosfamide (TLK286, TELCYTA)
BIOCHEMISTRY, 52 (45): 8069- 8078, 2013
DOI: 10.1021/bi4005705


Moorthy, NSHN; Cerqueira, NMFSA; Ramos, MJ; Fernandes, PA

Development of Ribonucleotide Reductase Inhibitor: A Review on Structure Activity Relationships
MINI-REVIEWS IN MEDICINAL CHEMISTRY, 13 (13): 1862- 1872, 2013 (Review Article)


Ribeiro, AJM; Alberto, ME; Ramos, MJ; Fernandes, PA; Russo, N

The Catalytic Mechanism of Protein Phosphatase 5 Established by DFT Calculations
CHEMISTRY-A EUROPEAN JOURNAL, 19 (42): 14081- 14089, 2013
DOI: 10.1002/chem.201301565


Cerqueira, NMFSA; Fernandes, PA; Gonzalez, PJ; Moura, JJG; Ramos, MJ

The Sulfur Shift: An Activation Mechanism for Periplasmic Nitrate Reductase and Formate Dehydrogenase
INORGANIC CHEMISTRY, 52(19): 10766- 10772, 2013
DOI: 10.1021/ic3028034


Sousa, SF; Pinto, GRP; Ribeiro, AJM; Coimbra, JTS; Fernandes, PA; Ramos, MJ

Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for copper complexes
JOURNAL OF COMPUTATIONAL CHEMISTRY, 34 (24): 2079- 2090, 2013 (Review Article)
DOI: 10.1002/jcc.23349


Oliveira, BL; Moreira, IS; Fernandes, PA; Ramos, MJ; Santos, I; Correia, JDG

Theoretical studies on the binding of rhenium(I) complexes to inducible nitric oxide synthase
JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 45: 13-25, 2013
DOI: 10.1016/j.jmgm.2013.07.007


Teixeira, N; Cruz, L; Bras, NF; Mateus, N; Ramos, MJ; de Freitas, V

Structural Features of Copigmentation of Oenin with Different Polyphenol Copigments
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY, 61 (28): 6942-6948, 2013
DOI: 10.1021/jf401174b


Carvalho, ATP; Teixeira, AFS; Ramos, MJ

Parameters for molecular dynamics simulations of iron-sulfur proteins
JOURNAL OF COMPUTATIONAL CHEMISTRY, 34 (18): 1540-1548, 2013
DOI: 10.1002/jcc.23287


Neves, RPP; Sousa, SF; Fernandes, PA; Ramos, MJ

Parameters for Molecular Dynamics Simulations of Manganese-Containing Metalloproteins
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9 (6): 2718-2732, 2013
DOI: 10.1021/ct400055v


Sousa, SF; Ribeiro, AJM; Coimbra, JTS; Neves, RPP; Martins, SA; Moorthy, NSHN; Fernandes, PA; Ramos, MJ

Protein-Ligand Docking in the New Millennium - A Retrospective of 10 Years in the Field
CURRENT MEDICINAL CHEMISTRY, 20 (18): 2296-2314, 2013


Ribeiro, AJM; Ramos, MJ; Fernandes, PA; Russo, N

A DFT study of the applicability of the charge balance model in two-metal enzymes: The case of cAMP-dependent protein kinase
CHEMICAL PHYSICS LETTERS, 571: 66-70, 2013
DOI: 10.1016/j.cplett.2013.03.085


Gesto, DS; Cerqueira, NMFSA; Fernandes, PA; Ramos, MJ

Unraveling the Enigmatic Mechanism of L-Asparaginase II with QM/QM Calculations
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 135 (19): 7146-7158, 2013
DOI: 10.1021/ja310165u


Moorthy, NSHN; Cerqueira, NMFSA; Ramos, MJ; Fernandes, PA

Aryl- and Heteroaryl-Thiosemicarbazone Derivatives and Their Metal Complexes: A Pharmacological Template
RECENT PATENTS ON ANTI-CANCER DRUG DISCOVERY, 8 (2): 168-182, 2013 (Review Article)


Oliveira, BL; Moreira, IS; Fernandes, PA; Ramos, MJ; Santos, I; Correia, JDG

Insights into the structural determinants for selective inhibition of nitric oxide synthase isoforms
JOURNAL OF MOLECULAR MODELING, 19 (4): 1537-1551, 2013
DOI: 10.1007/s00894-012-1677-8


Ornellas, FR; Ramos, MJ

Preface
THEORETICAL CHEMISTRY ACCOUNTS, 132 (3), 2013 (Editorial Material)
DOI: 10.1007/s00214-012-1319-3


Martins, SA; Perez, MAS; Moreira, IS; Sousa, SF; Ramos, MJ; Fernandes, PA

Computational Alanine Scanning Mutagenesis: MM-PBSA vs TI
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 9 (3): 1311-1319, 2013
DOI: 10.1021/ct4000372


Sousa, SF; Coimbra, JTS; Paramos, D; Pinto, R; Guimares, RS; Teixeira, V; Fernandes, PA; Ramos, MJ

Molecular dynamics analysis of a series of 22 potential farnesyltransferase substrates containing a CaaX-motif
JOURNAL OF MOLECULAR MODELING, 19 (2): 673-688, 2013
DOI: 10.1007/s00894-012-1590-1


Moreira, IS; Martins, JM; Ramos, RM; Fernandes, PA; Ramos, MJ

Are Hot-Spots Occluded from Water?
BIOPHYSICAL JOURNAL, 104 (2): 505A, 2013 (Meeting Abstract)


Moorthy, NSHN; Cerqueira, NMFSA; Ramos, MJ; Fernandes, PA

Combined ligand and structure based binding mode analysis of oxidosqualene cyclase inhibitors
RSC ADVANCES, 3 (45): 23409-23422, 2013
DOI: 10.1039/c3ra43670e


Moorthy, NSHN; Ramos, MJ; Fernandes, PA

Human Ether-a-Go-Go-Related Gene Channel Blockers and its Structural Analysis for Drug Design
CURRENT DRUG TARGETS, 14 (1): 102-113, 2013


Moreira, IS; Martins, JM; Ramos, RM; Fernandes, PA; Ramos, MJ

Understanding the importance of the aromatic amino-acid residues as hot-spots
BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, 1834 (1): 404-414, 2013
DOI: 10.1016/j.bbapap.2012.07.005




Copyright © 2014 Maria João Ramos