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 2015-2016

Santos-Martins; Fernandes, PA; Ramos, MJ

Calculation of distribution coefficients in the SAMPL5 challenge from atomic solvation parameters and surface areas

JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN, 30: 1079-1086, 2016

DOI: 10.1007/s10822-016-9951-y


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

Binding mode of conformations and structure-based pharmacophore development for farnesyltransferase inhibitors

MEDICINAL CHEMISTRY RESEARCH, 25: 1340-1357, 2016

DOI: 10.1007/s00044-016-1578-y


Cerqueira, NMFSA; Oliveira, EF; Gesto, DS; Santos-Martins, D; Moreira, C; Moorthy, HN; Ramos, MJ; Fernandes, PA

Cholesterol Biosynthesis: A Mechanistic Overview

BIOCHEMISTRY, 55: 5483-5506, 2016

DOI: 10.1021/acs.biochem.6b00342


Moreira, C; Ramos, MJ; Fernandes, PA

Glutamine Synthetase Drugability beyond Its Active Site: Exploring Oligomerization Interfaces and Pockets

MOLECULES, 21, 2016

DOI: 10.3390/molecules21081028


Oliveira, EF; Santos-Martins, D; Ribeiro, AM; Bras, NF; Cerqueira, NS; Sousa, SF; Ramos, MJ; Fernandes, PA

HMG-CoA Reductase inhibitors: an updated review of patents of novel compounds and formulations (2011-2015)

EXPERT OPINION ON THERAPEUTIC PATENTS, 26: 1257-1272, 2016

DOI: 10.1080/13543776.2016.1216977


Sousa, SF; Sousa, JFM; Barbosa, ACC; Ferreira, CE; Neves, RPP; Ribeiro, AJM; Fernandes, PA; Ramos, MJ

Improving the Biodesulfurization of Crude Oil and Derivatives: A QM/MM Investigation of the Catalytic Mechanism of NADH-FMN Oxidoreductase (DszD)

JOURNAL OF PHYSICAL CHEMISTRY A, 120: 5300-5306, 2016

DOI: 10.1021/acs.jpca.6b01536


Sousa, RP; Fernandes, PA; Ramos, MJ; Bras, NF

Insights into the reaction mechanism of 3-O-sulfotransferase through QM/MM calculations

PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 18: 11488-11496, 2016

DOI: 10.1039/c5cp06224a


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

Molecular dynamic simulations and structure-based pharmacophore development for farnesyltransferase inhibitors discovery

JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY, 31: 1428-1442, 2016

DOI: 10.3109/14756366.2016.1144593


Oliveira, EF; Cerqueira, NMFSA; Ramos, MJ; Fernandes, PA

QM/MM study of the mechanism of reduction of 3-hydroxy-3-methylglutaryl coenzyme A catalyzed by human HMG-CoA reductase

CATALYSIS SCIENCE & TECHNOLOGY, 6: 7172-7185, 2016

DOI: 10.1039/c6cy00356g


Moreira, C; Ramos, MJ; Fernandes, PA

Reaction Mechanism of Mycobacterium Tuberculosis Glutamine Synthetase Using Quantum Mechanics/Molecular Mechanics Calculations

CHEMISTRY-A EUROPEAN JOURNAL, 22: 9218-9225, 2016

DOI: 10.1002/chem.201600305


Llinas, P; Chenon, M; Nguyen, TQ; Moreira, C; de Regibus, A; Coquard, A; Ramos, MJ; Guerois, R; Fernandes, PA; Menetrey, J

Structure of a truncated form of leucine zipper II of JIP3 reveals an unexpected antiparallel coiled-coil arrangement

ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, 72: 198-206, 2016

DOI: 10.1107/S2053230X16001576


Moniz, T; Coimbra, JTS; Bras, NF; Cunha-Silva, L; Ramos, MJ; Fernandes, PA; de Castro, B; Rangel, M

Synthesis and structural characterization, by spectroscopic and computational methods, of two fluorescent 3-hydroxy-4-pyridinone chelators bearing sulphorhodamine B and naphthalene

RSC ADVANCES, 6: 4200-4211, 2016

DOI: 10.1039/c5ra23217a


Bras, NF; Ferreira, P; Calixto, AR; Jaspars, M; Houssen, W; Naismith, JH; Fernandes, PA; Ramos, MJ

The Catalytic Mechanism of the Marine-Derived Macrocyclase PatGmac

CHEMISTRY-A EUROPEAN JOURNAL, 22: 13089-13097, 2016

DOI: 10.1002/chem.201601670


Neves, Rui P. P.; Fernandes, Pedro A.; Ramos, Maria J.

Unveiling the Catalytic Mechanism of NADP(+)-Dependent Isocitrate Dehydrogenase with QM/MM Calculations

ACS CATALYSIS, 6: 357-368, 2016

DOI: 10.1021/acscatal.5b01928


Piekarski, DG; Ramos, MJ; Diaz-Tendero, S

Dynamics of excited clusters of beta-alanine in the gas phase

JOURNAL OF PHYSICS: CONFERENCE SERIES, PTS 1-12, 635, 2015

DOI: 10.1088/1742-6596/635/3/032089


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

Periplasmic Nitrate Reductase and Formate Dehydrogenase: Similar Molecular Architectures with Very Different Enzymatic Activities

ACCOUNTS OF CHEMICAL RESEARCH, 48: 2875-2884, 2015 (Review Article)

DOI: 10.1021/acs.accounts.5b00333


Oliveira, BL; Morais, M; Mendes, F; Moreira, IS; Cordeiro, C; Fernandes, PA; Ramos, MJ; Alberto, R; Santos, I; Correia, JDG

Re(I) and Tc(I) Complexes for Targeting Nitric Oxide Synthase: Influence of the Chelator in the Affinity for the Enzyme

CHEMICAL BIOLOGY & DRUG DESIGN, 86: 1072-1086, 2015

DOI: 10.1111/cbdd.12575


Sousa, SF; Ramos, MJ; Lim, C; Fernandes, PA

Relationship between Enzyme/Substrate Properties and Enzyme Efficiency in Hydrolases

ACS CATALYSIS, 5: 5877-5887, 2015

DOI: 10.1021/acscatal.5b00923


Ribeiro, AJM; Santos-Martins, D; Russo, N; Rarnos, MJ; Fernandes, PA

Enzymatic Flexibility and Reaction Rate: A QM/MM Study of HIV-1 Protease

ACS CATALYSIS, 5: 5617-5626, 2015

DOI: 10.1021/acscatal.5b00759


Sousa, SF; Coimbra, JTS; Fernandes, PA; Marino, T; Ramos, MJ; Russo, N

Molecular Dynamics Analysis of FAAH Complexed with Anandamide

FRONTIERS IN QUANTUM METHODS AND APPLICATIONS IN CHEMISTRY AND PHYSICS, 29: 56-67, 2015

DOI: 10.1007/978-3-319-14397-2_7


Cerqueira, NMFSA; Gesto, D; Oliveira, EF; Santos-Martins, D; Bras, NF; Sousa, SF; Fernandes, PA; Ramos, MJ

Receptor-based virtual screening protocol for drug discovery

ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 582: 56-67, 2015 (Review Article)

DOI: 10.1016/j.abb.2015.05.011


Pinto, GP; Ribeiro, AJM; Ramos, MJ; Fernandes, PA; Toscano, M; Russo, N

New insights in the catalytic mechanism of tyrosine ammonia-lyase given by QM/MM and QM cluster models

ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS, 582: 107-115, 2015

DOI: 10.1016/j.abb.2015.03.002

Shi, YX; Liang, RZ; Martin, KA; Weston, N; Gonzalez-Calera, S; Ganguly, R; Li, YX; Lu, YP; Ribeiro, AJM; Ramos, MJ; Fernandes, PA; Garcia, F

Synthesis and Hydrolytic Studies on the Air-Stable [(4-CN-PhO)(E)P(mu-(NBu)-Bu-t)](2) (E = O, S, and Se) Cyclodiphosphazanes

INORGANIC CHEMISTRY, 54 (13): 6423-6432, 2015

DOI: 10.1021/acs.inorgchem.5b00735

Ribeiro, AJM; Yang, LF; Ramos, MJ; Fernandes, PA; Liang, ZX; Hirao, H

Insight into Enzymatic Nitrile Reduction: QM/MM Study of the Catalytic Mechanism of QueF Nitrile Reductase

ACS CATALYSIS, 5 (6): 3740-3751, 2015

DOI: 10.1021/acscatal.5b00528


Pinto, GP; Bras, NF; Perez, MAS; Fernandes, PA; Russo, N; Ramos, MJ; Toscano, M

Establishing the Catalytic Mechanism of Human Pancreatic alpha-Amylase with QM/MM Methods

JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 11 (6): 2508-2516, 2015

DOI: 10.1021/acs.jctc.5b00222


Cerqueira, NMFSA; Coelho, C; Bras, NF; Fernandes, PA; Garattini, E; Terao, M; Romao, MJ; Ramos, MJ

Insights into the structural determinants of substrate specificity and activity in mouse aldehyde oxidases

JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY, 20 (2): 209-217, 2015

DOI: 10.1007/s00775-014-1198-2


Moreira, IS; Martins, JM; Coimbra, JTS; Ramos, MJ; Fernandes, PA

A new scoring function for protein-protein docking that identifies native structures with unprecedented accuracy

PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 17 (4): 2378-2387

DOI: 10.1039/c4cp04688a


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

Ligand based analysis on HMG-CoA reductase inhibitors

CHEMOMETRICS AND INTELLIGENT LABORATORY SYSTEMS, 140: 102-116, 2015

DOI: 10.1016/j.chemolab.2014.11.009




Copyright © 2014 Maria João Ramos