Publications 2017

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 2017-2018

Fernandes, HS; Ramos, MJ; Cerqueira, NMFSA
Catalytic Mechanism of the Serine Hydroxymethyltransferase: A Computational ONIOM QM/MM Study
ACS CATALYSIS, 8: 10096-10110, 2018
DOI: 10.1021/acscatal.8b02321

Medina, FE; Neves, RPP; Ramos, MJ; Fernandes, PA
QM/MM Study of the Reaction Mechanism of the Dehydratase Domain from Mammalian Fatty Acid Synthase
ACS CATALYSIS, 8: 10267-10278, 2018
DOI: 10.1021/acscatal.8b02616

Ramos, MJ; Fernandes, PA
Structure, Dynamics, and Energetics of ATP Hydrolysis by ABC Transporters
ACS CENTRAL SCIENCE, 4: 1300-1302, 2018
DOI: 10.1021/acscentsci.8b00631

Barbosa, ACC; Neves, RPP; Sousa, SF; Ramos, MJ; Fernandes, PA
Mechanistic Studies of a Flavin Monooxygenase: Sulfur Oxidation of Dibenzothiophenes by DszC
ACS CATALYSIS, 8: 9298-9311, 2018
DOI: 10.1021/acscatal.8b01877

Silva, AMN; Coimbra, JTS; Castro, MM; Oliveira, A; Bras, NF; Fernandes, PA; Ramos, MJ; Rangel, M
Determining the glycation site specificity of human holo-transferrin
JOURNAL OF INORGANIC BIOCHEMISTRY, 186: 95-102, 2018
DOI: 10.1016/j.jinorgbio.2018.05.016

Simoes, ICM; Coimbra, JTS; Neves, RPP; Costa, IPD; Ramos, MJ; Fernandes, PA
Properties that rank protein: protein docking poses with high accuracy
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 20: 20927-20942, 2018
DOI: 10.1039/c8cp03888k

Friedman, R; Khalid, S; Aponte-Santamaria, C; Arutyunova, E; Becker, M; Boyd, KJ; Christensen, M; Coimbra, JTS; Concilio, S; Daday, C; van Eerden, FJ; Fernandes, PA; Grater, F; Hakobyan, D; Heuer, A; Karathanou, K; Keller, F; Lemieux, MJ; Marrink, SJ; May, ER; Mazumdar, A; Naftalin, R; Pickholz, M; Piotto, S; Pohl, P; Quinn, P; Ramos, MJ; Schiott, B; Sengupta, D; Sessa, L; Vanni, S; Zeppelin, T; Zoni, V; Bondar, AN; Domene, C
Understanding Conformational Dynamics of Complex Lipid Mixtures Relevant to Biology
JOURNAL OF MEMBRANE BIOLOGY, 251: 609-631, 2018
DOI: 10.1007/s00232-018-0050-y

Bras, NF; Fernandes, PA; Ramos, MJ
Understanding the Rate-Limiting Step of Glycogenolysis by Using QM/MM Calculations on Human Glycogen Phosphorylase
CHEMMEDCHEM, 13: 1608-1616, 2018
DOI: 10.1002/cmdc.201800218

Dalla Torre, G; Mujika, JI; Formoso, E; Matito, E; Ramos, MJ; Lopez, X
Tuning the affinity of catechols and salicylic acids towards Al(III): characterization of Al-chelator interactions
DALTON TRANSACTIONS, 47, 9592-9607, 2018
DOI: 10.1039/c8dt01341a

Fernandes, HS; Ramos, MJ; Cerqueira, NMFSA
molUP: A VMD plugin to handle QM and ONIOM calculations using the gaussian software
JOURNAL OF COMPUTATIONAL CHEMISTRY, 39, 1344-1353, 2018
DOI: 10.1002/jcc.25189

Paiva, P; Sousa, SF; Ramos, MJ; Fernandes, PA
Understanding the Catalytic Machinery and the Reaction Pathway of the Malonyl-Acetyl Transferase Domain of Human Fatty Acid Synthase
ACS CATALYSIS, 8, 4860-4872, 2018
DOI: 10.1021/acscatal.8b00577

Biernacki, K; Sousa, SF; Gales, L; Ramos, MJ; Magalhaes, AL
Transport Properties of Light Gases in Nanochannels of L-Leu-L-Ser Dipeptide Crystals: A Comparative Study by Molecular Dynamics Simulations
CHEMISTRYSELECT, 3, 5517-5525, 2018
DOI: 10.1002/slct.201800559

Paiva, P; Costa, IPD; Ferreira, CE; Ferreira, P; Pereira, AT; Cerqueira, NMFSA; Fernandes, PA; Ramos, MJ
Studies on neuraminidase inhibition
INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, 118, SI e25592, 2018
DOI: 10.1002/qua.25592

Santos-Martins, D; Calixto, AR; Fernandes, PA; Ramos, MJ
A Buried Water Molecule Influences Reactivity in a alpha-Amylase on a Subnanosecond Time Scale
ACS CATALYSIS, 8, 4055-406, 2018
DOI: 10.1021/acscatal.7b04400

Ferreira, P; Cerqueira, NMFSA; Bras, NF; Fernandes, PA; Ramos, MJ
Parametrization of Molybdenum Cofactors for the AMBER Force Field
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 14, 2538-2548, 2018
DOI: 10.1021/acs.jctc.8b00137

Zuniga, MA; Alderete, JB; Jana, GA; Fernandez, PA; Ramos, MJ; Jimenez, VA
Modulation of lateral and longitudinal interdimeric interactions in microtubule models by Laulimalide and Peloruside A association: A molecular modeling approach on the mechanism of microtubule stabilizing agents
CHEMICAL BIOLOGY & DRUG DESIGN, 91, 1042-1055, 2018
DOI: 10.1111/cbdd.13168

Jana, GA; Mendoza, F; Osorio, MI; Alderete, JB; Fernandes, PA; Ramos, MJ; Jimenez, VA
A QM/MM approach on the structural and stereoelectronic factors governing glycosylation by GTF-SI from Streptococcus mutans
ORGANIC & BIOMOLECULAR CHEMISTRY, 16, 2438-2447, 2018
DOI: 10.1039/c8ob00284c

Bras, NF; Santos-Martins, D; Fernandes, PA; Ramos, MJ
Mechanistic Pathway on Human alpha-Glucosidase Maltase-Glucoamylase Unveiled by QM/MM Calculations
JOURNAL OF PHYSICAL CHEMISTRY B, 122, 3889-3899, 2018
DOI: 10.1021/acs.jpcb.8b01321

Almeida, JR; Mendes, B; Lancellotti, M; Marangoni, S; Vale, N; Passos, O; Ramos, MJ; Fernandes, PA; Gomes, P; Da Silva, SL
A novel synthetic peptide inspired on Lys49 phospholipase A(2) from Crotalus oreganus abyssus snake venom active against multidrug-resistant clinical isolates
EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY, 149, 248-256, 2018
DOI: 10.1016/j.ejmech.2018.02.055

Cerqueira, NMFSA; Fernandes, PA; Ramos, MJ
Protocol for Computational Enzymatic Reactivity Based on Geometry Optimisation
CHEMPHYSCHEM, 19, 669-689, 2018
DOI: 10.1002/cphc.201700339

Cerqueira, NMFSA; Fernandes, PA; Ramos, MJ
Visualizing the Microscopic World
INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES, 10: 105-110, 2018
DOI: 10.1007/s12539-017-

Bras, NF; Fernandes, PA; Ramos, MJ; Schwartz, SD
Mechanistic Insights on Human Phosphoglucomutase Revealed by Transition Path Sampling and Molecular Dynamics Calculations
CHEMISTRY-A EUROPEAN JOURNAL, 24: 1978-1987, 2018
DOI: 10.1002/chem.201705090

Viegas, MF; Neves, RPP; Ramos, MJ; Fernandes, PA
Modeling of Human Fatty Acid Synthase and &ITin Silico&IT Docking of Acyl Carrier Protein Domain and Its Partner Catalytic Domains
JOURNAL OF PHYSICAL CHEMISTRY B, 122: 77-85, 2018
DOI: 10.1021/acs.jpcb.7b09645

Coimbra, JTS; Bras, NF; Fernandes, PA; Rangel, M; Ramos, MJ Membrane partition of bis-(3-hydroxy-4pyridinonato) zinc(ii) complexes revealed by molecular dynamics simulations
RSC ADVANCES, 8: 27081-27090, 2018
DOI: 10.1039/c8ra03602k

Ferreira, P; Sousa, SF; Fernandes, PA; Ramos, MJ
Improving the Catalytic Power of the DszD Enzyme for the Biodesulfurization of Crude Oil and Derivatives
CHEMISTRY-A EUROPEAN JOURNAL, 23: 17231-17241, 2017
DOI: 10.1002/chem.201704057 Published: DEC 6 2017

Calixto, AR; Ramos, MJ; Fernandes, PA
Influence of Frozen Residues on the Exploration of the PES of Enzyme Reaction Mechanisms
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 13: 5486-5495, 2017

Moreira, C; Ramos, MJ; Fernandes, PA
Clarifying the Catalytic Mechanism of Human Glutamine Synthetase: A QM/MM Study
JOURNAL OF PHYSICAL CHEMISTRY B, 121: 6313-6320, 2017
DOI: 10.1021/acs.jpcb.7b02543

Sousa, CF; Coimbra, JTS; Ferreira, M; Ramos, MJ; Fernandes, PA; Gameiro, P
Exploring the permeation of free and copper-complexed fluoroquinolones across the bacterial membrane
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 46: S269-S269, 2017

alpha-Glucosidase inhibition by flavonoids: an in vitro and in silico structure-activity relationship study
Proenca, C; Freitas, M; Ribeiro, D; Oliveira, EFT; Sousa, JLC; Tome, SM; Ramos, MJ; Silva, AMS; Fernandes, PA; Fernandes, E
JOURNAL OF ENZYME INHIBITION AND MEDICINAL CHEMISTRY, 32: 1216-1228, 2017
DOI: 10.1080/14756366.2017.1368503