Publicações

Irina S. Moreira, Pedro Alexandrino Fernandes, Maria J. Ramos

Computational Alanine Scanning Mutagenesis – an improved methodological approach

J. Comput. Chem., Vol.28,
Pages 644-654, 2007

Sérgio F. Sousa, Pedro Alexandrino Fernandes, Maria J. Ramos

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, Vol.117,
Pages 171-181, 2007

Irina S. Moreira, Pedro Alexandrino Fernandes, Maria J. Ramos

Hot spots computational identification- application to the complex formed between the hen egg-white lysozyme (HEL) and the antibody HyHEL-10

Int. J. Quantum Chem.,
Nr.107, Pages 299-310, 2007

Alexandra T. P. Carvalho, Pedro Alexandrino Fernandes, Maria J. Ramos

Parameterization Of AZT- A Widely Used Nucleoside Inhibitor Of HIV-1 Reverse Transcriptase

Int. J. of Quantum Chem.,
Nr.107, Pages 292-298, 2007

Nuno M. F. S. A. Cerqueira, Pedro Alexandrino Fernandes, Maria João Ramos

Ribonucleotide Reductase Review – New insights in the gemcitabine inhibitory mechanism

Chemistry - A European Journal,
Nr.DOI: 10.1002/chem.200700260., 2007

Nuno M. F. S. A. Cerqueira, Pedro Alexandrino Fernandes, Maria João Ramos

Ribonucleotide Reductase Review – New insights in the gemcitabine inhibitory mechanism

Chemistry - A European Journal,
Nr.DOI: 10.1002/chem.200700260., 2007

Nuno M. F. S. A. Cerqueira, Pedro Alexandrino Fernandes, Maria João Ramos

Ribonucleotide Reductase: A critical enzyme for cancer chemotherapy and antiviral agents

Recent patents in anticancer research, Vol.2,
Pages 11-29, 2007

Sérgio F. Sousa, Pedro Alexandrino Fernandes, Maria J. Ramos

The carboxylate shift in zinc enzymes: a computational study

Journal of the American Chemical Society, Vol.129,
Pages 1378-1385, 2007

Sérgio F. Sousa, Pedro Alexandrino Fernandes, Maria J. Ramos

Theoretical Studies on Farnesyltransferase: The Distances Paradox Explained

Proteins: Structure, Function and Bioinformatics, Vol.66,
Pages 205-218, 2007

Irina S. Moreira, Pedro Alexandrino Fernandes, Maria J. Ramos

Unravelling Hot Spots - a comprehensive and exhaustive computational mutagenesis study

Theor. Chem. Acc.,
Nr.117, Pages 99-113, 2007

Irina S. Moreira, Pedro Alexandrino Fernandes, Maria J. Ramos

Vascular endothelial growth factor (VEGF) Inhibition - A Critical Review

Anticancer Agents Med. Chem., Vol.7,
Pages 223-245, 2007

Irina S. Moreira, Pedro Alexandrino Fernandes, Maria J. Ramos

Computational Determination of the Relative Free Energy of Binding- Application to Alanine Scanning Mutagenesis

Molecular Materials with Specific Interactions
Vol.4, W. Andrzej Sokalski (Editor), Springer,
2007

Irina S. Moreira, Pedro Alexandrino Fernandes, Maria J. Ramos

Accuracy of the Numerical Differentiation of the Poisson-Boltzmann Equation

J. Molec. Struct. - THEOCHEM,
Nr.729, Pages 11-18, 2006

Maria J. Ramos, Pedro Alexandrino Fernandes

Atomic-Level Rational Drug Design

Curr. Comput.-Aided Drug Design,
Nr.3, Pages 325, 2006

Bruno Tamames, Pedro Alexandrino Fernandes, Maria J. Ramos

Catalysis and Inhibition of HIV-1 Protease

Curr. Bioact. Compounds,
Nr.2, Pages 243, 2006

Alexandra T. Marques, Agostinho Antunes, Pedro Alexandrino Fernandes, Maria J. Ramos

Comparative evolutionary genomics of the HADH2 gene encoding amyloid beta-binding alcohol dehydrogenase/17beta-hydroxysteroid dehydrogenase type 10 (ABAD/HSD10)

BMC Genomics,
Nr.7, Pages 202, 2006

Susana Pereira, Pedro Alexandrino Fernandes, Maria J. Ramos

Computational Studies on Class I Ribonucleotide Reductase – Understanding the Mechanisms of Action and Inhibition of a Cornerstone Enzyme for the Treatment of Cancer

Eur. Biophys. J.,
Nr.35, Pages 125, 2006

Ricardo J. F. Branco, Pedro Alexandrino Fernandes, Maria J. Ramos

Cu, Zn Superoxide Dismutase: Distorted Active Site Binds Substrate With no Significant Energetic Cost

Theor. Chem. Acc.,
Nr.115, Pages 27, 2006

Nuno M. F. S. A. Cerqueira, Pedro Alexandrino Fernandes, Leif Eriksson, Maria J. Ramos

Dehydration Of Ribonucleotides Catalysed By Ribonucleotide Reductase: The Role Of The Enzyme

Biophys. J.,
Nr.90, Pages 2109, 2006

Irina S. Moreira, Pedro Alexandrino Fernandes, Maria J. Ramos

Detailed microscopic study of the full ZipA:FtsZ interface

Proteins,
Nr.63, Pages 811, 2006

Alexandra T. P. Carvalho, Pedro Alexandrino Fernandes, Maria J. Ramos

Determination of the ∆pKa between the active site cysteines of Thioredoxin and DsbA

J. Comput. Chem.,
Nr.27, Pages 966, 2006

Nuno M. F. S. A. Cerqueira, Pedro Alexandrino Fernandes, Maria J. Ramos

Enzyme Ribonucleotide Reductase:Unraveling an enigmatic paradigm of enzyme inhibition by furanone derivatives

J. Phys. Chem B.,
Nr.110, Pages 21272, 2006

Alexandra T. P. Carvalho, Pedro Alexandrino Fernandes, Maria J. Ramos

Insights on resistance of RT: The different patterns of interaction of NRTIs in the dNTP binding site relative to the normal substrate

J. Med. Chem., Vol.49,
Pages 7675, 2006

Pedro Alexandrino Fernandes, Araújo M. L. A. C., Barbosa, A. J. M., Alves C. N., Ferreira Z. Q., Gonzalez C. R.-N., Lima C. F. R. A. C., Loureiro S. I. E., Magalhães J. M. T., Maia F. C.,, Marta A. S. Perez, Peredo E. M. M., Sara A. Moura, Rodrigues T. A. Q., da Silva A. M. P., da Silva C. A. M., da Silva J. P. A., Maria J. Ramos

Lead Optimisation: Improving the Affinity of the Antiretrovirals Nelfinavir and Amprenavir for HIV-1 Protease

Lett. Drug Design & Discov.,
Nr.3, Pages 338, 2006

Alexandra T. P. Carvalho, Pedro Alexandrino Fernandes, Maria J. Ramos

Molecular Dynamics Model Of Unliganded HIV-1 Reverse Transcriptase

Med. Chem.,
Nr.2, Pages 491, 2006

Ricardo J. F. Branco, Pedro Alexandrino Fernandes, Maria N. D. S. Cordeiro, Maria J. Ramos

Molecular Dynamics Simulation of the Enzyme Cu,Zn Superoxide Dismutase

J. Phys. Chem. B, Vol.110,
Pages 16754, 2006

Alexandra T. P. Carvalho, Pedro Alexandrino Fernandes, Maria J. Ramos

Molecular Insights Into The Mechanisms Of HIV-1 Reverse Transcriptase Resistance To Nucleoside Analogues

Mini-Rev. Med. Chem.,
Nr.6, Pages 549, 2006

Sérgio F. Sousa, Pedro Alexandrino Fernandes, Maria J. Ramos

Protein–Ligand Docking: Current Status and Future Challenges

Proteins: Structure, Function and Bioinformatics, Vol.65,
Pages 15-26, 2006

Alexandra T. P. Carvalho, Pedro Alexandrino Fernandes, Maria J. Ramos

The complex similarities and differences within the members of the thioredoxin superfamily

Progress Byophys. Molec. Biol.,
Nr.91, Pages 229-248, 2006

Alexandra T. P. Carvalho, Pedro Alexandrino Fernandes, Maria J. Ramos

Theoretical Study of the Unusual Protonation Properties of the Active Site Cysteines in Thioredoxin

J. Phys. Chem. B,
Nr.110, Pages 5758, 2006

Irina S. Moreira, Pedro Alexandrino Fernandes, Maria J. Ramos

Unravelling 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”

J. Phys. Chem. B,
Nr.110, Pages 10962, 2006

Enzyme Ribonucleotide Reductase. The paradigm of enzyme inhibition by furanone derivatives

Vol.A61, Nuno M. F. S. A. Cerqueira (Editor), Pedro Alexandrino Fernandes (Editor), Maria João Ramos (Editor), Acta. cryst.,
Nr.C496 – 497, 2005

Ricardo J. F. Branco, Pedro Alexandrino Fernandes, Maria J. Ramos

Density-Functional Calculations of the Cu, Zn Superoxide Dismutase Redox Potential: The Influence of Active Site Distortion

J. Molec. Struct. - THEOCHEM,
Nr.729, Pages 141, 2005

Nuno M. F. S. A. Cerqueira, Pedro Alexandrino Fernandes, Maria J. Ramos

Enzyme Ribonucleotide Reductase. The paradigm of enzyme inhibition by furanone derivatives

Acta. Cryst., Vol.A61,
Pages C496 – 497, 2005

Sérgio F. Sousa, Pedro Alexandrino Fernandes, Maria J. Ramos

Farnesyltransferase - New Insights into the Zinc-Coordination Sphere Paradigm: Evidence for a Carboxylate-Shift Mechanism

Biophysical Journal, Vol.88,
Pages 483-494, 2005

Sérgio F. Sousa, Pedro Alexandrino Fernandes, Maria J. Ramos

Farnesyltransferase: Theoretical studies on peptide substrate entrance thiol or thiolate coordination?

Journal of Molecular Structure - THEOCHEM, Vol.729,
Pages 125-129, 2005

Maria J. Ramos, Alexandre L. Magalhães, André Melo, Pedro Alexandrino Fernandes

Foreward

Journal of Molecular Structure (Theochem), Vol.729,
Pages vii, 2005

Maria J. Ramos, Pedro Alexandrino Fernandes

Modeling and Research in the Classroom

J. Chem. Ed.,
Nr.82, Pages 1021, 2005

Pedro Alexandrino Fernandes, Ana R. R. Maia, André A. S. Almeida, Bruno F. B. Silva, Carla M. S. Ribeiro, César F. B. Ribeiro, David S. M. Ribeiro, Diana A.P. Fonseca, Elsa S. Henriques, Eva M. S. Cunha, Filipe R. N. C. Maia, Joana A. A. Pereira, João P. G. Pacheco, Joaquim A. A. D., Maria J. Ramos

New Designs For Inhibitors of the NF-kB:DNA Binding

Theor. Chem. Acc.,
Nr.113, Pages 197, 2005

Nuno M. F. S. A. Cerqueira, Susana Pereira, Pedro Alexandrino Fernandes, Maria J. Ramos

Overview of Ribonucleotide Reductase Inhibitors: an Appealing Target in Anti Cancer Therapy

Curr. Med. Chem.,
Nr.12, Pages 1283, 2005

Susana Pereira, Pedro Alexandrino Fernandes, Maria J. Ramos

Theoretical Study on the Inhibition of Ribonucleotide Reductase by 2’-mercapto-2’-deoxyribonucleoside-5’-diphosphates

J. Am. Chem. Soc.,
Nr.127, Pages 5174, 2005

Sérgio Filipe Sousa, Pedro Alexandrino Fernandes, Maria João Ramos

Unravelling the Mechanism of the Farnesyltransferase Enzyme

Journal of Biological Inorganic Chemistry, Vol.10,
Pages 3-10, 2005

Pedro Alexandrino Fernandes, Ana I. S. Cruz, Ana R. R. Maia, André A. S. Almeida, André M. N. da Silva, Bruno F. B. Silva, Carla M. S. Ribeiro, César F. B. Ribeiro, Eva M. S. Cunha, Filipe R. N. C. Maia, João A. C. Tedim, Joaquim A. A. D. Ferreira, Lígia C. Gomes, Liliana R. C. Matos

Design of 2-Cyclopentenone Derivatives with Enhanced NF-kB:DNA Binding Inhibitory Properties

J. Molec. Struct. - THEOCHEM,
Nr.685, Pages 73, 2004

Susana Pereira, Pedro Alexandrino Fernandes, Maria João Ramos

Mechanism for Ribonucleotide Reductase Inactivation by the Anticancer Drug Gemcitabine

J. Comput. Chem.,
Nr.25, Pages 1286, 2004

Pedro Alexandrino Fernandes, André Melo, Maria João Ramos

Modelling chemical and biological systems. A successful course for undergraduates

Journal of Chemical Education, Vol.81,
Pages 72-75, 2004

Nuno M. F. S. A. Cerqueira, Pedro Alexandrino Fernandes, Leif Eriksson, Maria João Ramos

Ribonucleotide Activation by Enzyme Ribonucleotide Reductase: Understanding the Role of the Enzyme

J. Comput. Chem.,
Nr.25, Pages 2031, 2004

Pedro Alexandrino Fernandes, Maria João Ramos

Theoretical Insights into the Mechanism for Thiol/Disulfide Exchange

Chem. Eur. J.,
Nr.10, Pages 257, 2004

Susana Pereira, Pedro Alexandrino Fernandes, Maria João Ramos

Theoretical Study of Ribonucleotide Reductase Mechanism-Based Inhibition by 2’-azido-2’-deoxyribonucleoside 5’-diphosphates

J. Comput. Chem.,
Nr.25, Pages 227, 2004

Nuno M. F. S. A. Cerqueira, Pedro Alexandrino Fernandes, Leif Eriksson, Maria João Ramos

Theoretical Study of the Mechanism of Ribonucleotide Reductase: New insights into a critical biological control step

J. Molec. Struct. – THEOCHEM,
Nr.709, Pages 53, 2004

Pedro J. Silva, Pedro Alexandrino Fernandes, Maria João Ramos

A theoretical study of radical-only and combined radical-carbocationic mechanisms of arachidonic acid cyclooxygenation by prostaglandin H synthase

Theor. Chem. Acc.,
Nr.110, Pages 345, 2003

Pedro Alexandrino Fernandes, Alexandra T. P. Carvalho, Alexandra T. Marques, A. L. Pereira, A. P. Madeira, A. S. Ribeiro, A. Carvalho, E. Ricardo, F. Pinto, H. Santos, H. Mangericão, H. Martins, H. Pinto, H. Santos, Irina S. Moreira, M. J. Azeredo, R. Abreu, R. Oliveira, S. Sousa, R. Silva, Z. Mourão, Maria J. Ramos

New Design for MRI Contrast Agents

J. Comp. Aided Mol. Design,
Nr.17, Pages 463, 2003

Maria F. A. Lucas, Pedro Alexandrino Fernandes, Maria João Ramos

Piruvate Formate Lyase: A New Perspective

J. Phys. Chem. B.,
Nr.107, Pages 5751, 2003

Pedro Alexandrino Fernandes, Maria João Ramos

Theoretical Studies on the Mechanism of Inhibition of Ribonucleotide Reductase by (E)-2’-Fluoromethylene-2’-deoxycitidine-5’-diphosphate

J. Am. Chem. Soc.,
Nr.125, Pages 6311, 2003

Pedro Alexandrino Fernandes, Maria João Ramos

Theoretical Studies on the Paradigm of Inhibition of Ribonucleotide Reductase by 2’-Substituted Substrate Analogs

Chem. Eur. J.,
Nr.9, Pages 5961, 2003

Pedro Alexandrino Fernandes, Leif Eriksson, Maria João Ramos

The Reduction of Ribonucleotides Catalysed by the Enzyme Ribonucleotide Reductase

Theor. Chem. Acc.,
Nr.108, Pages 352, 2002

Pedro Alexandrino Fernandes, Maria J. Ramos

Simulação Computacional de SIstemas Químicos e Biológicos

Internet, 2002

Influence of the Supporting Electrolyte in the Properties of Liquid|Liquid Interfaces

Modeling Complex Systems - 6th Granada Lectures on Computational Physic
Vol.574, Maria N. D. S. Cordeiro (Editor), Pedro Alexandrino Fernandes (Editor), Jose A. N. F. Gomes (Editor), American Institute of Physics,
Nr.254, 2001

Pedro Alexandrino Fernandes, Maria N. D. S. Cordeiro, Jose A. N. F. Gomes

The Liquid|Liquid Interface Across Two Immiscible Electrolyte Solutions

J. Phys. Chem. B,
Nr.105, Pages 981, 2001

Pedro Alexandrino Fernandes

2. Reacções de Transferência Iónica Através de Interfaces entre Líquidos Imiscíveis

Faculdade de Ciências da Universidade do Porto, 2000

Jose A. N. F. Gomes, Pedro Alexandrino Fernandes, Maria N. D. S. Cordeiro

Simulation of Liquid|Liquid Interfaces and Ion Transfer

Abstracts of papers of the American Chemical Society, Vol.,220,
Pages 46-COLL, 2000

Pedro Alexandrino Fernandes, Maria N. D. S. Cordeiro, Jose A. N. F. Gomes

Transfer of Ions Across a Liquid|Liquid Interface: Investigation of the Influence of the Ion's Size and Charge by Molecular Dynamics Simulations

J. Phys. Chem. B,
Nr.104, Pages 2278, 2000

Pedro Alexandrino Fernandes, Maria N. D. S. Cordeiro, Jose A. N. F. Gomes

Molecular Dynamics Simulation of Liquid|2-Heptanone, Pure and Saturated with Water

J. Phys. Chem. B,
Nr.103, Pages 1176, 1999

Pedro Alexandrino Fernandes, Maria N. D. S. Cordeiro, Jose A. N. F. Gomes

Molecular Dynamics Simulation of the Water|1,2- dichloroethane Interface

J. Molec. Struct. - THEOCHEM,
Nr.463, Pages 151, 1999

Pedro Alexandrino Fernandes, Maria N. D. S. Cordeiro, Jose A. N. F. Gomes

Molecular Dynamics Simulation of the Water|2-Heptanone Liquid|liquid Interface

J. Phys. Chem. B,
Nr.103, Pages 6290, 1999

Pedro Alexandrino Fernandes, Maria N. D. S. Cordeiro, Maria João Ramos

Molecular Dynamics Study of the Transfer of Iodide Ion Across Two Liquid|liquid Interfaces

J. Phys. Chem. B,
Nr.103, Pages 8960, 1999

Pedro Alexandrino Fernandes, Alfredo P. Carvalho, João P. P. Ramalho

Path Integral Monte Carlo Simulations: Study of the Efficiency of Energy Estimators

J. Chem. Phys.,
Nr.103, Pages 5720, 1995