andre.melo

André Alberto de Sousa Melo
Assistant Professor
Integrated Member
Research Group
Theoretical & Computational Biochemistry
Departamento de Química e Bioquímica, Faculdade de Ciências da Universidade do Porto, Rua do Campo Alegre, 4169-007 Porto, Portugal
220 402 503
- ext 30503
Research Interests
Quantum calculations

Molecular simulations

Ionic liquids

Molecular association processes
Main publications
Teixeira, F., Melo, A., Cordeiro, M.N.D.S., “Aza-Diels-Alder addition of cyclopentadiene to propynyliminoglyoxylates”, Computational and Theoretical Chemistry, 1012, 54-59 (2013).

Luan, F., Melo, A., Borges, F., Cordeiro, M.N.D.S., “Affinity prediction on A3 adenosine receptor antagonists: The chemometric approach”, Bioorganic and Medicinal Chemistry, 19, 6853-6859 (2011).

Lima, C.F.R.A.C., Rocha, M.A.A., Melo, A., Gomes, L.R., Low, J.N., Santos, L.M.N.B.F., “Structural and thermodynamic characterization of polyphenylbenzenes”, Journal of Physical Chemistry A, 115, 11876-11888 (2011).

Carvalho, A.R.F., Oliveira, J., De Freitas, V., Mateus, N., Melo, A., “On the contribution of intramolecular kinetics properties of an important rotamer of vinylpyranoanthocyanin-phenol pigment (portisin)”, International Journal of Quantum Chemistry, 111 (7-8), 1355-1360 (2011).

Teixeira, F., Melo, A., Cordeiro, M.N.D.S., “Response to Comment on Uncertainties in scaling factors for ab initio vibrational zero-point energies' and Calibration sets and the accuracy of vibrational scaling factors: A case study with the X3LYP hybrid functional' [J. Chem. Phys. 134, 167101 (2011)]”, Journal of Chemical Physics, 134, art. no. 167103, (2011).

Gaspar, A., Teixeira, F., Uriarte, E., Milhazes, N., Melo, A., Cordeiro, M.N.D.S., Ortuso, F., Alcaro, S., Borges, F., “Towards the Discovery of a Novel Class of Monoamine Oxidase Inhibitors: Structure-Property-Activity and Docking Studies on Chromone Amides”, ChemMedChem, 6, 628-632 (2011).

Marques, J.R.F., da Fonseca, R.R., Drury, B., Melo, A., “Conformational characterization of disulfide bonds: A tool for protein classification”, Journal of Theoretical Biology, 267, 388-395 (2010).

Marques, J.R.F., da Fonseca, R.R., Drury, B., Melo, A., “Amino acid patterns around disulfide bonds” International Journal of Molecular Sciences, 11, 4673-4686 (2010).

Lima, C.F.R.A.C., Sousa, C.A.D., Rodriguez-Borges, J.E., Melo, A., Gomes, L.R., Low, J.N., Santos, L.M.N.B.F., “The role of aromatic interactions in the structure and energetics of benzyl ketones”, Physical Chemistry Chemical Physics, 12 (37), 11228-11237 (2010).

Teixeira, F., Melo, A., Cordeiro, M.N.D.S., “Calibration sets and the accuracy of vibrational scaling factors: A case study with the X3LYP hybrid functional”, Journal of Chemical Physics, 133, art. no. 114109 (2010).

Carvalho, A.R.F., Melo, A., ”Quantum Semiempirical Energy Based (SEEB) descriptors performance with benzamidine inhibitors of trypsin”, Molecular Informatics, 29, 525-531 (2010).

Carvalho, A.R.F., Oliveira, J., Freitas, V.d., Mateus, N., Melo, A., “A theoretical interpretation of the color of two classes of pyranoanthocyanins”, Journal of Molecular Structure: THEOCHEM, 948, 61-64 (2010).

Mourão, Z.S., Melo, A., “Energy decomposition analysis of cis and trans isomers of 1,2-dihaloethylenes and 2-butene”, Journal of Molecular Structure: THEOCHEM, 946, 7-12 (2010).

Carvalho, A.R.F., Oliveira, J., de Freitas, V., Silva, A., Mateus, N., Melo, A., “A computational study of vinylpyranoanthocyanin-phenolic pigments (portisins)”, Journal of Molecular Structure: THEOCHEM, 946, 113-118 (2010).

Carvalho, A.R.F., Oliveira, J., De Freitas, V., Mateus, N., Melo, A., “Unusual color change of vinylpyranoanthocyanin?phenolic pigments”, Journal of Agricultural and Food Chemistry, 58, 4292-4297 (2010)

Teixeira, F., Rodríguez-Borges, J.E., Melo, A., Cordeiro, M.N.D.S., “Stereoselectivity of the aza-Diels-Alder reaction between cyclopentadiene and protonated phenylethylimine derived from glyoxylates. A density functional theory study”, Chemical Physics Letters, 477, 60-64 (2009).

Preto, M.A.C., Melo, A., Rodrigues, L.M., Maia, H.L.S., Ramos, M.J., “Structural insight on the activity of type 1 angiotensin II peptide antagonists using MD simulations”, Journal of Physical Chemistry B, 112, 13620-13628 (2008).

Carvalho, A.R.F., Puga, A.T., Melo, A., “Exact and effective pair-wise potential for protein-ligand interactions obtained from a semiempirical energy partition”, International Journal of Molecular Sciences, 9, 1652-1664 (2008).

da Fonseca, R.R., Antunes, A., Melo, A., Ramos, M.J., “Structural divergence and adaptive evolution in mammalian cytochromes P450 2C”, Gene, 387, 58-66 (2007).

da Fonseca, R., Melo, A., Iori, F., Menziani, C., Ramos, M.J., “Molecular interactions between human cytochrome P450 1A2 and flavone derivatives”, Medicinal Chemistry, 2, 401-406 (2006).

Melo, A., Alfaia, A.J.I., Reis, J.C.R., Calado, A.R.T., “Unusual solvent effect on a SN2 reaction. A quantum-mechanical and kinetic study of the menshutkin reaction between 2-amino-l- methylbenzimidazole and iodomethane in the gas phase and in acetonitrile”, Journal of Physical Chemistry B, 110, 1877-1888 (2006).

Preto, M.A.C., Melo, A., Maia, H.L.S., Mavromoustakos, T., Ramos, M.J., “Molecular dynamics simulations of angiotensin II in aqueous and dimethyl sulfoxide environments”, Journal of Physical Chemistry B, 109, 17743-17751 (2005).

Ramos, M.J., Magalhães, A.L., Melo, A.S., Fernandes, P.A., “Foreword”, Journal of Molecular Structure: THEOCHEM, 729 (2005).

Carvalho, A.R.F., Melo, A., “Energy partitioning in association processes”, International Journal of Quantum Chemistry, 104, 240-248 (2005).

da Fonseca, R., Marini, M., Melo, A., Menziani, M.C., Ramos, M.J.
Computational insight into anti-mutagenic properties of CYP1A flavonoid ligands”, Medicinal chemistry, 1, 355-360 (2005).

Ramos, M.J., Fernandes, P.A., Melo, A., “Modeling chemical and biological systems: A successful course for undergraduate students”, Journal of Chemical Education, 81, 72-75 (2004).

Preto, M.A.C., Melo, A., Costa, S.P.G., Maia, H.L.S., Ramos, M.J., “Parametrization of Synthetic Amino Acids”, Journal of Physical Chemistry B, 107, 14556-14562 (2003).

Da Fonseca, R., Menziani, M.C., Melo, A., Ramos, M.J., “Modelling the metabolic action of human and rat CYP1A2 and its relationship with the carcinogenicity of heterocyclic amines”, Molecular Physics, 101 (17), 2731-2741 (2003).

Mateus, N., Carvalho, E., Carvalho, A.R.F., Melo, A., González-Paramás, A.M., Santos-Buelga, C., Silva, A.M.S., De Freitas, V., “Isolation and structural characterization of new acylated anthocyanin-vinyl-flavanol pigments occurring in aging red wines”, Journal of Agricultural and Food Chemistry, 51, 277-282 (2003).

Melo, A., Ramos, M.J., “Theoretical study of the amino acid interactions in the binding region of the trypsin-pancreatic trypsin inhibitor complex”, Journal of Molecular Structure: THEOCHEM, 580, 251-262 (2002).

Ramos, M.J., Melo, A., Henriques, E.S., “Modelling enzyme - Ligand interactions”, in "Theoretical biochemistry - processes and properties of biological systems", Theoretical and Computational Chemistry Book Series, Vol. 9, L. A. Eriksson (Editor), Elsevier, Amsterdam, 539-595, (2001).

Henriques, E.S., Floriano, W.B., Reuter, N., Melo, A., Brown, D., Gomes, J.A.N.F., Maigret, B., Nascimento, M.A.C., Ramos, M.J., “The search for a new model structure of β-factor XIIa”, Journal of Computer-Aided Molecular Design, 15, 309-322 (2001).

Melo, A., Puga, A.T., Gentil, F., Brito, N., Alves, A.P., Ramos, M.J., “Byte Structure Variable Length Coding (BS-VLC): A New Specific Algorithm Applied in the Compression of Trajectories Generated by Molecular Dynamics”, Journal of Chemical Information and Computer Sciences, 40, 559-566 (2000)

Ramos, M.J., Melo, A., Henriques, E.S., Gomes, J.A.N.F., Reuter, N., Maigret, B., Floriano, W.B., Nascimento, M.A.C., “Modeling enzyme-inhibitor interactions in serine proteases”, International Journal of Quantum Chemistry, 74, 299-314 (1999).

Melo, A., Ramos, M.J., “A new partitioning scheme for molecular interacting systems within a multiconfigurational or monoconfigurational Hartree-Fock formalism”, International Journal of Quantum Chemistry, 72, 157-176 (1999)

Melo, A., Ramos, M.J., Floriano, W.B., Gomes, J.A.N.F., Leao, J.F.R., Magalhaes, A.L., Maigret, B., Nascimento, M.C., Reuter, N., “Theoretical study of arginine-carboxylate interactions”, Journal of Molecular Structure: THEOCHEM, 463, 81-90 (1999)

Melo, A., Ramos, M.J., “The nature of trypsin-pancreatic trypsin inhibitor binding: Free energy calculation of Tyr39 → Phe39 mutation in trypsin", Journal of Peptide Research, 50, 382-387 (1997).

Melo, A., Ramos, M.J., “Proton transfer in arginine-carboxylate interactions”, Chemical Physics Letters, 245, 498-502 (1995).

Melo, A., Gomes, J.A.N.F. G., "Theoretical study of ionization potentials in monosubstituted benzenes", International Journal of Quantum Chemistry, 46, 651-669 (1993).