• Genetic diversity of the melanocortin-1 receptor in an admixed population of Rio de Janeiro: Structural and functional impacts of Cys35Tyr variant. PLoS One. NEITZKE-MONTINELLI, V.; GOMES, P.S.F.C.; PASCUTTI, P.G.; MOURA-NETO, R.S.; SILVA, R.

• A molecular docking integrated platform for virtual screening of bioactive compounds. BIOTECNOLOGÍA APLICADA. NARANJO-FELICIANO, D; ALVAREZ, L.I.; RAMOS, R.C.; ALVAREZ, L.H.; FIGUEROA, J.B.; GOMES, D.E.B.; VALIENTE, P.A.; CALVET, H.; PASCUTTI, P.G.
• A novel receptor for platelet-activating factor and lysophosphatidylcholine in Trypanosoma cruzi. MOLECULAR MICROBIOLOGY. COELHO, F.S.; FRAGOSO, S.P.; LOPES, A.H.; OLIVEIRA, M.M.; VIEIRA, D.P.; TORRES, P.H.M.; MOREIRA, I.C.F.; MARTINS-DUARTE, E.S.; GONÇALVES, I.C.; CABANELAS, A.; PASCUTTI, P.G.
• Computational study on the allosteric mechanism of Leishmania major IF4E-1 by 4E-interacting protein-1: Unravelling the determinants of m7GTP cap recognition. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL. ALVAREZ, L.H.; OLIVEIRA, A.B.; GONZÁLEZ, J.E.H.; CHAHINE, J.; PASCUTTI, P.G.; DE ARAUJO, A.S.; DE SOUZA, F.P.
• Improving Blind Docking in DOCK6 through an Automated Preliminary Fragment Probing Strategy. MOLECULES. JOFILY, P.; PASCUTTI, P.G.; TORRES, P.H.M.
• In silico identification of noncompetitive inhibitors targeting an uncharacterized allosteric site of falcipain-2. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN. GONZÁLEZ, J.E.H.; SALAS-SARDUY, E.; ALVAREZ, L.H.; GOMES, D.E.B.; PASCUTTI, P.G; OOSTENBRINK, C.; LEITE, V.B.P
• ProtCHOIR: a tool for proteome-scale generation of homo-oligomers. Briefings in Bioinformatics. TORRES, P.H.M.; ROSSI, A.D.; BLUNDELL, T.L.
• The p38 MAPK Inhibitors and Their Role in Inflammatory Diseases. ChemistrySelect. MACHADO, T.R.; MACHADO, T.R.; PASCUTTI, P.G.

• Enzymatic and structural properties of human glutamine:fructose-6-phosphate amidotransferase 2 (hGFAT2). JOURNAL OF BIOLOGICAL CHEMISTRY. OLIVEIRA, I.A.; ALLONSO, D.; FERNANDES, T.V.A.; LUCENA, D.M.S.; VENTURA, G.T.; DIAS, W.B.; MOHANA-BORGES, R.; PASCUTTI, P.G.; TODESCHINI, A.R.
• Physicochemical and structural properties of lunasin revealed by spectroscopic, chromatographic and molecular dynamics approaches. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS. DE SOUZA, S.M.A.; FERNANDES, T.V.A.; KALUME, D.E.; LIMA, L.M.T.R.; PASCUTTI, P.G.; DE SOUZA, T.L.F.
• Pisum sativum Defensin 1 Eradicates Mouse Metastatic Lung Nodules from B16F10 Melanoma Cells. INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES. DO AMARAL, V.S.G.; MONTEIRO, R.Q.; KURTENBACH, E.; SANTOS, S.A.C.S.; DE ANDRADE, P.C.; NOWATZKI, J.; JÚNIOR, N.S.; DE MEDEIROS, L.N.; GITIRANA, L.B.; PASCUTTI, P.G.; ALMEIDA, V.H.
• Theoretical studies and NMR assay of coumarins and neoflavanones derivatives as potential inhibitors of acetylcholinesterase. COMPUTATIONAL BIOLOGY AND CHEMISTRY. DE SOUZA, L.G.; MORAES, P.F.; LEÃO, R.A.C.; COSTA, P.R.R; SOARES, R.O.; PASCUTTI, P.G.; FIGUEROA-VILLAR, J.D.; RENNÓ, M.N.
• Water Bridges Play a Key Role in the Affinity and Selectivity for the Malarial Protease Falcipain-2. Journal of Chemical Information and Modeling. GONZALEZ, J.E.H.; ALVAREZ, L.H.; LEITE, V.B.P.; PASCUTTI, P.G.

• Dissecting a novel allosteric mechanism of cruzain: A computer-aided approach. PLoS One. ALVAREZ, L.H.; GOMES, D.E.B.; GONZÁLEZ, J.E.H.; PASCUTTI, P.G.
• Prediction of Non-Competitive Inhibitor Binding Mode Reveals Promising Site for Allosteric Modulation of Falcipain-2. JOURNAL OF PHYSICAL CHEMISTRY B. GONZALEZ, J.E.H.; ALVAREZ, L.H.; PASCUTTI, P.G.; LEITE, V.B.P.

• Identification of (4-(9H-fluoren-9-yl) piperazin-1-yl) methanone derivatives as falcipain 2 inhibitors active against Plasmodium falciparum cultures. BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS. GONZÁLEZ, J.E.; SALAS-SARDUY, E.; RAMÍREZ, L.F.H.; PASCUAL, M.J.; ÁLVAREZ, D.E.; PABÓN, A.; LEITE, V.B.P.; PASCUTTI, P.G.; VALIENTE, P.A.
• Investigation of the binding mode of a novel cruzain inhibitor by docking, molecular dynamics, ab initio and MM/PBSA calculations. JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN. MARTINS, L.C.; TORRES, P.H.M.; DE OLIVEIRA, R.B.; PASCUTTI, P.G.; CINO, E.A.; FERREIRA, R.S.

• Insights into cytochrome bc1 complex binding mode of antimalarial 2-hydroxy-1,4-naphthoquinones through molecular modelling. Memórias do Instituto Oswaldo Cruz. SODERO, A.C.R.; ABRAHIM-VIEIRA, B.; TORRES, P.H.M.; PASCUTTI, P.G.; GARCIA, C.R.S.; FERREIRA, V.F.; DA ROCHA, D.R.; FERREIRA, S.B.; SILVA JR, F.P.
• Predicting binding modes of reversible peptide-based inhibitors of falcipain-2 consistent with structure-activity relationships. PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS. GONZÁLEZ, J.E.H.; ALVAREZ, L.H.; PASCUTTI, P.G.; VALIENTE, P.A.

• Alternative Model for RND-Type Efflux Pump. JOURNAL OF THE BRAZILIAN CHEMICAL SOCIETY. TORRES, P.H.M.; PASCUTTI, P.G.; BISCH, P.M.; DA SILVA, M.L.
• Dataset showing the impact of the protonation states on molecular dynamics of HIV protease. DATA IN BRIEF. SOARES, R.O.; TORRES, P.H.M.; DA SILVA, M.L.; PASCUTTI, P.G.
• Insight on Mutation-Induced Resistance from Molecular Dynamics Simulations of the Native and Mutated CSF-1R and KIT. Plos One. GOMES, P.S.F.C.; DE BEAUCHÊNE, I.C.; PANEL, N.; LOPEZ, S.; DE SEPULVEDA, P.; PASCUTTI, P.G.; SOLARY, E.; TCHERTANOV, L.
• Machine Learning and Applications in Bioinformatics.. SEMIOSES (RIO DE JANEIRO). DIAS, M.F.R.; PASCUTTI, P.G.; DA SILVA, M.L.
• Non-competitive Inhibitor of Nucleoside Hydrolase from Leishmania donovani Identified by Fragment-based Drug Discovery. RSC Advances: an international journal to further the chemical sciences. ALVES, M.A.; LIMA, L.M.; TINOCO, L.; NIRMA, C.; MOREIRA, M.M.; SOARES, R.O.; PASCUTTI, P.G.; NOEL, F.; COSTA, P.; SANT?ANNA, C.; BARREIRO, E.J.
• Unraveling HIV Protease Flaps Dynamics by Constant pH Molecular Dynamics Simulations. Journal of Structural Biology (Print). SOARES, R.O.; TORRES, P.H.M.; DA SILVA, M.L.; PASCUTTI, P.G.

• Allosteric regulation of the Plasmodium falciparum cysteine protease falcipain-2 by heme. Archives of Biochemistry and Biophysics (Print). MARQUES, A.F.; GOMES, P.S.F.C; OLIVEIRA, P.L.; ROSENTHAL, P.J.; PASCUTTI, P.G.; LIMA, L.M.T.
• Insights into the Interactions of Fasciola hepatica Cathepsin L3 with a Substrate and Potential Novel Inhibitors through In Silico Approaches. PLoS Neglected Tropical Diseases (Online). ALVAREZ, L.H.; FELICIANO, D.N.; GONZÁLEZ, J.E.H.; SOARES, R.O.; GOMES, D.E.B.; PASCUTTI, P.G.
• Molecular Dynamics Simulations of the Free and Inhibitor-Bound Cruzain Systems in Aqueous Solvent: Insights on the Inhibition Mechanism in Acidic pH. Journal of Biomolecular Structure & Dynamics. HOELZ, L.V.B.; LEAL, V.F.; RODRIGUES, C.R.; PASCUTTI, P.G.; ALBUQUERQUE, M.G.; MURI, E.M.F.; DIAS, L.R.S.

• Anti-Prion Activity of a Panel of Aromatic Chemical Compounds: In Vitro and In Silico Approaches. Plos One. FERREIRA, N.C.; HUGHSON, A.G.; RAYMOND, L.D.; PASCUTTI, P.G.; CAUGHEY, B.; CORDEIRO, Y.; MARQUES, I.A.; CONCEIÇÃO, W.A.; MACEDO, B.; MACHADO, C.S.; MASCARELLO, A.; CHIARADIA-DELATORRE, L.D.; YUNES, R.A.; NUNES, R.J.
• Conformational Changes in Human Hsp70 Induced by High Hydrostatic Pressure Produce Oligomers with ATPase Activity but without Chaperone Activity. BIOCHEMISTRY. ARAUJO, T.L.S.; BORGES, J.C.; RAMOS, C.H.; MEYER-FERNANDES, J.R.; JUNIOR, R.S.O.; PASCUTTI, P.G.; FOGUEL, D.; PALHANO, F.L.
• Differential Effects of CSF-1R D802V and KIT D816V Homologous Mutations on Receptor Tertiary Structure and Allosteric Communication. Plos One. GOMES, P.S.F.C.; PANEL, N.; LAINE, E.; PASCUTTI, P.G.; SOLARY, E.; TCHERTANOV, L.
• Impact of M36I polymorphism on the interaction of HIV-1 protease with its substrates: insights from molecular dynamics. BMC Genomics. COSTA, M.G.S.; BENETTI-BARBOSA, T.G.; DESDOUITS, N.; BLONDEL, A.; BISCH, P.M.; PASCUTTI, P.G.; BATISTA, P.R.
• New treatments for Chagas disease and the relationship between chagasic patients and cancers. Cancer Research Journal. OLIVEIRA, V.M.; MENDES, L.T.; ALMEIDA, D.J.; HOELZ, L.V.B.; TORRES, P.H.M.; PASCUTTI, P.G.; FREITAS, G.B.L.
• Structural and Functional Analysis of a Platelet-Activating Lysophosphatidylcholine of Trypanosoma cruzi. PLoS Neglected Tropical Diseases (Online). GAZOS-LOPOES, F.; SOUTO-PADRON, T.; MONTEIRO, R.Q.; LOPES, A.H.; ALMEIDA, I.C.; OLIVEIRA, M.M.; HOELZ, L.V.B.; VIEIRA, D.P.; MARQUES, A.F.; NAKAYASU, E.S.; GOMES, M.T.; SALLOUM, N.G.; PASCUTTI, P.G.

• Desenvolvimento de ferramentas multimidiáticas para o ensino de bioquímica. Revista Práxis (Volta Redonda.Impresso). DIAS, G.S.; OLIVEIRA, F.S.; BIANCONI, M.L.; PASCUTTI, P.G.
• Receptores Acoplados à Proteína G. Revista Virtual de Química. HOELZ, L.V.B.; FREITAS, G.B.; TORRES, P.H.M.; FERNANDES, T.V.A.; SILVA, J.F.M.; ALBURQUERQUE, M.G.; PASCUTTI, P.G.; Alencastro R B
• Structural analysis of Pla protein from the biological warfare agent Yersinia pestis : docking and molecular dynamics of interactions with the mammalian plasminogen system. JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS. RUBACK, E.; LOBO, L.A.; FRANÇA, T.C.C.; PASCUTTI, P.G.

• GSAFold: A new application of GSA to protein structure prediction. Proteins (Print). MELO, M.C.R.; BERNARDI, R.C.; FERNANDES, T.V.A.; PASCUTTI, P.G.
• Hybrid QM/MM Molecular Dynamics Study of Benzocaine in a Membrane Environment: How Does a Quantum Mechanical Treatment of Both Anesthetic and Lipids Affect Their Interaction. Journal of Chemical Theory and Computation. BERNARDI, R.C.; PASCUTTI, P.G.
• Molecular Dynamics Simulations of Peptide Inhibitors Complexed With Trypanosoma cruzi Trypanothione Reductase. Chemical Biology & Drug Design. PITA, S.S.R.; BATISTA, P.R.; ALBUQUERQUE, M.G.; PASCUTTI, P.G.
• Pharmacophore Analysis of Trypanosoma cruzi Trypanothione Reductase (TR) Complexed with Peptide Mimetic Inhibitors. Revista Virtual de Química. PITA, S.S.R.; PASCUTTI, P.G.
• The role of helices 5 and 6 on the human β 1-adrenoceptor activation mechanism. Molecular Simulation (Print). HOELZ, L.V.B.; RIBEIRO, A.A.S.T.; BERNARDI, R.C.; HORTA, B.A.C.; ALBUQUERQUE, M.G.; DA SILVA, J.F.M.; PASCUTTI, P.G.; DE ALENCASTRO, R.B.
• The Structural Dynamics of the Flavivirus Fusion Peptide?Membrane Interaction. Plos One. MENDES, Y.S.; OLIVEIRA, A.C.; ALVES, N.S.; SOUZA, T.L.F.; SOUZA JR, I.P.; BIANCONI, M.L.; BERNARDI, R.C.; PASCUTTI, P.G.; SILVA, J.L.; SILVA, J.L.; GOMES, A.M.O.

• Alvos Terapêuticos na Doença de Chagas: a Tripanotiona Redutase como Foco. Revista Virtual de Química. PITA, S.S.R.; PASCUTTI, P.G.
• Computational Perspectives into Plasmepsins Structure-Function Relationship: Implications to Inhibitors Design. JOURNAL OF TROPICAL MEDICINE. GIL L., A.; VALIENTE, P.A.; PASCUTTI, P.G.; PONS, T.
• Conformational Variability of Organophosphorus Hydrolase upon Soman and Paraoxon Binding. Journal of Physical Chemistry. B. GOMES, D.E.B.; LINS, R.D.; PASCUTTI, P.G.; LEI, C.; SOARES, T.A.
• Dynamical behaviour of the human ? -adrenoceptor under agonist binding. Molecular Simulation (Print). HOELZ, L.V.B.; BERNARDI, R.C.; HORTA, B.A.C.; ARAÚJO, J.Q.; ALBUQUERQUE, M.G.; DA SILVA, J.F.M.; PASCUTTI, P.G.; DE ALENCASTRO, R.B.
• Free Energy Profiles along Consensus Normal Modes Provide Insight into HIV-1 Protease Flap Opening. Journal of Chemical Theory and Computation. BATISTA, P.R.; PANDEY, G.; PASCUTTI, P.G.; BISCH, P.M.; PERAHIA, D.; ROBERT, C.H.
• High temperatures enhance cooperative motions between CBM and catalytic domains of a thermostable cellulase: mechanism insights from essential dynamics. PCCP. Physical Chemistry Chemical Physics (Print). BATISTA, P.R.; Costa, M.G.S.; PASCUTTI, P.G.; BISCH, P.M.; DE SOUZA, W.
• Molecular dynamics simulations and QM/MM studies of the reactivation by 2-PAM of tabun inhibited human acethylcolinesterase. Journal of the Brazilian Chemical Society (Impresso). GONÇALVES, A.S.; FRANÇA, T.C.C.; FIGUEROA-VILLAR, J.D.; PASCUTTI, P.G.
• Structural analysis of the N-terminal fragment of the antiangiogenic protein endostatin: A molecular dynamics study. Proteins (Print). TORRES, P.H.; Sousa, G.L.S.C.; PASCUTTI, P.G.

• Conformational Analysis of Toxogonine, TMB-4 and HI-6 using PM6 and RM1 methods. Journal of the Brazilian Chemical Society (Impresso). GONÇALVES, A.S.; FRANÇA, T.C.C.; FIGUEROA-VILLAR, J.D.; PASCUTTI, P.G.
• Conformational selection, dynamic restriction and the hydrophobic effect coupled to stabilization of the BIR3 domain of the human X-linked inhibitor of apoptosis protein by the tetrapeptide AVPI. Biophysical Chemistry (Print). DE SOUZA, T.L.F.; SANCHES, D.; GONÇALVEZ, R.B.; PITA, S.S.R.; PASCUTTI, P.G.; BIANCONI, M.L.; DE ALMEIDA, F.C.L.; SILVA, J.L.; DE OLIVEIRA, A.C.
• Consensus modes, a robust description of protein collective motions from multiple-minima normal mode analysis¿application to the HIV-1 protease. PCCP. Physical Chemistry Chemical Physics. BATISTA, P.R.; ROBERT, C.H.; MARÉCHAL, J.D.; HAMIDA-REDAI, M.B.; PASCUTTI, P.G.; BISCH, P.M.; PERAHIA, D.
• Design, docking studies and molecular dynamics of new potential selective inhibitors of Plasmodium falciparum serine hydroxymethyltransferase. Molecular Simulation. DA SILVA, M.L.; GONÇALVES, A.S.; BATISTA, P.R.; FIGUEROA-VILLAR, J.D.; PASCUTTI, P.G.; FRANCA, T.C.C.
• How does heparin prevent the pH inactivation of cathepsin B? Allosteric mechanism elucidated by docking and molecular dynamics. BMC Genomics. COSTA, M.G.S.; BATISTA, P.R.; SHIDA, C.S.; ROBERT, C.H.; BISCH, P.M.; PASCUTTI, P.G.
• New parameterization approaches of the LIE method to improve free energy calculations of PlmII-Inhibitors complexes. Journal of Computational Chemistry. VALIENTE, P.A.; GIL L., A.; BATISTA, P.R.; CAFFARENA, E.R.; PONS, T.; PASCUTTI, P.G.
• Self-affine analysis of protein energy. PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS. FIGUEIRÊDO, P.H.; MORET, M.A.; PASCUTTI, P.G.; NOGUEIRA, E.; COUTINHO, S.
• Solvation of anionic water-soluble porphyrins: A computational study. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY. GUIZADO, T.R.C.; LOURO, S.R.W.; PASCUTTI, P.G.; ANTENEODO, C.
• The Role of Nonbonded Interactions in the Conformational Dynamics of Organophosphorous Hydrolase Adsorbed onto Functionalized Mesoporous Silica Surfaces. Journal of Physical Chemistry. B. GOMES, D.E.B.; LINS, R.D.; PASCUTTI, P.G.; LEI, C.; SOARES, T.A.
• Understanding the HIV-1 protease nelfinavir resistance mutation D30N in subtypes B and C through molecular dynamics simulations. Journal of Molecular Graphics & Modelling. SOARES, R.O.; BATISTA, P.R.; COSTA, M.G.S.; DARDENNE, L.E.; PASCUTTI, P.G.; SOARES, M.A.

• Dissociation of molecular aggregates under high hydrostatic pressure: the influence of water structure on Benzene cluster solubility. Journal of the Brazilian Chemical Society (Impresso). GONÇALVES, A.S.; CAFFARENA, E.R.; PASCUTTI, P.G.
• Molecular Dynamics Study of Biomembrane-Local Anesthetics Interactions. Molecular Physics. BERNARDI, R.C.; GOMES, D.E.B.; TAFT, C.A.; OTA, A.T.; PASCUTTI, P.G.
• Self-similarity and protein compactness. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics (Print). MORET, M.A.; SANTANA, M.C.; ZEBENDE, G.F.; PASCUTTI, P.G.

• Computational study of the solvation of protoporphyrin IX and its Fe 2+ complex. International Journal of Quantum Chemistry. GUIZADO, T.C.; PITA, S.R.; LOURO, S.R.W.; PASCUTTI, P.G.
• Molecular Models to Emulate Confinement Effects on the Internal Dynamics of Organophosphorous Hydrolase. Lecture Notes in Computer Science (LNCS). GOMES, D.E.B.; LINS, R.D.; PASCUTTI, P.G.; STRAATSMA, T.P.; SOARES, A.T.
• Predicting functional residues in Plasmodium falciparum plasmepsins by combining sequence and structural analysis with molecular dynamics simulations. Proteins. VALIENTE, P.A.; BATISTA, P.R.; PUPO, A.; PONS, T.; VALENCIA, A.; PASCUTTI, P.G.
• Studies of molecular docking between fibroblast growth factor and heparin using generalized simulated annealing. International Journal of Quantum Chemistry. PITA, S.S.R.; FERNANDES, T.V.A.; CAFFARENA, E.R.; PASCUTTI, P.G.

• Density functional and molecular dynamics simulations of local anesthetics in 0.9% NaCl solution. Molecular Simulation. BERNARDI, R.C.; GOMES, D.E.B.; ITO, A.S.; OTA, A.T.; PASCUTTI, P.G.; TAFT, C.
• Water solvent and local anesthetics: A computational study. International Journal of Quantum Chemistry. BERNARDI, R.C.; GOMES, D.E.B.; PASCUTTI, P.G.; ITO, A.S.; TAFT, C.A.; OTA, A.T.

• Classical and quantum conformational analysis using Generalized Genetic Algorithm. Physica. A. MORET, M.; PASCUTTI, P.G.; BISCH, P.M.; MUNDIM, M.; MUNDIM, K.
• Generalized simulated annealing applied to protein folding studies. Journal of Computational Chemistry. AGOSTINI, F.P.; SOARES-PINTO, D.O.; MORET, M.A.; OSTHOFF, C.; PASCUTTI, P.G.
• Molecular dynamics of the interaction of Plasmodium falciparum and human serine hydroxymethyltransferase with 5-formyl-6-hydrofolic acid analogues: design of new potential antimalarials. Journal of the Brazilian Chemical Society. FRANÇA, T.C.C.; WILTER, A.; RAMALHO, T.C.; PASCUTTI, P.G.; FIGUEROA-VILLAR, J.D.
• Molecular Dynamics Simulations Applied to the Study of Subtypes of HIV-1 Protease Common to Brazil, Africa, and Asia. Cell Biochemistry and Biophysics. BATISTA, P.R.; WILTER, A.; DURHAM, E.H.A.B.; PASCUTTI, P.G.
• Theoretical studies on water-tetracaine interaction. International Journal of Quantum Chemistry. BERNARDI, R.C.; GOMES, D.E.B.; PASCUTTI, P.G.; ITO, A.S.; OTA, A.T.

• A three-dimensional structure of serine hydroxymethyltransferase in complex with glycine and 5-formyl-tetrahydrofolate. Homology modeling and molecular dynamics. Biophysical Chemistry. FRANCA, T.; PASCUTTI, P.G.; RAMALHO, T.; FIGUEROA-VILLAR, J.
• Binding mode of e-64 to Malaria and Chagas disease cysteine proteases. European Biophysics Journal With Biophysics Letters. GOMES, D.E.B.; PASCUTTI, P.G.
• Mapping of important residues in interface area of Pla protein from Yersinia pestis with mammalian Plasmin(ogen) by Molecular Dynamics simulations. European Biophysics Journal With Biophysics Letters. SANTOS, E.R.D.O.S.; PASCUTTI, P.G.
• Peptide conformational search using Generalized Simulated Annealing method. European Biophysics Journal With Biophysics Letters. PASCUTTI, P.G.; AGOSTINI, F.P.; OSTHOFF, C.; MUNDIM, K.C.; MORET, M.A.
• Stochastic strategy to analyze protein folding. Physica. A. MORET, M.; BISCH, P.M,; NOGUEIRA JR, E.; PASCUTTI, P.G.
• Structural analysis of Pla protein from Y. pestis: Docking and molecular dynamics of interactions with mammalian plasminogen system. FEBS Journal. SANTOS, E.R.D.O.S.; PASCUTTI, P.G.
• The BioPAUÁ Project: A Portal for Molecular Dynamics Using Grid Environment. Lecture Notes in Computer Science. SILVA, A.W.S.D.A.; PASCUTTI, P.G.; OSTHOFF, C.; OLIVEIRA, C.; GOMES, D.E.B.; HILL, E.; DARDENNE, L.E.; BARROS, P.M.; LOUREIRO, P.A.L.; NOVAES, R.

• A Grid Alternative Solution for Protein Folding Studies Applications. Revista Tecnologia da Informação. AGOSTINI, F.P.; OSTHOFF, C.; VASSALO, A.; SOARES-PINTO, D.O.; PASCUTTI, P.G.
• Molecular dynamics simulations of a DPPC bilayer with a GROMOS parameter set optimized for long alkanes. European Biophysics Journal. LOUREIRO, P.A.; BISCH, P.M.; PASCUTTI, P.G.
• Nonspecific interaction forces at water-membrane interface by forced molecular dynamics simulations. Journal of Computational Chemistry. LORENZO, A.C.; PASCUTTI, P.G.; BISCH, P.M.

• Molecular Modeling and Dynamics of the Sodium Channel Inactivation Gate. Biophysical Journal. SIROTA, F.; PASCUTTI, P.G.; ANTENEODO, C.
• New Stochastic Strategy to Analyze Helix Folding. Biophysical Journal. MORET, M.; BISCH, P.M.; MUNDIM, K.C.; PASCUTTI, P.G.

• Molecular dynamics of the sodium channel inactivation gate in a dielectric discontinuity medium. Biophysical Journal. LEITE, F.S.; PASCUTTI, P.G.; ANTENEODO, C.
• Multifractality, Levinthal paradox, and energy hypersurface. Physical Review E - Statistical Physics, Plasmas, Fluids and Related Interdisciplinary Topics. MORET, M.A.; PASCUTTI, P.G.; MUNDIM, K.C.; BISCH, P.M.; NOGUEIRA, E.

• Molecular dynamics simulation of alfa-melanocyte stimulating hormone in a water-membrane model interfaces. European Biophysics Journal. PASCUTTI, P.G.; EL-JAIK, L.J.; MUNDIM, K.C.; ITO, A.S.; BISCH, P.M.
• Polarization effects on peptide conformations at water-membrane interface by molecular dynamics simulation. Journal of Computational Chemistry. PASCUTTI, P.G.; MUNDIM, K.C.; ITO, A.S.; BISCH, P.M.

• Stochastic molecular optimization using generalized simulated annealing. Journal of Computational Chemistry. MORET, M.A.; PASCUTTI, P.G.; BISCH, P.M.; MUNDIM, K.C.

• Molecular Dynamics Simulations of Peptide-Membrane Interactions. Biophysical Journal. PASCUTTI, P.G.; CASSIANO, M.M.; ITO, A.S.; BISCH, P.M.

• Molecular dynamics of peptides at membrane-water interfaces. Progress in Biophysics and Molecular Biology. PASCUTTI, P.G.; AÊAS, E.P.G.; ITO, A.S.; MUNDIM, K.C.; BISCH, P.M.

• Molecular Dynamics Simulations of Signal Sequences at a Membrane/Water Interface. JOURNAL OF PHYSICAL CHEMISTRY. AREAS, E.P.G.; PASCUTTI, P.G.; SCHREIER, S.; MUNDIM, K.C.; BISCH, P.M.
• On the contribution of electon transfer reactions to the quenching of triptophan fluorescence. Journal of Chemical Physics. GOLDMAN, C.; PASCUTTI, P.G.; PIQUINI, P.; ITO, A.S.

• Molecular dynamics at a cytoplasm/membrane interface of a signal sequence from an e.coli maltoporin. Brazilian Journal of Medical and Biological Research. ARÊAS, E.P.G.; PASCUTTI, P.G.; SCHREIER, S.; MUNDIM, K.C.; BISCH, P.M.

• EPR study of melanin-protein interaction: Photoinduced free radicals and progressive microwave power saturation. Journal of Photochemistry and Photobiology. B, Biology. PASCUTTI, P.G.; ITO, A.S.
• Kinetic studies of the photodecomposition of dipyridamole in solution: Interaction with lysophosphatidylcholine and bovine serum albumin. Spectrochimica Acta. Part A, Molecular Spectroscopy. BORISEVITCH, I.E.; PASCUTTI, P.G.; TABAK, M.