Artigos Publicados

• Exploring the folding landscape of leptin: Insights into threading pathways.

da Silva, F. B., Simien, J. M., Viegas, R. G., Haglund, E., & Leite, V. B. P. (2024).

Journal of Structural Biology. https://doi.org/10.1016/j.jsb.2023.108054

• Exploring the molecular pathways of the activation process in PPARγ recurrent bladder cancer mutants. 

de Oliveira, V. M., Malospirito, C. C., da Silva, F. B., Videira, N. B., Dias, M. M. G., Sanches, M. N., Leite, V. B. P., & Figueira, A. C. M. (2024).

The Journal of Chemical Physics. https://doi.org/10.1063/5.0232041

• Molecular dynamics simulations illuminate the role of sequence context in the ELF3-PrD-based temperature sensing mechanism in plants. 

Lindsay, R. J., Viegas, R. G., Leite, V. B., Wigge, P. A., & Hanson, S. M. (2024). 

ELife. https://doi.org/10.7554/elife.102410.1

• Probing Mastoparan-like Antimicrobial Peptides Interaction with Model Membrane Through Energy Landscape Analysis. 

Martins, I. B. S., Viegas, R. G., Sanches, M. N., de Araujo, A. S., & Leite, V. B. P. (2024).

Journal of Physical Chemistry B. https://doi.org/10.1021/acs.jpcb.3C05852

• Forensic analysis of microtraces using image recognition through machine learning.

Rodrigues, C. H. P., Sousa, M. D. da C., dos Santos, M. A., Filho, P. A. F., Velho, J. A., Leite, V. B. P., & Bruni, A. T. (2024).

Microchemical Journal. https://doi.org/10.1016/j.microc.2024.111780

• Understanding the Energy Landscape of Intrinsically Disordered Protein Ensembles.

Viegas, R. G., Martins, I. B. S., & Leite, V. B. P. (2024). 

Journal of Chemical Information and Modeling. https://doi.org/10.1021/acs.jcim.4C00080

• ELViM: Exploring Biomolecular Energy Landscapes through Multidimensional Visualization.

Viegas, R. G., Martins, I. B. S., Sanches, M. N., Oliveira Junior, A. B., Camargo, J. B. de, Paulovich, F. v., & Leite, V. B. P. (2024). 

Journal of Chemical Information and Modeling. https://doi.org/10.1021/acs.jcim.4C00034

• Probing the Energy Landscape of Spectrin R15 and R16 and the Effects of Non-native Interactions.

da Silva, F. B., Martins de Oliveira, V., de Oliveira Junior, A. B., Contessoto, V. de G., & Leite, V. B. P. (2023).

The Journal of Physical Chemistry B, 6. https://doi.org/10.1021/acs.jpcb.2c06178

• Processing of Composite Electrodes of Carbon Nanotube Fabrics and Inorganic Matrices via Rapid Joule Heating.

da Silva, F. B., Martins de Oliveira, V., de Oliveira Junior, A. B., Contessoto, V. de G., & Leite, V. B. P. (2023b). 

Journal of Physical Chemistry B. https://doi.org/10.1021/acs.jpcb.2C06178

• Unveiling Metastable Ensembles of GRB2 and the Relevance of Interdomain Communication during Folding.

Dias, R. V. R., Pedro, R. P., Sanches, M. N., Moreira, G. C., Leite, V. B. P., Caruso, I. P., de Melo, F. A., & de Oliveira, L. C. (2023). 

Journal of Chemical Information and Modeling. https://doi.org/10.1021/acs.jcim.3C00955

• Exploring the Folding Mechanism of Dimeric Superoxide Dismutase.

Mouro, P. R., Sanches, M. N., Leite, V. B. P., & Chahine, J. (2023).

Journal of Physical Chemistry B. https://doi.org/10.1021/acs.jpcb.2C08877

• Characterizing the Folding Transition-State Ensembles in the Energy Landscape of an RNA Tetraloop. 

Viegas, R. G., Sanches, M. N., Chen, A. A., Paulovich, F. v., Garcia, A. E., & Leite, V. B. P. (2023).

Journal of Chemical Information and Modeling. https://doi.org/10.1021/acs.jcim.3C00426

• PH and the Breast Cancer Recurrent Mutation D538G Affect the Process of Activation of Estrogen Receptor α.

de Oliveira, V. M., Dias, M. M. G., Avelino, T. M., Videira, N. B., da Silva, F. B., Doratioto, T. R., Whitford, P. C., Leite, V. B. P., & Figueira, A. C. M. (2022).

Biochemistry. https://doi.org/10.1021/acs.biochem.1C00806

• Intrinsically disordered proteins: Ensembles at the limits of Anfinsen’s dogma.

Kulkarni, P., Leite, V. B. P., Roy, S., Bhattacharyya, S., Mohanty, A., Achuthan, S., Singh, D., Appadurai, R., Rangarajan, G., Weninger, K., Orban, J., Srivastava, A., Jolly, M. K., Onuchic, J. N., Uversky, V. N., & Salgia, R. (2022).

Biophysics Reviews. https://doi.org/10.1063/5.0080512

• Examining the Ensembles of Amyloid-β Monomer Variants and Their Propensities to Form Fibers Using an Energy Landscape Visualization Method.

Sanches, M. N., Knapp, K., Oliveira, A. B., Wolynes, P. G., Onuchic, J. N., & Leite, V. B. P. (2022). 

Journal of Physical Chemistry B. https://doi.org/10.1021/acs.jpcb.1C08525

• Resolving the fine structure in the energy landscapes of repeat proteins.

Sanches, M. N., Parra, R. G., Viegas, R. G., Oliveira, A. B., Wolynes, P. G., Ferreiro, D. U., & Leite, V. B. P. (2022). 

QRB Discovery. https://doi.org/10.1017/qrd.2022.4

• Coarse-Grained Simulations of Protein Folding: Bridging Theory and Experiments. 

Contessoto, V. G., de Oliveira, V. M., & Leite, V. B. P. (2022). 

Methods in Molecular Biology. https://doi.org/10.1007/978-1-0716-1716-8_16

• Examining the Ensembles of Amyloid-β Monomer Variants and Their Propensities to Form Fibers Using an Energy Landscape Visualization Method. 

Sanches, M. N., Knapp, K., Oliveira, A. B., Wolynes, P. G., Onuchic, J. N., & Leite, V. B. P. (2022). 

Journal of Physical Chemistry B. https://doi.org/10.1021/acs.jpcb.1C08525

• Small Neutral Crowding Solute Effects on Protein Folding Thermodynamic Stability and Kinetics.

Contessoto, V. G., Ferreira, P. H. B., Chahine, J., Leite, V. B. P., & Oliveira, R. J. (2021).

Journal of Physical Chemistry B. https://doi.org/10.1021/acs.jpcb.1C07663

• Electrostatic interaction optimization improves catalytic rates and thermotolerance on xylanases.

de Godoi Contessoto, V., Ramos, F. C., de Melo, R. R., de Oliveira, V. M., Scarpassa, J. A., de Sousa, A. S., Zanphorlin, L. M., Slade, G. G., Leite, V. B. P., & Ruller, R. (2021). 

Biophysical Journal. https://doi.org/10.1016/j.bpj.2021.03.036

• Protein conformational dynamics and phenotypic switching.

Kulkarni, P., Achuthan, S., Bhattacharya, S., Jolly, M. K., Kotnala, S., Leite, V. B. P., Mohanty, A., Orban, J., Roy, S., Rangarajan, G., & Salgia, R. (2021).

Biophysical Reviews 2021 13:6. https://doi.org/10.1007/S12551-021-00858-X

• Improving the thermostability of xylanase a from bacillus subtilis by combining bioinformatics and electrostatic interactions optimization. 

Ngo, K., da Silva, F. B., Leite, V. B. P., Contessoto, V. G., & Onuchic, J. N. (2021). 

Journal of Physical Chemistry B. https://doi.org/10.1021/acs.jpcb.1C01253

• In silico Evaluation of Cucurbit[6]uril as a Potential Detector for Cocaine and Its Adulterants Lidocaine, Caffeine, and Procaine. 

Rodrigues, C. H. P., Hernández-González, J. E., Pedrina, N. J., Leite, V. B. P., & Bruni, A. T. (2021). 

Journal of the Brazilian Chemical Society. https://doi.org/10.21577/0103-5053.20200231

• Can NMR spectroscopy discriminate between NPS amphetamines and cathinones? An evaluation by in silico studies and chemometrics.

Rodrigues, C. H. P., Leite, V. B. P., & Bruni, A. T. (2021).

Chemometrics and Intelligent Laboratory Systems. https://doi.org/10.1016/j.chemolab.2021.104265

• Synthetic fentanyls evaluation and characterization by infrared spectroscopy employing in silico methods.

Sinhorini, L. F. C., Rodrigues, C. H. P., Leite, V. B. P., & Bruni, A. T. (2021). 

Computational and Theoretical Chemistry. https://doi.org/10.1016/j.comptc.2021.113378

• In silico identification of noncompetitive inhibitors targeting an uncharacterized allosteric site of falcipain-2.

Hernández González, J. E., Salas-Sarduy, E., Hernández Alvarez, L., Barreto Gomes, D. E., Pascutti, P. G., Oostenbrink, C., & Leite, V. B. P. (2021). 

Journal of Computer-Aided Molecular Design. https://doi.org/10.1007/s10822-021-00420-7

• Rational Design of Chymotrypsin Inhibitor 2 by Optimizing Non-Native Interactions. 

B. Da Silva, F., M. De Oliveira, V., Sanches, M. N., Contessoto, V. G., & Leite, V. B. P. (2020). 

Journal of Chemical Information and Modeling. https://doi.org/10.1021/acs.jcim.9B00911

• PH and Charged Mutations Modulate Cold Shock Protein Folding and Stability: A Constant pH Monte Carlo Study.

de Oliveira, V. M., Caetano, D. L. Z., da Silva, F. B., Mouro, P. R., de Oliveira, A. B., de Carvalho, S. J., & Leite, V. B. P. (2020). 

Journal of Chemical Theory and Computation. https://doi.org/10.1021/acs.jctc.9B00894

• Modeling Chikungunya control strategies and Mayaro potential outbreak in the city of Rio de Janeiro. 

Dodero-Rojas, E., Ferreira, L. G., Leite, V. B. P., Onuchic, J. N., & Contessoto, V. G. (2020). 

PLOS ONE. https://doi.org/10.1371/journal.pone.0222900

• Water bridges play a key role in Affinity and Selectivity for Malarial Protease Falcipain-2. 

Hernández González, J. E., Hernández Alvarez, L., Leite, V. B. P., & Pascutti, P. G. (2020). 

Journal of Chemical Information and Modeling. https://doi.org/10.1021/acs.jcim.0C00294

• Exploring Folding Aspects of Monomeric Superoxide Dismutase. 

Mouro, P. R., Povinelli, A. P. R., Leite, V. B. P., & Chahine, J. (2020). 

Journal of Physical Chemistry B. https://doi.org/10.1021/acs.jpcb.9B09640

• Prediction of Noncompetitive Inhibitor Binding Mode Reveals Promising Site for Allosteric Modulation of Falcipain-2.

Hernández González, J. E., Hernández Alvarez, L., Pascutti, P. G., & Leite, V. B. P. (2019). 

Journal of Physical Chemistry B. https://doi.org/10.1021/acs.jpcb.9B05021

• Distinguishing Biomolecular Pathways and Metastable States. 

Oliveira, A. B., Yang, H., Whitford, P. C., & Leite, V. B. P. (2019). 

Journal of Chemical Theory and Computation. https://doi.org/10.1021/acs.jctc.9B00704

• Diffusion of tRNA inside the ribosome is position-dependent. 

Yang, H., Bandarkar, P., Horne, R., Leite, V. B. P., Chahine, J., & Whitford, P. C. (2019).

Journal of Chemical Physics. https://doi.org/10.1063/1.5113814

• Non-Native Cooperative Interactions Modulate Protein Folding Rates.

Bruno Da Silva, F., Contessoto, V. G., de Oliveira, V. M., Clarke, J., & Leite, V. B. P. (2018). 

Journal of Physical Chemistry B. https://doi.org/10.1021/acs.jpcb.8B08990

• In silico methods in forensic science: Quantum chemistry and multivariate analysis applied to infrared spectra of new amphetamine- and cathinone-derived psychoactive substances. 

Bruni, A. T., de Carvalho, P. O. M., Rodrigues, C. H. P., & Leite, V. B. P. (2018). 

Forensic Chemistry. https://doi.org/10.1016/j.forc.2018.03.006

• Introduction to the Protein Folding Problem: An Approach Using Simplified Computational Models.

Contessoto, V. de G., Junior, A. B. de O., Chahine, J., de Oliveira, R. J., & Leite, V. B. P. (2018). 

Revista Brasileira de Ensino de Física. https://doi.org/10.1590/1806-9126-RBEF-2018-0068

• TKSA-MC: A web server for rational mutation through the optimization of protein charge interactions.

Contessoto, V. G., de Oliveira, V. M., Fernandes, B. R., Slade, G. G., & Leite, V. B. P. (2018). 

Proteins: Structure, Function, and Bioinformatics. https://doi.org/10.1002/prot.25599

• Identification of (4-(9H-fluoren-9-yl) piperazin-1-yl) methanone derivatives as falcipain 2 inhibitors active against Plasmodium falciparum cultures.

Hernández-González, J. E., Salas-Sarduy, E., Hernández Ramírez, L. F., Pascual, M. J., Álvarez, D. E., Pabón, A., Leite, V. B. P., Pascutti, P. G., & Valiente, P. A. (2018).

Biochimica et Biophysica Acta (BBA) - General Subjects. https://doi.org/10.1016/j.bbagen.2018.09.015

• Effects of pH and Salt Concentration on Stability of a Protein G Variant Using Coarse-Grained Models.

Martins de Oliveira, V., Godoi Contessoto, V. de, Bruno da Silva, F., Zago Caetano, D. L., Jurado de Carvalho, S., & Pereira Leite, V. B. (2018).

Biophysical Journal. https://doi.org/10.1016/j.bpj.2017.11.012

• Differential Expression Analysis in RNA-seq Data Using a Geometric Approach.

Tambonis, T., Boareto, M., & Leite, V. B. P. (2018). 

Journal of Computational Biology. https://doi.org/10.1089/cmb.2017.0244

• Cold Shock Protein A from Corynebacterium pseudotuberculosis: Role of Electrostatic Forces in the Stability of the Secondary Structure.

Eberle, R., Arni, R., Kawai, L., Leite, V., Contessoto, V., Oliveira, V., Caruso, I., & Coronado, M. (2017). 

Protein & Peptide Letters. https://doi.org/10.2174/0929866524666170207153808

• NTL9 folding at constant pH: The importance of electrostatic interaction and pH dependence.

Contessoto, V. G., de Oliveira, V. M., de Carvalho, S. J., Oliveira, L. C., & Leite, V. B. P. (2016). 

Journal of Chemical Theory and Computation. https://doi.org/10.1021/acs.jctc.6B00399

• Quantifying Nonnative Interactions in the Protein-Folding Free-Energy Landscape. 

Mouro, P. R., de Godoi Contessoto, V., Chahine, J., Junio de Oliveira, R., & Pereira Leite, V. B. (2016). 

Biophysical Journal. https://doi.org/10.1016/j.bpj.2016.05.041

• Supervised Variational Relevance Learning, an analytic geometric feature selection with applications to omic datasets. 

Boareto, M., Cesar, J., Leite, V. B. P., & Caticha, N. (2015). 

IEEE/ACM Transactions on Computational Biology and Bioinformatics. https://doi.org/10.1109/tcbb.2014.2377750

• Analysis of the procedures used to evaluate suicide crime scenes in Brazil: A statistical approach to interpret reports.

Bruni, A. T., Velho, J. A., Ferreira, A. S. L., Tasso, M. J., Ferrari, R. S., Yoshida, R. L., Dias, M. S., & Leite, V. B. P. (2014). 

Journal of Forensic and Legal Medicine. https://doi.org/10.1016/j.jflm.2014.06.004

• Inferring a weighted elastic network from partial unfolding with coarse-grained simulations. 

de Mendonça, M. R., Rizzi, L. G., Contessoto, V., Leite, V. B. P., & Alves, N. A. (2014).

Proteins: Structure, Function, and Bioinformatics. https://doi.org/10.1002/prot.24381

• Probing Diffusive and Energetic Aspects of Ribosome Function. 

Noel, J. K., Leite, V. B. P., Chahine, J., & Whitford, P. C. (2014).

Biophysical Journal. https://doi.org/10.1016/j.bpj.2013.11.3369

• Capturing Transition Paths and Transition States for Conformational Rearrangements in the Ribosome.

Noel, J.K., Chahine, J., Leite, V. B. P., & Whitford, P. C. (2014).

Biophysical Journal. https://doi.org/10.1016/J.BPJ.2014.10.022

• Visualization of Protein Folding Funnels in Lattice Models. 

Oliveira, A. B., Fatore, F. M., Paulovich, F. v., Oliveira, O. N., & Leite, V. B. P. (2014). 

PLOS ONE. https://doi.org/10.1371/journal.pone.0100861

• Analyzing the effect of homogeneous frustration in protein folding.

Contessoto, V. G., Lima, D. T., Oliveira, R. J., Bruni, A. T., Chahine, J., & Leite, V. B. P. (2013).

Proteins: Structure, Function, and Bioinformatics. https://doi.org/10.1002/.24309

• Assembling a xylanase–lichenase chimera through all-atom molecular dynamics simulations.

Cota, J., Oliveira, L. C., Damásio, A. R. L., Citadini, A. P., Hoffmam, Z. B., Alvarez, T. M., Codima, C. A., Leite, V. B. P., Pastore, G., de Oliveira-Neto, M., Murakami, M. T., Ruller, R., & Squina, F. M. (2013). 

Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. https://doi.org/10.1016/j.bbapap.2013.02.030

• Modelo de Marcus, elementos de matriz de tunelamento, efeitos de solvente e controle nuclear em reações de transferência de elétrons.

de Paula, L. C., de Andrade, P. C. P., & Leite, V. B. P. (2013). 

Revista Brasileira de Ensino de Física. https://doi.org/10.1590/S1806-11172013000200015

• Characterization of a hexameric exo-acting GH51 α-l- arabinofuranosidase from the mesophilic bacillus subtilis.

Hoffmam, Z. B., Oliveira, L. C., Cota, J., Alvarez, T. M., Diogo, J. A., de Oliveira Neto, M., Citadini, A. P. S., Leite, V. B. P., Squina, F. M., Murakami, M. T., & Ruller, R. (2013). 

Molecular Biotechnology. https://doi.org/10.1007/S12033-013-9677-1

• The characterization of a thermostable and cambialistic superoxide dismutase from Thermus filiformis. 

Mandelli, F., Franco Cairo, J. P. L., Citadini, A. P. S., Büchli, F., Alvarez, T. M., Oliveira, R. J., Leite, V. B. P., Paes Leme, A. F., Mercadante, A. Z., & Squina, F. M. (2013). 

Letters in Applied Microbiology. https://doi.org/10.1111/lam.12071

• Relationship between global structural parameters and Enzyme Commission hierarchy: Implications for function prediction.

Boareto, M., Yamagishi, M. E. B., Caticha, N., & Leite, V. B. P. (2012)

Computational Biology and Chemistry. https://doi.org/10.1016/j.compbiolchem.2012.06.003

• Topography of funneled landscapes determines the thermodynamics and kinetics of protein folding.

Wang, J., Oliveira, R. J., Chu, X., Whitford, P. C., Chahine, J., Han, W., Wang, E., Onuchic, J. N., & Leite, V. B. P. (2012).

Proceedings of the National Academy of Sciences of the United States of America. https://doi.org/10.1073/pnas.1212842109

• Configuration-dependent diffusion dynamics of downhill and two-state protein folding. 

Xu, W., Lai, Z., Oliveira, R. J., Leite, V. B. P., & Wang, J. (2012). 

Journal of Physical Chemistry B. https://doi.org/10.1021/jp212132v

• Coordinate and time-dependent diffusion dynamics in protein folding.

Oliveira, R. J., Whitford, P. C., Chahine, J., Leite, V. B. P., & Wang, J. (2010). 

Methods. https://doi.org/10.1016/j.ymeth.2010.04.016

• The origin of nonmonotonic complex behavior and the effects of nonnative interactions on the diffusive properties of protein folding. 

Oliveira, R. J., Whitford, P. C., Chahine, J., Wang, J., Onuchic, J. N., & Leite, V. B. P. (2010).

Biophysical Journal. https://doi.org/10.1016/J.BPJ.2010.04.041

2010-2014

• Statistics and kinetics of single-molecule electron transfer dynamics in complex environments: A simulation model study. 

Paula, L. C., Wang, J., & Leite, V. B. P. (2008). 

Journal of Chemical Physics. https://doi.org/10.1063/1.3036421

• Configuration-dependent diffusion can shift the kinetic transition state and barrier height of protein folding.

Chahine, J., Oliveira, R. J., Leite, V. B. P., & Wang, J. (2007). 

Proceedings of the National Academy of Sciences. https://doi.org/10.1073/PNAS.0606506104

• Long term economic relationships from cointegration maps.

Vicente, R., Pereira, C. de B., Leite, V. B. P., & Caticha, N. (2007). 

Physica A: Statistical Mechanics and Its Applications. https://doi.org/10.1016/j.physa.2007.02.067

• Underlying dynamics of typical fluctuations of an emerging market price index: The Heston model from minutes to months. 

Vicente, R., de Toledo, C. M., Leite, V. B. P., & Caticha, N. (2006). 

Physica A: Statistical Mechanics and Its Applications. https://doi.org/10.1016/j.physa.2005.06.095

• Frustration and hydrophobicity interplay in protein folding and protein evolution. 

Oliveira, L. C., Silva, R. T. H., Leite, V. B. P., & Chahine, J. (2006). 

Journal of Chemical Physics. https://doi.org/10.1063/1.2335638

• Single molecule electron transfer dynamics in complex environments. 

Leite, V. B. P., Alonso, L. C. P., Newton, M., & Wang, J. (2005). 

Physical Review Letters. https://doi.org/10.1103/physrevlett.95.118301

• Probing the kinetics of single molecule protein folding. 

Leite, V. B. P., Onuchic, J. N., Stell, G., & Wang, J. (2004). 

Biophysical Journal. https://doi.org/10.1529/biophysj.104.046243

• Water at interfaces and its influence on the electrical properties of adsorbed films. 

Oliveira, O. N., Riul, A., & Leite, V. B. P. (2004).

Brazilian Journal of Physics. https://doi.org/10.1590/S0103-97332004000100011

• The energy landscape for solvent dynamics in electron transfer reactions: A minimalist model. 

Tanimura, Y., Leite, V. B. P., & Onuchic, J. N. (2002).

The Journal of Chemical Physics, 117(5), 2172–2179. https://doi.org/10.1063/1.1488588

• Conformational analysis: A new approach by means of chemometrics.

Bruni, A. T., Leite, V. B. P., & Ferreira, M. M. C. (2002). 

Journal of Computational Chemistry. https://doi.org/10.1002/JCC.10004

• Specific and Nonspecific Collapse in Protein Folding Funnels.

Chahine, J., Nymeyer, H., Leite, V. B., Socci, N. D., Socci, N. D., & Onuchic, J. N. (2002). 

Physical Review Letters. https://doi.org/10.1103/PhysRevLett.88.168101

• Soliton model for proton conductivity in Langmuir films.

Bazeia, D., Leite, V. B. P., Lima, B. H. B., & Moraes, F. (2001).

Chemical Physics Letters. https://doi.org/10.1016/S0009-2614(01)00425-0

• Electron transfer between adjacent layers in self-assembled films.

Leite, V. B. P., Ferreira, M., & Oliveira, O. N. (2000). 

Chemical Physics Letters. https://doi.org/10.1016/S0009-2614(99)01343-3