Marcelo D. Polêto

@usp.br

Research Associate - Department of Biotechnology
Universidade de São Paulo

Marcelo D. Polêto


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https://researchid.co/mdpoleto

RESEARCH, TEACHING, or OTHER INTERESTS

Biochemistry, Physical and Theoretical Chemistry, Biophysics, Renewable Energy, Sustainability and the Environment
31

Scopus Publications

752

Scholar Citations

13

Scholar h-index

17

Scholar i10-index

Scopus Publications

  • Weighted Ensemble Simulations With the Drude Polarizable Model
    Marcelo D. Polêto, Gabriel Monteiro da Silva, Brenda M. Rubenstein, Justin A. Lemkul
    Journal of Computational Chemistry, 2025
    Enhanced sampling methods have become powerful techniques to investigate complex systems and rare molecular events by facilitating greater access to configurational space. In parallel, the continuous development of polarizable force fields augments such techniques, allowing the investigation of the role of electronic polarization in transitional barriers that might be overlooked in nonpolarizable simulations. Together, improved sampling methods and polarizable force fields should accelerate computational discoveries. Here, we present an implementation of a weighted ensemble strategy for the Drude polarizable force field using the WESTPA software package in conjunction with the OpenMM simulation engine. We demonstrate its use for backbone conformational sampling in a model system (alanine dipeptide) and in studying functional sidechain rotations in an enzyme (Abl1 kinase). We further discuss possible consequences related to the inclusion of explicit electronic polarization in the model. This software implementation and validation should facilitate the use of WESTPA‐Drude strategies throughout the simulation community.
  • Structural Modeling of NTPDase-Substrate Complexes Preserving Catalytic Experimental Features
    João Victor B. de Moraes, Marcelo D. Polêto, Raissa B. de Castro, Gustavo C. Bressan, Raphael de S Vasconcellos, Jean Sévigny, Juliana R. Fietto
    ACS Omega, 2025
    High Resolution Image Download MS PowerPoint Slide Members of the ecto-nucleoside triphosphate diphosphohydrolase (E-NTPDase) family play a pivotal role in hydrolyzing nucleoside triphosphates and diphosphates, modulating purinergic and pyrimidinergic signaling pathways. The NTPDases have therapeutic potential; gaining structural insights into NTPDase-substrate complexes would be valuable for optimizing these enzymes for therapeutic applications. However, such insights remain limited, posing challenges for effective optimization. Molecular docking often fails to capture experimentally characterized substrate conformations, leading to biologically irrelevant models. To address this, we developed a computational strategy that preserves experimentally observed substrate features while leveraging the active site’s conservation across NTPDases. Our method identifies a canonical linear-like substrate conformation encompassing the phosphate tail and nucleobase ring conserved across experimental NTPDase structures. This approach enabled the modeling of Homo sapiens (Hs) NTPDases (HsNTPDase1–8) complexed with ATP, ADP, GTP, GDP, UTP, and UDP, accurately positioning metal ion cofactor and catalytic water molecules. The resulting models offer a reliable framework for studying enzyme–substrate interactions, paving the way for rational enzyme engineering and therapeutic exploration.
  • Structural and Electronic Properties of Poly(ethylene terephthalate) (PET) from Polarizable Molecular Dynamics Simulations
    Marcelo D. Polêto, Justin A. Lemkul
    Macromolecules, 2025
    The environmental and economic challenges posed by the widespread use and disposal of plastics, particularly poly(ethylene terephthalate) (PET), require innovative solutions to mitigate their impact. Such mitigation begins with understanding physical properties of the polymer that could enable new recycling technologies. Although molecular simulations have provided valuable insights into PET interactions with various PET hydrolases, current nonpolarizable force fields neglect the electronic polarization effects inherent to PET interactions. Here, we present parameters for PET polymer and its derivatives that are compatible with the Drude polarizable force field. Our parameter fitting protocol accurately reproduces electrostatic properties from quantum mechanical calculations. We then studied electronic properties of PET amorphous slabs and PET crystal units, revealing a crucial electronic polarization response of PET residues at the interface with water or vacuum, yielding insights into the modulation of electrostatic properties by solvent molecules. Finally, we showcase the interaction between a carbohydrate-binding protein and the PET crystal unit, revealing the role of electronic polarization in enhancing binding affinity. This study represents the first extension of the Drude polarizable force field to a synthetic polymer, offering a robust tool for exploring PET material properties and advancing the design of efficient (bio)technologies for addressing plastic pollution.
  • Synthesis of new non-natural l-glycosidic flavonoid derivatives and their evaluation as inhibitors of Trypanosoma cruzi ecto-nucleoside triphosphate diphosphohydrolase 1 (TcNTPDase1)
    Isadora Cunha Ribeiro, João Victor Badaró de Moraes, Christiane Mariotini-Moura, Marcelo Depolo Polêto, Nancy da Rocha Torres Pavione, Raissa Barbosa de Castro, Izabel Luzia Miranda, Suélen Karine Sartori, Kryssia Lohayne Santos Alves, Gustavo Costa Bressan, Raphael de Souza Vasconcellos, José Roberto Meyer-Fernandes, Gaspar Diaz-Muñoz, Juliana Lopes Rangel Fietto
    Purinergic Signalling, 2024
  • Structural Dynamics of the Methyl-Coenzyme M Reductase Active Site Are Influenced by Coenzyme F430 Modifications
    Marcelo D. Polêto, Kylie D. Allen, Justin A. Lemkul
    Biochemistry, 2024
    High Resolution Image Download MS PowerPoint Slide Methyl-coenzyme M reductase (MCR) is a central player in methane biogeochemistry, governing methanogenesis and the anaerobic oxidation of methane (AOM) in methanogens and anaerobic methanotrophs (ANME), respectively. The prosthetic group of MCR is coenzyme F 430, a nickel-containing tetrahydrocorphin. Several modified versions of F 430 have been discovered, including the 17 2 -methylthio-F 430 (mtF 430 ) used by ANME-1 MCR. Here, we employ molecular dynamics (MD) simulations to investigate the active site dynamics of MCR from Methanosarcina acetivorans and ANME-1 when bound to the canonical F 430 compared to 17 2 -thioether coenzyme F 430 variants and substrates (methyl-coenzyme M and coenzyme B) for methane formation. Our simulations highlight the importance of the Gln to Val substitution in accommodating the 17 2 methylthio modification in ANME-1 MCR. Modifications at the 17 2 position disrupt the canonical substrate positioning in M. acetivorans MCR. However, in some replicates, active site reorganization to maintain substrate positioning suggests that the modified F 430 variants could be accommodated in a methanogenic MCR. We additionally report the first quantitative estimate of MCR intrinsic electric fields that are pivotal in driving methane formation. Our results suggest that the electric field aligned along the CH 3 -S-CoM thioether bond facilitates homolytic bond cleavage, coinciding with the proposed catalytic mechanism. Structural perturbations, however, weaken and misalign these electric fields, emphasizing the importance of the active site structure in maintaining their integrity. In conclusion, our results deepen the understanding of MCR active site dynamics, the enzyme’s organizational role in intrinsic electric fields for catalysis, and the interplay between active site structure and electrostatics.
  • Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes
    Marcelo D. Polêto, Justin A. Lemkul
    Journal of Chemical Information and Modeling, 2023
    The formation of G-quadruplexes (GQs) occurs in guanine-rich sequences of DNA and RNA, producing highly stable and structurally diverse noncanonical nucleic acid structures. GQs play crucial roles in regulating transcription, translation, and replication and maintaining the genome, among others; thus, changes to their structures can lead to diseases such as cancer. Previous studies using polarizable molecular dynamics simulations have shown differences in ion binding properties between telomeric and telomeric repeat-containing RNA GQs despite architectural similarities. Here, we used volume-based metadynamics and repulsive potential simulations in conjunction with polarizable force fields to quantify the impact of ion binding on the GQ dynamics and ion binding free energies. Furthermore, we describe how GQs exert electric fields on their surroundings to link dynamics with variations in the electronic structure. Our findings provide new insights into the energetic, physical, and conformational properties of GQs and expose subtle but important differences between DNA and RNA GQs with the same fold.
  • Effects of the Cations Li+, Na+, K+, Mg2+, or Ca2+ on Physicochemical Properties of Xanthan Gum in Aqueous Medium – A view from Computational Molecular Dynamics Calculations
    Érica Cardoso Valente, Marcelo Depólo Polêto, Thomás Valente de Oliveira, Lucas de Souza Soares, Jane Sélia dos Reis Coimbra, Ana Paula Guimarães, Eduardo Basílio de Oliveira
    Food Biophysics, 2023
  • First evidence of a serine arginine protein kinase (SRPK) in leishmania braziliensis and its potential as therapeutic target
    Débora Cristina Pimentel, Juliana Rodrigues Leopoldo, Leilane Ferreira Teixeira, Marcus Vinícius de Andrade Barros, Ana Paula Martins de Souza, Thiago Souza Onofre, Rayane Luiza de Carvalho, Sara Andrade Machado, Isabelly Gonçalves Messias, Carla Cristina de Souza Pinto, Marcelo Depolo Poleto, Marcel Arruda Diogo, Christiane Mariotini-Moura, Gustavo Costa Bressan, Robson Ricardo Teixeira, Juliana Lopes Rangel Fietto, Raphael de Souza Vasconcellos
    Acta Tropica, 2023
  • Monomeric and dimeric states of human ZO1-PDZ2 are functional partners of the SARS-CoV-2 E protein
    Noah Giacon, Ettore Lo Cascio, Darcy S. Davidson, Marcelo D. Polêto, Justin A. Lemkul, Valeria Pennacchietti, Livia Pagano, Carlotta Zamparelli, Angelo Toto, Alessandro Arcovito
    Computational and Structural Biotechnology Journal, 2023
    The Envelope (E) protein of SARS-CoV-2 plays a key role in virus maturation, assembly, and virulence mechanisms. The E protein is characterized by the presence of a PDZ-binding motif (PBM) at its C-terminus that allows it to interact with several PDZ-containing proteins in the intracellular environment. One of the main binding partners of the SARS-CoV-2 E protein is the PDZ2 domain of ZO1, a protein with a crucial role in the formation of epithelial and endothelial tight junctions (TJs). In this work, through a combination of analytical ultracentrifugation analysis and equilibrium and kinetic folding experiments, we show that ZO1-PDZ2 domain is able to fold in a monomeric state, an alternative form to the dimeric conformation that is reported to be functional in the cell for TJs assembly. Importantly, surface plasmon resonance (SPR) data indicate that the PDZ2 monomer is fully functional and capable of binding the C-terminal portion of the E protein of SARS-CoV-2, with a measured affinity in the micromolar range. Moreover, we present a detailed computational analysis of the complex between the C-terminal portion of E protein with ZO1-PDZ2, both in its monomeric conformation (computed as a high confidence AlphaFold2 model) and dimeric conformation (obtained from the Protein Data Bank), by using both polarizable and nonpolarizable simulations. Together, our results indicate both the monomeric and dimeric states of PDZ2 to be functional partners of the E protein, with similar binding mechanisms, and provide mechanistic and structural information about a fundamental interaction required for the replication of SARS-CoV-2.
  • Integration of experimental data and use of automated fitting methods in developing protein force fields
    Marcelo D. Polêto, Justin A. Lemkul
    Communications Chemistry, 2022
    The development of accurate protein force fields has been the cornerstone of molecular simulations for the past 50 years. During this period, many lessons have been learned regarding the use of experimental target data and parameter fitting procedures. Here, we review recent advances in protein force field development. We discuss the recent emergence of polarizable force fields and the role of electronic polarization and areas in which additive force fields fall short. The use of automated fitting methods and the inclusion of additional experimental solution data during parametrization is discussed as a means to highlight possible routes to improve the accuracy of force fields even further.
  • TUPÃ: Electric field analyses for molecular simulations
    Marcelo D. Polêto, Justin A. Lemkul
    Journal of Computational Chemistry, 2022
  • Impacts of Ca2+ cation and temperature on bovine α-lactalbumin secondary structures and foamability – Insights from computational molecular dynamics
    Thomás Valente De Oliveira, Marcelo Depólo Polêto, Samuel Vieira Barbosa, Jane Sélia dos Reis Coimbra, Eduardo Basílio De Oliveira
    Food Chemistry, 2022
  • Making it Rain: Cloud-Based Molecular Simulations for Everyone
    Pablo R. Arantes, Marcelo D. Polêto, Conrado Pedebos, Rodrigo Ligabue-Braun
    Journal of Chemical Information and Modeling, 2021
  • Structural and molecular bases of angiotensin-converting enzyme inhibition by bovine casein-derived peptides: an in silico molecular dynamics approach
    Thomás Valente De Oliveira, Ana Paula Guimarães, Gustavo Costa Bressan, Elaine Rose Maia, Jane Sélia dos Reis Coimbra, Marcelo Depólo Polêto, Eduardo Basílio De Oliveira
    Journal of Biomolecular Structure and Dynamics, 2021
  • Entpdases from pathogenic trypanosomatids and purinergic signaling: Shedding light towards biotechnological applications
    Walmir da Silva, Nancy da Rocha Torres, Joice de Melo Agripino, Victor Hugo Ferraz da Silva, Anna Cláudia Alves de Souza, Isadora Cunha Ribeiro, Tatiana Aparecida de Oliveira, Luciana Angelo de Souza, Lethicia Kelly Ramos Andrade, João Victor Badaró de Moraes, Marcel Arruda Diogo, Raíssa Barbosa de Castro, Marcelo Depolo Polêto, Luis Carlos Crocco Afonso, Juliana Lopes Rangel Fietto
    Current Topics in Medicinal Chemistry, 2021
  • Rotational Profiler: A Fast, Automated, and Interactive Server to Derive Torsional Dihedral Potentials for Classical Molecular Simulations
    Victor H. Rusu, Denys E. S. Santos, Marcelo D. Poleto, Marcelo M. Galheigo, Antônio T. A. Gomes, Hugo Verli, Thereza A. Soares, Roberto D. Lins
    Journal of Chemical Information and Modeling, 2020
  • ConfID: An analytical method for conformational characterization of small molecules using molecular dynamics trajectories
    Marcelo D Polêto, Bruno I Grisci, Marcio Dorn, Hugo Verli
    Bioinformatics, 2020
  • Casein-Derived Peptides with Antihypertensive Potential: Production, Identification and Assessment of Complex Formation with Angiotensin I-Converting Enzyme (ACE) through Molecular Docking Studies
    Thomás Valente De Oliveira, Marcelo Depólo Polêto, Mara Rose De Oliveira, Thaís Jordânia Silva, Edvaldo Barros, Valéria Monteze Guimarães, Maria Cristina Baracat-Pereira, Monique Renon Eller, Jane Sélia dos Reis Coimbra, Eduardo Basílio De Oliveira
    Food Biophysics, 2020
  • The Lazy Life of Lipid-Linked Oligosaccharides in All Life Domains
    Pablo R. Arantes, Conrado Pedebos, Marcelo D. Polêto, Laércio Pol-Fachin, Hugo Verli
    Journal of Chemical Information and Modeling, 2020
  • Discovery of novel West Nile Virus protease inhibitor based on isobenzonafuranone and triazolic derivatives of eugenol and indan-1,3-dione scaffolds
    André S. de Oliveira, Poliana A. R. Gazolla, Ana Flávia C. da S. Oliveira, Wagner L. Pereira, Lívia C. de S. Viol, Angélica F. da S. Maia, Edjon G. Santos, Ítalo E. P. da Silva, Tiago A. de Oliveira Mendes, Adalberto M. da Silva, Roberto S. Dias, Cynthia C. da Silva, Marcelo D. Polêto, Róbson R. Teixeira, Sergio O. de Paula
    Plos One, 2019
  • Role of structural ions on the dynamics of the Pseudomonas fluorescens 07A metalloprotease
    Marcelo D. Polêto, Maura P. Alves, Rodrigo Ligabue-Braun, Monique R. Eller, Antonio Fernandes De carvalho
    Food Chemistry, 2019
  • Development of GROMOS-Compatible Parameter Set for Simulations of Chalcones and Flavonoids
    Pablo R. Arantes, Marcelo D. Polêto, Elisa B. O. John, Conrado Pedebos, Bruno I. Grisci, Marcio Dorn, Hugo Verli
    Journal of Physical Chemistry B, 2019
  • An Unusual Intramolecular Halogen Bond Guides Conformational Selection
    Roberta Tesch, Christian Becker, Matthias Philipp Müller, Michael Edmund Beck, Lena Quambusch, Matthäus Getlik, Jonas Lategahn, Niklas Uhlenbrock, Fanny Nascimento Costa, Marcelo D. Polêto, Pedro de Sena Murteira Pinheiro, Daniel Alencar Rodrigues, Carlos Mauricio R. Sant'Anna, Fabio Furlan Ferreira, Hugo Verli, Carlos Alberto Manssour Fraga, Daniel Rauh
    Angewandte Chemie International Edition, 2018
  • Influence of Na+ and Mg2+ ions on RNA structures studied with molecular dynamics simulations
    Nina M Fischer, Marcelo D Polêto, Jakob Steuer, David van der Spoel
    Nucleic Acids Research, 2018
  • Aromatic rings commonly used in medicinal chemistry: Force fields comparison and interactions with water toward the design of New Chemical Entities
    Marcelo D. Polêto, Victor H. Rusu, Bruno I. Grisci, Marcio Dorn, Roberto D. Lins, Hugo Verli
    Frontiers in Pharmacology, 2018
  • Homology modeling and molecular dynamics provide structural insights into tospovirus nucleoprotein
    Rayane Nunes Lima, Muhammad Faheem, João Alexandre Ribeiro Gonçalves Barbosa, Marcelo Depólo Polêto, Hugo Verli, Fernando Lucas Melo, Renato Oliveira Resende
    BMC Bioinformatics, 2016
  • Evaluation of a synthetic peptide from the Taenia saginata 18 kDa surface/secreted oncospheral adhesion protein for serological diagnosis of bovine cysticercosis
    Rafaella Paola Meneguete Guimarães-Peixoto, Paulo Sérgio Arruda Pinto, Marcus Rebouças Santos, Marcelo Depólo Polêto, Letícia Ferreira Silva, Abelardo Silva-Júnior
    Acta Tropica, 2016
  • ESI-MS/MS of expanded porphyrins: A look into their structure and aromaticity
    Catarina IV Ramos, Flávio Figueira, Marcelo D Polêto, Francisco ML Amado, Hugo Verli, João PC Tomé, M Graça PMS Neves
    Journal of Mass Spectrometry, 2016
  • Hexaphyrin derivatives for anion recognition in organic and aqueous media
    Flávio Figueira, Andreia S. F. Farinha, Paulino V. Muteto, Marcelo D. Polêto, Hugo Verli, M. Teresa S. R. Gomes, Augusto C. Tomé, José A. S. Cavaleiro, João P. C. Tomé
    Chemical Communications, 2016
  • A porcine circovirus-2 mutant isolated in Brazil contains low-frequency substitutions in regions of immunoprotective epitopes in the capsid protein
    Rafael Locatelli Salgado, Pedro Marcus Pereira Vidigal, Natalia F. Gonzaga, Luiz F. L. de Souza, Marcelo D. Polêto, Thiago Souza Onofre, Monique R. Eller, Carlos Eduardo Real Pereira, Juliana L. R. Fietto, Gustavo C. Bressan, Roberto M. C. Guedes, Márcia R. Almeida, Abelardo Silva Júnior
    Archives of Virology, 2015
  • Potential antileukemia effect and structural analyses of SRPK inhibition by N-(2-(Piperidin-1-yl)-5-(Trifluoromethyl)Phenyl) isonicotinamide (SRPIN340)
    Raoni Pais Siqueira, Éverton de Almeida Alves Barbosa, Marcelo Depólo Polêto, Germanna Lima Righetto, Thiago Vargas Seraphim, Rafael Locatelli Salgado, Joana Gasperazzo Ferreira, Marcus Vinícius de Andrade Barros, Leandro Licursi de Oliveira, Angelo Brunelli Albertoni Laranjeira, Márcia Rogéria Almeida, Abelardo Silva Júnior, Juliana Lopes Rangel Fietto, Jörg Kobarg, Eduardo Basílio de Oliveira, Robson Ricardo Teixeira, Júlio César Borges, Jose Andrés Yunes, Gustavo Costa Bressan
    Plos One, 2015

RECENT SCHOLAR PUBLICATIONS

  • Weighted ensemble simulations with the Drude polarizable model
    MD Polêto, GM Da Silva, BM Rubenstein, JA Lemkul
    Journal of Computational Chemistry 46 (30), e70264 , 2025
    2025
  • Structural Modeling of NTPDase-Substrate Complexes Preserving Catalytic Experimental Features
    JVB de Moraes, MD Polêto, RB de Castro, GC Bressan, ...
    ACS omega 10 (38), 43891-43902 , 2025
    2025
  • Running Gaussian-accelerated Molecular Dynamics Simulations in NAMD [Article v1. 0]
    HM Michel, MD Polêto, JA Lemkul
    Living journal of computational molecular science 6 (1), 3815 , 2025
    2025
    Citations: 1
  • Structural and electronic properties of poly (ethylene terephthalate)(PET) from polarizable molecular dynamics simulations
    MD Polêto, JA Lemkul
    Macromolecules 58 (1), 403-414 , 2024
    2024
    Citations: 10
  • Synthesis of new non-natural l -glycosidic flavonoid derivatives and their evaluation as inhibitors of Trypanosoma cruzi ecto-nucleoside triphosphate …
    IC Ribeiro, JVB de Moraes, C Mariotini-Moura, MD Polêto, ...
    Purinergic Signalling 20 (4), 399-419 , 2024
    2024
    Citations: 2
  • Structural Dynamics of the Methyl-Coenzyme M Reductase Active Site Are Influenced by Coenzyme F 430 Modifications
    MD Polêto, KD Allen, JA Lemkul
    Biochemistry 63 (14), 1783-1794 , 2024
    2024
    Citations: 8
  • Differences in Conformational Sampling and Intrinsic Electric Fields Drive Ion Binding in Telomeric and TERRA G-Quadruplexes
    MD Polêto, JA Lemkul
    Journal of chemical information and modeling 63 (21), 6851-6862 , 2023
    2023
    Citations: 4
  • Effects of the Cations Li + , Na + , K + , Mg 2+ , or Ca 2+ on Physicochemical Properties of Xanthan Gum in Aqueous Medium – A view from Computational Molecular …
    ÉC Valente, MD Polêto, TV De Oliveira, LS Soares, JS dos Reis Coimbra, ...
    Food Biophysics 18 (1), 32-47 , 2023
    2023
    Citations: 8
  • First evidence of a serine arginine protein kinase (SRPK) in leishmania braziliensis and its potential as therapeutic target
    DC Pimentel, JR Leopoldo, LF Teixeira, MV de Andrade Barros, ...
    Acta Tropica 238, 106801 , 2023
    2023
    Citations: 3
  • Monomeric and dimeric states of human ZO1-PDZ2 are functional partners of the SARS-CoV-2 E protein
    N Giacon, EL Cascio, DS Davidson, MD Polêto, JA Lemkul, ...
    Computational and Structural Biotechnology Journal 21, 3259-3271 , 2023
    2023
    Citations: 6
  • Sequence diversity and catalytic properties of phytases
    EBE Pires, MD Polêto, PMP Vidigal, MIB Aragão, TA Barros, RL Salgado, ...
    Research, Society and Development 11 (10), e427111032765-e427111032765 , 2022
    2022
  • TUPÃ: Electric field analyses for molecular simulations
    MD Polêto, JA Lemkul
    Journal of computational chemistry 43 (16), 1113-1119 , 2022
    2022
    Citations: 30
  • Integration of experimental data and use of automated fitting methods in developing protein force fields
    MD Polêto, JA Lemkul
    Communications chemistry 5 (1), 38 , 2022
    2022
    Citations: 43
  • Impacts of Ca2+ cation and temperature on bovine α-lactalbumin secondary structures and foamability–Insights from computational molecular dynamics
    TV De Oliveira, MD Polêto, SV Barbosa, JS dos Reis Coimbra, ...
    Food chemistry 367, 130733 , 2022
    2022
    Citations: 12
  • Making it rain: cloud-based molecular simulations for everyone
    PR Arantes, MD Polêto, C Pedebos, R Ligabue-Braun
    Journal of Chemical Information and Modeling 61 (10), 4852-4856 , 2021
    2021
    Citations: 140
  • Structural and molecular bases of angiotensin-converting enzyme inhibition by bovine casein-derived peptides: an in silico molecular dynamics approach
    TV De Oliveira, AP Guimaraes, GC Bressan, ER Maia, JSR Coimbra, ...
    Journal of Biomolecular Structure and Dynamics 39 (4), 1386-1403 , 2021
    2021
    Citations: 7
  • ENTPDases from pathogenic trypanosomatids and purinergic signaling: shedding light towards biotechnological applications
    W da Silva, N da Rocha Torres, J de Melo Agripino, VHF da Silva, ...
    Current Topics in Medicinal Chemistry 21 (3), 213-226 , 2021
    2021
    Citations: 13
  • Rotational profiler: A fast, automated, and interactive server to derive torsional dihedral potentials for classical molecular simulations
    VH Rusu, DES Santos, MD Poleto, MM Galheigo, ATA Gomes, H Verli, ...
    Journal of Chemical Information and Modeling 60 (12), 5923-5927 , 2020
    2020
    Citations: 7
  • ConfID : an analytical method for conformational characterization of small molecules using molecular dynamics trajectories
    MD Polêto, BI Grisci, M Dorn, H Verli
    Bioinformatics 36 (11), 3576-3577 , 2020
    2020
    Citations: 6
  • Casein-derived peptides with antihypertensive potential: Production, identification and assessment of complex formation with angiotensin I-converting enzyme (ACE) through …
    TV De Oliveira, MD Polêto, MR De Oliveira, TJ Silva, E Barros, ...
    Food Biophysics 15 (2), 162-172 , 2020
    2020
    Citations: 25

MOST CITED SCHOLAR PUBLICATIONS

  • Making it rain: cloud-based molecular simulations for everyone
    PR Arantes, MD Polêto, C Pedebos, R Ligabue-Braun
    Journal of Chemical Information and Modeling 61 (10), 4852-4856 , 2021
    2021
    Citations: 140
  • Influence of Na + and Mg 2+ ions on RNA structures studied with molecular dynamics simulations
    NM Fischer, MD Polêto, J Steuer, D van der Spoel
    Nucleic acids research 46 (10), 4872-4882 , 2018
    2018
    Citations: 107
  • Potential Antileukemia Effect and Structural Analyses of SRPK Inhibition by N -(2-(Piperidin-1-yl)-5-(Trifluoromethyl)Phenyl)Isonicotinamide (SRPIN340)
    RP Siqueira, ÉAA Barbosa, MD Polêto, GL Righetto, TV Seraphim, ...
    PloS one 10 (8), e0134882 , 2015
    2015
    Citations: 97
  • Aromatic rings commonly used in medicinal chemistry: force fields comparison and interactions with water toward the design of new chemical entities
    MD Polêto, VH Rusu, BI Grisci, M Dorn, RD Lins, H Verli
    Frontiers in pharmacology 9, 395 , 2018
    2018
    Citations: 80
  • Integration of experimental data and use of automated fitting methods in developing protein force fields
    MD Polêto, JA Lemkul
    Communications chemistry 5 (1), 38 , 2022
    2022
    Citations: 43
  • TUPÃ: Electric field analyses for molecular simulations
    MD Polêto, JA Lemkul
    Journal of computational chemistry 43 (16), 1113-1119 , 2022
    2022
    Citations: 30
  • Discovery of novel West Nile Virus protease inhibitor based on isobenzonafuranone and triazolic derivatives of eugenol and indan-1, 3-dione scaffolds
    AS de Oliveira, PAR Gazolla, AFCS Oliveira, WL Pereira, LC de S. Viol, ...
    PLoS One 14 (9), e0223017 , 2019
    2019
    Citations: 30
  • Casein-derived peptides with antihypertensive potential: Production, identification and assessment of complex formation with angiotensin I-converting enzyme (ACE) through …
    TV De Oliveira, MD Polêto, MR De Oliveira, TJ Silva, E Barros, ...
    Food Biophysics 15 (2), 162-172 , 2020
    2020
    Citations: 25
  • An unusual intramolecular halogen bond guides conformational selection
    R Tesch, C Becker, MP Müller, ME Beck, L Quambusch, M Getlik, ...
    Angewandte Chemie International Edition 57 (31), 9970-9975 , 2018
    2018
    Citations: 21
  • Role of structural ions on the dynamics of the pseudomonas fluorescens 07a metalloprotease
    MD Polêto, MP Alves, R Ligabue-Braun, MR Eller, AF De Carvalho
    Food Chemistry , 2019
    2019
    Citations: 17
  • [28] Hexaphyrin derivatives for anion recognition in organic and aqueous media
    F Figueira, ASF Farinha, PV Muteto, MD Polêto, H Verli, MTSR Gomes, ...
    Chemical Communications 52 (10), 2181-2184 , 2016
    2016
    Citations: 17
  • ENTPDases from pathogenic trypanosomatids and purinergic signaling: shedding light towards biotechnological applications
    W da Silva, N da Rocha Torres, J de Melo Agripino, VHF da Silva, ...
    Current Topics in Medicinal Chemistry 21 (3), 213-226 , 2021
    2021
    Citations: 13
  • Homology modeling and molecular dynamics provide structural insights into tospovirus nucleoprotein
    RN Lima, M Faheem, JARG Barbosa, MD Polêto, H Verli, FL Melo, ...
    BMC bioinformatics 17 (Suppl 18), 489 , 2016
    2016
    Citations: 13
  • Impacts of Ca2+ cation and temperature on bovine α-lactalbumin secondary structures and foamability–Insights from computational molecular dynamics
    TV De Oliveira, MD Polêto, SV Barbosa, JS dos Reis Coimbra, ...
    Food chemistry 367, 130733 , 2022
    2022
    Citations: 12
  • Development of GROMOS-compatible parameter set for simulations of chalcones and flavonoids
    PR Arantes, MD Poleto, EBO John, C Pedebos, BI Grisci, M Dorn, H Verli
    The Journal of Physical Chemistry B 123 (5), 994-1008 , 2019
    2019
    Citations: 12
  • Structural and electronic properties of poly (ethylene terephthalate)(PET) from polarizable molecular dynamics simulations
    MD Polêto, JA Lemkul
    Macromolecules 58 (1), 403-414 , 2024
    2024
    Citations: 10
  • Evaluation of a synthetic peptide from the Taenia saginata 18 kDa surface/secreted oncospheral adhesion protein for serological diagnosis of bovine cysticercosis
    RPM Guimarães-Peixoto, PSA Pinto, MR Santos, MD Polêto, LF Silva, ...
    Acta tropica 164, 463-468 , 2016
    2016
    Citations: 10
  • The lazy life of lipid-linked oligosaccharides in all life domains
    PR Arantes, C Pedebos, MD Polêto, L Pol-Fachin, H Verli
    Journal of chemical information and modeling 60 (2), 631-643 , 2019
    2019
    Citations: 9
  • Structural Dynamics of the Methyl-Coenzyme M Reductase Active Site Are Influenced by Coenzyme F 430 Modifications
    MD Polêto, KD Allen, JA Lemkul
    Biochemistry 63 (14), 1783-1794 , 2024
    2024
    Citations: 8
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