Matheus Ferraz
PhD in computational chemistry, bioinformatician with experience in industry
Research Expertise
Publications
The ongoing evolution of variants of concern and interest of SARS-CoV-2 in Brazil revealed by convergent indels in the amino (N)-terminal domain of the spike protein
Virus Evolution / Aug 14, 2021
Resende, P. C., Naveca, F. G., Lins, R. D., Dezordi, F. Z., Ferraz, M. V. F., Moreira, E. G., Coêlho, D. F., Motta, F. C., Paixão, A. C. D., Appolinario, L., Lopes, R. S., Mendonça, A. C. da F., da Rocha, A. S. B., Nascimento, V., Souza, V., Silva, G., Nascimento, F., Neto, L. G. L., da Silva, F. V., … Wallau, G. L. (2021). The ongoing evolution of variants of concern and interest of SARS-CoV-2 in Brazil revealed by convergent indels in the amino (N)-terminal domain of the spike protein. Virus Evolution, 7(2). https://doi.org/10.1093/ve/veab069
Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil
Microbiology Spectrum / Feb 23, 2022
Naveca, F. G., Nascimento, V., Souza, V., Corado, A. de L., Nascimento, F., Silva, G., Mejía, M. C., Brandão, M. J., Costa, Á., Duarte, D., Pessoa, K., Jesus, M., Gonçalves, L., Fernandes, C., Mattos, T., Abdalla, L., Santos, J. H., Martins, A., Chui, F. M., … Bello, G. (2022). Spread of Gamma (P.1) Sub-Lineages Carrying Spike Mutations Close to the Furin Cleavage Site and Deletions in the N-Terminal Domain Drives Ongoing Transmission of SARS-CoV-2 in Amazonas, Brazil. Microbiology Spectrum, 10(1). https://doi.org/10.1128/spectrum.02366-21
Immune evasion of SARS-CoV-2 variants of concern is driven by low affinity to neutralizing antibodies
Chemical Communications / Jan 01, 2021
Ferraz, M. V. F., Moreira, E. G., Coêlho, D. F., Wallau, G. L., & Lins, R. D. (2021). Immune evasion of SARS-CoV-2 variants of concern is driven by low affinity to neutralizing antibodies. Chemical Communications, 57(49), 6094–6097. https://doi.org/10.1039/d1cc01747k
Molecular basis of Tityus stigmurus alpha toxin and potassium channel kV1.2 interactions
Journal of Molecular Graphics and Modelling / Mar 01, 2019
Freire, M. C. L. C., Silva de Menezes, Y. A., Ferreira Ferraz, M. V., Bezerra da Cruz, C. H., De Santis Ferreira, L., de Freitas Fernandes-Pedrosa, M., & Barbosa, E. G. (2019). Molecular basis of Tityus stigmurus alpha toxin and potassium channel kV1.2 interactions. Journal of Molecular Graphics and Modelling, 87, 197–203. https://doi.org/10.1016/j.jmgm.2018.11.012
The influence of biotinylation on the ability of a computer designed protein to detect B-cells producing anti-HIV-1 2F5 antibodies
Journal of Molecular Graphics and Modelling / Dec 01, 2019
Coêlho, D. F., Ferraz, M. V. F., Marques, E. T. A., Lins, R. D., & Viana, I. F. T. (2019). The influence of biotinylation on the ability of a computer designed protein to detect B-cells producing anti-HIV-1 2F5 antibodies. Journal of Molecular Graphics and Modelling, 93, 107442. https://doi.org/10.1016/j.jmgm.2019.107442
SARS-CoV-2 VOCs Immune Evasion from Previously Elicited Neutralizing Antibodies Is Mainly Driven by Lower Cross-Reactivity Due to Spike RBD Electrostatic Surface Changes
Mar 31, 2021
Ferraz, M., MOREIRA, E., Coêlho, D. F., Wallau, G., & Lins, R. (2021). SARS-CoV-2 VOCs Immune Evasion from Previously Elicited Neutralizing Antibodies Is Mainly Driven by Lower Cross-Reactivity Due to Spike RBD Electrostatic Surface Changes. https://doi.org/10.26434/chemrxiv.14343743
Identification of potential Staphylococcus aureus dihydrofolate reductase inhibitors using QSAR, molecular docking, dynamics simulations and free energy calculation
Journal of Biomolecular Structure and Dynamics / Mar 31, 2022
Matos, I. de A., Goes Pinto, A. C., Ferraz, M. V. F., Adan, W. C. S., Rodrigues, R. P., dos Santos, J. X., Kitagawa, R. R., Lins, R. D., Oliveira, T. B., & Costa Junior, N. B. da. (2022). Identification of potential Staphylococcus aureus dihydrofolate reductase inhibitors using QSAR, molecular docking, dynamics simulations and free energy calculation. Journal of Biomolecular Structure and Dynamics, 41(9), 3835–3846. https://doi.org/10.1080/07391102.2022.2057361
An artificial neural network model to predict structure-based protein–protein free energy of binding from Rosetta-calculated properties
Physical Chemistry Chemical Physics / Jan 01, 2023
Ferraz, M. V. F., Neto, J. C. S., Lins, R. D., & Teixeira, E. S. (2023). An artificial neural network model to predict structure-based protein–protein free energy of binding from Rosetta-calculated properties. Physical Chemistry Chemical Physics, 25(10), 7257–7267. https://doi.org/10.1039/d2cp05644e
Association strength of E6 to E6AP/p53 complex correlates with HPV‐mediated oncogenesis risk
Biopolymers / Aug 18, 2022
Ferraz, M. V. F., Viana, I. F. T., Coêlho, D. F., da Cruz, C. H. B., de Arruda Lima, M., de Luna Aragão, M. A., & Lins, R. D. (2022). Association strength of E6 to E6AP/p53 complex correlates with HPV‐mediated oncogenesis risk. Biopolymers, 113(10). Portico. https://doi.org/10.1002/bip.23524
Unraveling the Role of Nanobodies Tetrad on Their Folding and Stability Assisted by Machine and Deep Learning Algorithms
Advances in Bioinformatics and Computational Biology / Jan 01, 2020
Ferraz, M. V. F., dos Santos Adan, W. C., & Lins, R. D. (2020). Unraveling the Role of Nanobodies Tetrad on Their Folding and Stability Assisted by Machine and Deep Learning Algorithms. Lecture Notes in Computer Science, 93–104. https://doi.org/10.1007/978-3-030-65775-8_9
Prediction of Absolute Protein-Protein Binding Free Energy by a Super Learner Model
Aug 14, 2023
Chaves, E., Mhrous, E., Nascimento-Filho, M., Cruz, C., Ferraz, M., & Lins, R. (2023). Prediction of Absolute Protein-Protein Binding Free Energy by a Super Learner Model. https://doi.org/10.26434/chemrxiv-2023-zq1nj
Inhibition of 3-Hydroxykynurenine Transaminase from Aedes aegypti and Anopheles gambiae: A Mosquito-Specific Target to Combat the Transmission of Arboviruses
ACS Bio & Med Chem Au / Feb 16, 2023
Maciel, L. G., Ferraz, M. V. F., Oliveira, A. A., Lins, R. D., dos Anjos, J. V., Guido, R. V. C., & Soares, T. A. (2023). Inhibition of 3-Hydroxykynurenine Transaminase from Aedes aegypti and Anopheles gambiae: A Mosquito-Specific Target to Combat the Transmission of Arboviruses. ACS Bio & Med Chem Au, 3(2), 211–222. https://doi.org/10.1021/acsbiomedchemau.2c00080
Artificial Neural Network to Predict Structure-based Protein-protein Free Energy of Binding from Rosetta-calculated Properties
Aug 09, 2022
Ferraz, M., Neto, J., Lins, R., & Teixeira, E. (2022). Artificial Neural Network to Predict Structure-based Protein-protein Free Energy of Binding from Rosetta-calculated Properties. https://doi.org/10.26434/chemrxiv-2022-zhd87
Discovery of Diverse Natural Products as Inhibitors of SARS-CoV2 Mpro Protease through Virtual Screening
Discovery of Diverse Natural Products as Inhibitors of SARS-CoV2 Mpro Protease through Virtual Screening. (n.d.). https://doi.org/10.1021/acs.jcim.1c00951.s001
CHIKUNGUNYA: DA EPIDEMIOLOGIA AO DESENVOLVIMENTO DE VACINAS
Fatores de virulência microbianos e terapias emergentes / Apr 14, 2022
Purificação Júnior, A. F. da, Azevedo, E. A. N., Lins Neto, R. D., & Viana, I. F. T. (2022). CHIKUNGUNYA: DA EPIDEMIOLOGIA AO DESENVOLVIMENTO DE VACINAS. Fatores de Virulência Microbianos e Terapias Emergentes, 215–232. https://doi.org/10.47174/lap2020.ed.00000105
Characterizing Binding Kinetics and Thermodynamics of Computer-Designed Nanobodies Targeting SARS-CoV-2 RBD
Biophysical Journal / Feb 01, 2021
Ferraz, M., & Lins, R. (2021). Characterizing Binding Kinetics and Thermodynamics of Computer-Designed Nanobodies Targeting SARS-CoV-2 RBD. Biophysical Journal, 120(3), 21a–22a. https://doi.org/10.1016/j.bpj.2020.11.393
TRIAGEM VIRTUAL PARA IDENTIFICAÇÃO DE INIBIDORES DA ACETILCOLINESTERASE.
Anais dos Seminários de Iniciação Científica / Nov 01, 2017
Silva, K. S. (2017). TRIAGEM VIRTUAL PARA IDENTIFICAÇÃO DE INIBIDORES DA ACETILCOLINESTERASE. Anais Dos Seminários de Iniciação Científica, 21. https://doi.org/10.13102/semic.v0i21.2304
Education
Federal University of Pernambuco
Ph.D., Chemistry / June, 2023
Experience
HEIDELBERG INSTITUTE FOR THEORETICAL STUDIES
Visiting scientst
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