Matheus Ferraz

PhD in computational chemistry, bioinformatician with experience in industry

Research Interests

Computational Chemistry
Protein Design
Machine Learning
Virology
Microbiology
Infectious Diseases
Cell Biology
Microbiology (medical)
Genetics
Ecology
Physiology
Materials Chemistry
Metals and Alloys
Surfaces, Coatings and Films
Ceramics and Composites
Electronic, Optical and Magnetic Materials
Catalysis
Computer Graphics and Computer-Aided Design
Physical and Theoretical Chemistry
Spectroscopy
Molecular Biology
Structural Biology
Organic Chemistry
Biomaterials
Biochemistry
Biophysics
Pharmaceutical Science
Drug Discovery

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

Recife

Experience

HEIDELBERG INSTITUTE FOR THEORETICAL STUDIES

Visiting scientst

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