Matheus Ferraz

Computational Biophysics and Protein Design

About


Molecular simulations of biological systems provide an enhanced view of biochemical phenomena at the atomic scale, which is often inaccessible to experimental assessment. Currently, these methods have evolved to a level in which they are used not only to understand but also to predict macroscopic properties from molecular systems. Its applications extend to diverse fields, comprising biophysics, nanoscience, material physics, and a myriad of multidisciplinary areas at the interface of chemistry, physics, and biology. 

During my Ph.D. studies, under the supervision of Dr. Roberto Lins, I have combined multiple computational techniques to understand how proteins interact with their targets, by characterizing their binding kinetics and thermodynamics, to subsequently design novel proteins against infectious diseases (COVID-19, Zika, Dengue). Furthermore, we have been particularly keen on the development of computational tools to predict the binding free energies of Gibbs between protein pairs. 

Among the computational techniques I have used, I would like to mention molecular dynamics simulations, molecular docking, Brownian dynamics, enhanced sampling methods (e.g. metadynamics, and steered molecular dynamics), protein engineering with the Rosetta package, and machine learning. 



Publications


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


Felipe Gomes Naveca, Valdinete Nascimento, Victor Souza, André de Lima Corado, Fernanda Nascimento, George Silva, Matilde Contreras Mejía, Maria Júlia Brandão, Ágatha Costa, Débora Duarte, Karina Pessoa, Michele Jesus, Luciana Gonçalves, Cristiano Fernandes, Tirza Mattos, Ligia Abdalla, João Hugo Santos, Alex Martins, Fabiola Mendonça, Chui Fernando Fonseca Val, Gisely Cardoso de Melo, Mariana Simão Xavier, Vanderson de Souza Sampaio Maria Paula Mourão, Marcus Vinícius Lacerda Érika Lopes Rocha Batista, Alessandro Leonardo Álvares Magalhães, Nathânia Dábilla, Lucas Carlos Gomes Pereira, Fernando Vinhal Fabio Miyajima, Fernando Braga Stehling Dias, Eduardo Ruback dos Santos, Danilo Coêlho Matheus Ferraz, Roberto Lins, Gabriel Luz Wallau, Edson Delatorre, Tiago Gräf, Marilda Mendonça Siqueira, Paola Cristina Resende, Gonzalo Bell

MICROBIOLOGY SPECTRUM, 2022


Association strength of E6 to E6AP/p53 complex correlates with HPV-mediated oncogenesis risk


MATHEUS VITOR FERREIRA; FERRAZ, ISABELLE FREIRE TABOSA ; VIANA, DANILO FERNANDES ; COÊLHO, CARLOS HENRIQUE BEZERRA ; DA CRUZ, MAÍRA ; DE ARRUDA LIMA, MADSON ALLAN ; DE LUNA ARAGÃO, Roberto Dias Lins

Biopolymers, 2022


Identification of potential dihydrofolate reductase inhibitors using QSAR, molecular docking, dynamics simulations and free energy calculation


ISAAC DE ARAUJO ; MATOS, ANA CAROLINA ; GOES PINTO, MATHEUS VITOR FERREIRA ; FERRAZ, WENNY CAMILLA SANTOS ; ADAN, RICARDO PEREIRA ; RODRIGUES, JULIANE XAVIER ; DOS SANTOS, RODRIGO REZENDE ; KITAGAWA, ROBERTO DIAS LINS ;, TIAGO BRANQUINHO ; OLIVEIRA, NIVAN BEZERRA DA COSTA JUNIOR

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 2022


Immune Evasion of SARS-CoV-2 Variants of Concern is Driven by Low Affinity to Neutralizing Antibodies


Matheus Ferraz, Emerson Moreira, Danilo Coêlho, Gabriel Wallau, Roberto Lins

Chemical Communications, 2021


Unraveling the Role of Nanobodies Tetrad on Their Folding and Stability Assisted by Machine and Deep Learning Algorithms


Matheus Ferraz, W. Camilla Adan, Roberto Lins

Lecture Notes in Computer Science, 2020


The influence of biotinylation on the ability of a computer designed protein to detect B-cells producing anti-HIV-1 2F5 antibodies


Danilo Coêlho, Matheus Ferraz, Ernesto Marques, Roberto Lins, Isabelle Viana

Journal of Molecular Graphics and Modelling, 2019


Molecular basis of Tityus stigmurus alpha toxin and potassium channel kV1.2 interactions


Marjorie Freire, Yamara Menezes, Matheus Ferraz, Carlos Cruz, Leandro Ferreira, Matheus Pedrosa, Euzébio Barbosa

Journal of Molecular Graphics and Modelling, 2019

Courses


Numerical Analysis, UFPE (In portuguese)

Volunteer Monitor (2015)

On a 12 hours/week basis, used to provide extra classes and support on the course projects. The course syllabus consisted of classical algorithms to approach mathematical solutions. The projects were conducted in C programming language.


Molecular Biophysical Chemistry, UFPE Graduation (In Portuguese)

Invited Lecture

I have lectured to the post-graduation course in the chemistry department of the UFPE two classes regarding free energy calculations by molecular dynamics simulations, and enhanced sampling techniques.


Contact


Matheus Ferraz

Computational Biophysics


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