About
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
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
Matheus Ferraz, José Neto, Roberto Lins, Erico Teixeira
ChemRxiv, 2022
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
Matheus Ferraz, Emerson Moreira, Danilo Coêlho, Gabriel Wallau, Roberto Lins
Chemical Communications, 2021
Paola Resende et al.
Virus Evolution, 2021
Matheus Ferraz, W. Camilla Adan, Roberto Lins
Lecture Notes in Computer Science, 2020
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
Projects
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
Molecular and Cellular Modeling Group
Heidelberg Institute for Theoretical Studies, Heidelberg, Germany