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.
I am currently a research scientist (Structural bioinformatician) at NEC OncoImmunity AS (Norway/Germany). I combine machine learning and physics-based multiscale modeling for vaccine development, drug discovery, protein design, and for the molecular understanding of viral and drug mechanisms of action. My main focus is on antibody fragments, immunogens, and ADCs. Expertise includes computational structural biology and computational biophysics methods like protein structure prediction, de novo molecular design, flexible docking, structure- and ligand-based drug design, molecular dynamics simulations, enhanced sampling, free energies calculations, unbinding kinetics parameters computation, computational protein design and quantum chemical calculations.
I supervise one master student from the University of Oslo on an antibody design project.
Publications
Antônio Purificação, Matheus Ferraz, Marjorie Freire, Isabelle Viana, Roberto Lins
In preparation, 2024
Matheus Ferraz, Camilla Adan, Tayná Lima, Adriele Santos, Sérgio de Paula, Rafael Dhalia, Gabriel Wallau, Rebecca Wade, Isabelle Viana, Roberto Lins
BioRxiv (Under review on Plos Computational Biology), 2024
Giulia. ; PAIARDI, Matheus; FERRAZ, Marco ; RUSNATI, Rebecca WADE
PNAS, 2024
Prediction of absolute protein-protein binding free energy by a super learner model.
E.; Chaves, E.; Mhrous, M.; Nascimento-Filho, C.; Cruz, M.; Ferraz, R Lins
ChemRxiv (preprint), 2023
Advances in the phytochemical screening and biological potential of propolis
SILVIO ; DE ALMEIDA'JUNIOR, MATHEUS VITOR FERREIRA ; FERRAZ, ALEX ROBERTO ; DE OLIVEIRA, FABÍOLA PANSANI ; MANIGLIA, JAIRO KENUPP ; BASTOS, RICARDO ANDRADE FURTADO
FUNDAMENTAL & CLINICAL PHARMACOLOGY, 2023
MATHEUS; FERRAZ, JOSÉ ; SOARES, ROBERTO ; LINS, ERICO . TEIXEIRA
PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2023
TAYNÁ E. ; LIMA, MATHEUS V.F. ; FERRAZ, CARLOS A.A. ; BRITO, PAMELLA B. ; XIMENES, CAROLLINE A. ; MARIZ, CYNTHIA ; BRAGA, GABRIEL L. ; WALLAU, ISABELLE F.T. ; VIANA, ROBERTO D. . LINS
ANAIS DA ACADEMIA BRASILEIRA DE CIÊNCIAS, 2023
LARISSA G. ; MACIEL, MATHEUS V. F. ; FERRAZ, ANDREW A. ; OLIVEIRA, ROBERTO D. ; LINS, JANAÍNA V. ; DOS ANJOS, RAFAEL V. C. ; GUIDO, THEREZA A. SOARES
ACS Bio & Med Chem Au, 2023
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
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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.
