Computational Design of a Protein Binder Targeting the Chikungunya Virus E2B Domain Using Random Acceleration Molecular Dynamics and Interaction Fingerprint Analysis

Antônio Purificação, Matheus Ferraz, Marjorie Freire, Isabelle Viana, Roberto Lins

In preparation, 2024

Design of nanobody targeting SARS-CoV-2 spike glycoprotein using CDR-grafting assisted by molecular simulation and machine learning

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

The accomplices: Heparan sulfates and N-glycans foster SARS-CoV-2 spike:ACE2 receptor binding and virus priming

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

Artificial Neural Network to Predict Structure-based Protein-protein Free Energy of Binding from Rosetta calculated Properties

MATHEUS; FERRAZ, JOSÉ ; SOARES, ROBERTO ; LINS, ERICO . TEIXEIRA

PHYSICAL CHEMISTRY CHEMICAL PHYSICS, 2023

Determination of prognostic markers for COVID-19 disease severity using routine blood tests and machine learning

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

Inhibition of 3-Hydroxykynurenine Transaminase from Aedes aegypti and Anopheles gambiae: A Mosquito-Specific Target to Combat the Transmission of Arboviruses

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

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

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

Paola Resende et al.

Virus Evolution, 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