Design of nanobody targeting SARS-CoV-2 spike glycoprotein using CDR-grafting assisted by molecular simulation and machine learning
Ferraz, Matheus V.F., Adan, W. Camilla S., Lima, Tayná E., Santos, Adriele J.C., de Paula, Sérgio O., Dhalia, Rafael, Wallau, Gabriel L., Wade, Rebecca C., Viana, Isabelle F.T., Lins, Roberto D.
PLOS Computational Biology, 2025
DOI

Therapeutical Potential and Immunomodulatory Profile of Arthrospira platensis Compounds against Chagas Disease
da Silva, Maria Rafaele Oliveira Bezerra, Silva, Ana Carla da, Torreão, Byannca de Carvalho, Costa, Romero Marcos Pedrosa Brandão, Bezerra, Raquel Pedrosa, Silva, Silvana de Fátima Ferreira da, Oliva, Maria Luiza Vilela, Xavier, Lícya Samara da Silva, Viana, Isabelle F.T., Lins, Roberto Dias, Lorena, Virginia Maria Barros de, Viana Marques, Daniela de Araújo
ACS Infectious Diseases, 2025
DOI

Estimating Absolute Protein–Protein Binding Free Energies by a Super Learner Model
Chaves, Elton J. F., Sartori, João, Santos, Whendel M., Cruz, Carlos H. B., Mhrous, Emmanuel N., Nacimento-Filho, Manassés F., Ferraz, Matheus V. F., Lins, Roberto D.
Journal of Chemical Information and Modeling, 2025
DOI

Structure‐based computational design of antibody mimetics: challenges and perspectives
Chaves, Elton J. F., Coêlho, Danilo F., Cruz, Carlos H. B., Moreira, Emerson G., Simões, Júlio C. M., Nascimento‐Filho, Manassés J., Lins, Roberto D.
FEBS Open Bio, 2024
DOI

Design of nanobody targeting SARS-CoV-2 spike glycoprotein using CDR-grafting assisted by molecular simulation and machine learning
Ferraz, Matheus V. F., Adan, W. Camilla S., Lima, Tayná E., Santos, Adriele J. C., de Paula, Sérgio O., Dhalia, Rafael, Wallau, Gabriel L., Wade, Rebecca C., Viana, Isabelle F. T., Lins, Roberto D.
, 2024
DOI

Evolutionary deletions within the SARS-CoV-2 genome as signature trends for virus fitness and adaptation
Jeronimo, Pedro Miguel Carneiro, Aksenen, Cleber Furtado, Duarte, Igor Oliveira, Lins, Roberto D., Miyajima, Fabio
Journal of Virology, 2024
DOI

Enhanced immunogenicity and protective efficacy in mice following a Zika DNA vaccine designed by modulation of membrane-anchoring regions and its association to adjuvants
Teixeira, Franciane Mouradian Emidio, Oliveira, Luana de Mendonça, Branco, Anna Cláudia Calvielli Castelo, Alberca, Ricardo Wesley, Sousa, Emanuella Sarmento Alho de, Leite, Bruno Henrique de Sousa, Adan, Wenny Camilla dos Santos, Duarte, Alberto José da Silva, Lins, Roberto Dias, Sato, Maria Notomi, Viana, Isabelle Freire Tabosa
Frontiers in Immunology, 2024
DOI

Determination of prognostic markers for COVID-19 disease severity using routine blood tests and machine learning
LIMA, TAYNÁ E., FERRAZ, MATHEUS V.F., BRITO, CARLOS A.A., XIMENES, PAMELLA B., MARIZ, CAROLLINE A., BRAGA, CYNTHIA, WALLAU, GABRIEL L., VIANA, ISABELLE F.T., LINS, ROBERTO D.
Anais da Academia Brasileira de Ciências, 2024
DOI

Prediction of Absolute Protein-Protein Binding Free Energy by a Super Learner Model
Chaves, Elton, Mhrous, Emmanuel, Nascimento-Filho, Manasses, Cruz, Carlos, Ferraz, Matheus, Lins, Roberto
, 2023
DOI

Inhibition of 3-Hydroxykynurenine Transaminase from Aedes aegypti and Anopheles gambiae: A Mosquito-Specific Target to Combat the Transmission of Arboviruses
Maciel, Larissa G., Ferraz, Matheus V. F., Oliveira, Andrew A., Lins, Roberto D., dos Anjos, Janaína V., Guido, Rafael V. C., Soares, Thereza A.
ACS Bio & Med Chem Au, 2023
DOI

Artificial Neural Network to Predict Structure-based Protein-protein Free Energy of Binding from Rosetta calculated Properties
Matheus Ferraz, Jos{\'{e}} Soares, Roberto Lins, Erico Teixeira
Physical Chemistry Chemical Physics, 2023
DOI

In vitro neutralisation of Zika virus by an engineered protein targeting the viral envelope fusion loop
Isabelle FT Viana, Carlos HB da Cruz, Diogo Athayde, W. Camila Adan, Licya Samara Silva Xavier, Margarida Archer Fraz{\~{a}}o, Roberto Lins
Molecular Systems Design {\&}amp$\mathsemicolon$ Engineering, 2023
DOI

LAMP-1 Chimeric to HIV-1 p55Gag in the Immunization of Neonate Mice Induces an Early Germinal Center Formation and AID Expression
Teixeira, Franciane Mouradian Emidio, Oliveira, Luana de Mendonça, Pietrobon, Anna Julia, Salles, Érika Machado de, D’Império Lima, Maria Regina, Viana, Isabelle Freire Tabosa, Lins, Roberto Dias, Rigato, Paula Ordonhez, Marques, Ernesto Torres de Azevedo, da Silva Duarte, Alberto José, Sato, Maria Notomi
Vaccines, 2022
DOI

GM}2/{GM}3 controls the organizational status of {CD}82/Met microdomains: further studies in {GM}2/{GM}3 complexation
Ronan C. M. Santos, Daniela M. S. Lucena, Hector F. B. R. Loponte, Frederico Alisson-Silva, Wagner B. Dias, Roberto D. Lins, Adriane R. Todeschini
Glycoconjugate Journal, 2022
DOI

Identification of potential $\less$i$\greater$Staphylococcus aureus$\less$/i$\greater$ 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 and Dynamics, 2022
DOI

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, Andr{\'{e}} de Lima Corado, Fernanda Nascimento, George Silva, Matilde Contreras Mej{\'{\i}}a, Maria J{\'{u}}lia Brand{\~{a}}o, {\'{A}}gatha Costa, D{\'{e}}bora Duarte, Karina Pessoa, Michele Jesus, Luciana Gon{\c{c}}alves, Cristiano Fernandes, Tirza Mattos, Ligia Abdalla, Jo{\~{a}}o Hugo Santos, Alex Martins, Fabiola Mendon{\c{c}}a Chui, Fernando Fonseca Val, Gisely Cardoso de Melo, Mariana Sim{\~{a}}o Xavier, Vanderson de Souza Sampaio, Maria Paula Mour{\~{a}}o, Marcus Vin{\'{\i}}cius Lacerda, {\'{E}}rika Lopes Rocha Batista, Alessandro Leonardo {\'{A}}lvares Magalh{\~{a}}es, Nath{\^{a}}nia D{\'{a}}billa, Lucas Carlos Gomes Pereira, Fernando Vinhal, Fabio Miyajima, Fernando Braga Stehling Dias, Eduardo Ruback dos Santos, Danilo Co{\^{e}}lho, Matheus Ferraz, Roberto Lins, Gabriel Luz Wallau, Edson Delatorre, Tiago Gräf, Marilda Mendon{\c{c}}a Siqueira, Paola Cristina Resende, Gonzalo Bello
Microbiology Spectrum, 2022
DOI

Are Zika virus cross-reactive antibodies against aquaporin-4 associated to Neuromyelitis Optica Spectrum Disorder?
Jo{\~{a}}o P.M. Brainer-Lima, Bruno H.S. Leite, Catarina M.C.S. de Ara{\'{u}}jo, Rafael Dhalia, Danilo F. C{\^{o}}elho, Franciane M.E. Teixeira, Anna Cl{\'{a}}udia C.C. Branco, Maria N. Sato, Ernesto T.A. Marques, Roberto D. Lins, Isabelle F.T. Viana
Journal of Neuroimmunology, 2021
DOI

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 Cristina Resende, Felipe G Naveca, Roberto D Lins, Filipe Zimmer Dezordi, Matheus V. F Ferraz, Emerson G Moreira, Danilo F Co{\^{e}}lho, Fernando Couto Motta, Anna Carolina Dias Paix{\~{a}}o, Luciana Appolinario, Renata Serrano Lopes, Ana Carolina da Fonseca Mendon{\c{c}}a, Alice Sampaio Barreto da Rocha, Valdinete Nascimento, Victor Souza, George Silva, Fernanda Nascimento, Lidio Gon{\c{c}}alves Lima Neto, Fabiano Vieira da Silva, Irina Riediger, Maria do Carmo Debur, Anderson Brandao Leite, Tirza Mattos, Cristiano Fernandes da Costa, Felicidade Mota Pereira, Cliomar Alves dos Santos, Darcita Buerger Rovaris, Sandra Bianchini Fernandes, Adriano Abbud, Claudio Sacchi, Ricardo Khouri, Andr{\'{e}} Felipe Leal Bernardes, Edson Delatorre, Tiago Gräf, Marilda Mendon{\c{c}}a Siqueira, Gonzalo Bello, Gabriel L Wallau
Virus Evolution, 2021
DOI

Repositioning Lopinavir, an HIV Protease Inhibitor, as a Promising Antifungal Drug: Lessons Learned from Candida albicans—In Silico, In Vitro and In Vivo Approaches
Santos, André L. S., Braga-Silva, Lys A., Gonçalves, Diego S., Ramos, Lívia S., Oliveira, Simone S. C., Souza, Lucieri O. P., Oliveira, Vanessa S., Lins, Roberto D., Pinto, Marcia R., Muñoz, Julian E., Taborda, Carlos P., Branquinha, Marta H.
Journal of Fungi, 2021
DOI

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
Ferraz, Matheus, MOREIRA, EMERSON, Coêlho, Danilo F., Wallau, Gabriel, Lins, Roberto
, 2021
DOI

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
Ferraz, Matheus, MOREIRA, EMERSON, Coêlho, Danilo F., Wallau, Gabriel, Lins, Roberto
, 2021
DOI

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 Cristina Resende, Felipe G Naveca, Roberto D. Lins, Filipe Zimmer Dezordi, Matheus V. F. Ferraz, Emerson G. Moreira, Danilo F. Co{\^{e}}lho, Fernando Couto Motta, Anna Carolina Dias Paix{\~{a}}o, Luciana Appolinario, Renata Serrano Lopes, Ana Carolina da Fonseca Mendon{\c{c}}a, Alice Sampaio Barreto da Rocha, Valdinete Nascimento, Victor Souza, George Silva, Fernanda Nascimento, Lidio Gon{\c{c}}alves Lima Neto, Fabiano Vieira da Silva, Irina Riediger, Maria do Carmo Debur, Anderson Brandao Leite, Tirza Mattos, Cristiano Fernandes da Costa, Felicidade Mota Pereira, Cliomar Alves dos Santos, Darcita Buerger Rovaris, Sandra Bianchini Fernandes, Adriano Abbud, Claudio Sacchi, Ricardo Khouri, Andr{\'{e}} Felipe Leal Bernardes, Edson Delatorre, Tiago Gräf, Marilda Mendon{\c{c}}a Siqueira, Gonzalo Bello, Gabriel L Wallau
, 2021
DOI

Identification of a Zika {NS}2B Epitope for Which Absence of {IgG} Response Is Associated with Severe Neurological Symptoms and the Design of a Biomarker Capable of Discriminatory Diagnostics Between Severe and Non4 Severe Clinical Phenotypes
Felix Loeffler, Isabelle F. T. Viana, Nico Fischer, Danilo F. Coe{\^}lho, Carolina Santos, Antonio Purificacao Jr, Catarina Araujo, Bruno Leite, Ricardo Dur{\~{a}}es-Carvalho, Thereza Magalhaes, Clarice Morais, Marli Ten{\'{o}}rio Cordeiro, Roberto Lins, Ernesto T.A. Marques, Thomas Jaenisch
, 2021
DOI

Characterizing Binding Kinetics and Thermodynamics of Computer-Designed Nanobodies Targeting {SARS}-{CoV}-2 {RBD
Matheus Ferraz, Roberto Lins
Biophysical Journal, 2021
DOI

Identification of a Zika {NS}2B epitope as a biomarker for severe clinical phenotypes
Felix F. Loeffler, Isabelle F. T. Viana, Nico Fischer, Danilo F. Co{\^{e}}lho, Carolina S. Silva, Ant{\^{o}}nio F. Purifica{\c{c}}{\~{a}}o, Catarina M. C. S. Ara{\'{u}}jo, Bruno H. S. Leite, Ricardo Dur{\~{a}}es-Carvalho, Tereza Magalh{\~{a}}es, Clarice N. L. Morais, Marli T. Cordeiro, Roberto D. Lins, Ernesto T. A. Marques, Thomas Jaenisch
{RSC} Medicinal Chemistry, 2021
DOI

Immune evasion of {SARS}-{CoV}-2 variants of concern is driven by low affinity to neutralizing antibodies
Matheus V. F. Ferraz, Emerson G. Moreira, Danilo F. Co{\^{e}}lho, Gabriel L. Wallau, Roberto D. Lins
Chemical Communications, 2021
DOI

SARS-CoV-2 recombinant proteins stimulate distinct cellular and humoral immune response profiles in samples from COVID-19 convalescent patients
Silva, Laís Teodoro da, Ortega, Marina Mazzilli, Tiyo, Bruna Tiaki, Viana, Isabelle Freire Tabosa, Lima, Tayná Evily de, Tozetto-Mendoza, Tania Regina, Oliveira, Luanda Mara da Silva, Teixeira, Franciane Mouradian Emidio, Lins, Roberto Dias, Almeida, Alexandre de, Mendes-Correa, Maria Cassia, da Silva Duarte, Alberto Jose, Oshiro, Telma Miyuki
Clinics, 2021
DOI

Rotational Profiler: A Fast, Automated, and Interactive Server to Derive Torsional Dihedral Potentials for Classical Molecular Simulations
Victor H. Rusu, Denys E. S. Santos, Marcelo D. Poleto, Marcelo M. Galheigo, Ant{\^{o}}nio T. A. Gomes, Hugo Verli, Thereza A. Soares, Roberto D. Lins
Journal of Chemical Information and Modeling, 2020
DOI

Differential Frequencies of {HLA}-{DRB}1, {DQA}1, and {DQB}1 Alleles and Haplotypes Are Observed in the Arbovirus-Related Neurological Syndromes
Paulin Sonon, Maria L{\'{u}}cia Brito Ferreira, Renata Santos Almeida, Neifi Hassan Saloum Deghaide, Glauco Henrique Willcox, Elizabeth Lima Guimar{\~{a}}es, Ant{\^{o}}nio Fernando da Purifica{\c{c}}{\~{a}}o J{\'{u}}nior, Marli Ten{\'{o}}rio Cordeiro, Carlos Alexandre Antunes de Brito, Maria de F{\'{a}}tima Milit{\~{a}}o de Albuquerque, Roberto D Lins, Eduardo A Donadi, Norma Lucena-Silva
The Journal of Infectious Diseases, 2020
DOI

Unveiling the Influence of Nanobodies Dynamic Properties on Function and Antigen Binding Energy
Wenny Camilla dos Santos Adan, Matheus Vitor Ferreira Ferraz, Roberto Lins
, 2020
DOI

NWChem: Past, present, and future
Aprà, E., Bylaska, E. J., de Jong, W. A., Govind, N., Kowalski, K., Straatsma, T. P., Valiev, M., van Dam, H. J. J., Alexeev, Y., Anchell, J., Anisimov, V., Aquino, F. W., Atta-Fynn, R., Autschbach, J., Bauman, N. P., Becca, J. C., Bernholdt, D. E., Bhaskaran-Nair, K., Bogatko, S., Borowski, P., Boschen, J., Brabec, J., Bruner, A., Cauët, E., Chen, Y., Chuev, G. N., Cramer, C. J., Daily, J., Deegan, M. J. O., Dunning, T. H., Dupuis, M., Dyall, K. G., Fann, G. I., Fischer, S. A., Fonari, A., Früchtl, H., Gagliardi, L., Garza, J., Gawande, N., Ghosh, S., Glaesemann, K., Götz, A. W., Hammond, J., Helms, V., Hermes, E. D., Hirao, K., Hirata, S., Jacquelin, M., Jensen, L., Johnson, B. G., Jónsson, H., Kendall, R. A., Klemm, M., Kobayashi, R., Konkov, V., Krishnamoorthy, S., Krishnan, M., Lin, Z., Lins, R. D., Littlefield, R. J., Logsdail, A. J., Lopata, K., Ma, W., Marenich, A. V., Martin del Campo, J., Mejia-Rodriguez, D., Moore, J. E., Mullin, J. M., Nakajima, T., Nascimento, D. R., Nichols, J. A., Nichols, P. J., Nieplocha, J., Otero-de-la-Roza, A., Palmer, B., Panyala, A., Pirojsirikul, T., Peng, B., Peverati, R., Pittner, J., Pollack, L., Richard, R. M., Sadayappan, P., Schatz, G. C., Shelton, W. A., Silverstein, D. W., Smith, D. M. A., Soares, T. A., Song, D., Swart, M., Taylor, H. L., Thomas, G. S., Tipparaju, V., Truhlar, D. G., Tsemekhman, K., Van Voorhis, T., Vázquez-Mayagoitia, Á., Verma, P., Villa, O., Vishnu, A., Vogiatzis, K. D., Wang, D., Weare, J. H., Williamson, M. J., Windus, T. L., Woliński, K., Wong, A. T., Wu, Q., Yang, C., Yu, Q., Zacharias, M., Zhang, Z., Zhao, Y., Harrison, R. J.
The Journal of Chemical Physics, 2020
DOI

SuAVE}: A Tool for Analyzing Curvature-Dependent Properties in Chemical Interfaces
Denys E. S. Santos, Frederico J. S. Pontes, Roberto D. Lins, Kaline Coutinho, Thereza A. Soares
Journal of Chemical Information and Modeling, 2019
DOI

Unraveling the Role of Nanobodies Tetrad on Their Folding and Stability Assisted by Machine and Deep Learning Algorithms
Matheus Vitor Ferreira Ferraz, Wenny Camilla dos Santos Adan, Roberto Dias Lins
, 2020
DOI

Study protocol for the multicentre cohorts of Zika virus infection in pregnant women, infants, and acute clinical cases in Latin America and the Caribbean: the {ZIKAlliance} consortium
Vivian I. Avelino-Silva, , Philippe Mayaud, Adriana Tami, Maria C. Miranda, Kerstin D. Rosenberger, Neal Alexander, Luis Nacul, Aluisio Segurado, Moritz Pohl, Sarah Bethencourt, Luis A. Villar, Isabelle F. T. Viana, Renata Rabello, Carmen Soria, Silvia P. Salgado, Eduardo Gotuzzo, Mar{\'{\i}}a G. Guzm{\'{a}}n, Pedro A. Mart{\'{\i}}nez, Hugo L{\'{o}}pez-Gatell, Jennifer Hegewisch-Taylor, Victor H. Borja-Aburto, Cesar Gonzalez, Eduardo M. Netto, Paola M. Saba Villarroel, Bruno Hoen, Patr{\'{\i}}cia Brasil, Ernesto T. A. Marques, Barry Rockx, Marion Koopmans, Xavier de Lamballerie, Thomas Jaenisch
{BMC} Infectious Diseases, 2019
DOI

The influence of biotinylation on the ability of a computer designed protein to detect B-cells producing anti-{HIV}-1 2F5 antibodies
Danilo F. Co{\^{e}}lho, Matheus V.F. Ferraz, Ernesto T.A. Marques, Roberto D. Lins, Isabelle F.T. Viana
Journal of Molecular Graphics and Modelling, 2019
DOI

Influence of directional positive Darwinian selection-driven evolution on arboviruses Dengue and Zika virulence and pathogenesis
Ricardo Dur{\~{a}}es-Carvalho, Louisa F. Ludwig-Begall, Marco Salemi, Roberto D. Lins, Ernesto T.A. Marques
Molecular Phylogenetics and Evolution, 2019
DOI

Duffy binding-like 1$\upalpha$ adhesin from Plasmodium falciparum recognizes {ABH} histo-blood group saccharide in a type specific manner
Isadora A. Oliveira, La{\'{e}}rcio Pol-Fachin, Sebasti{\~{a}}o T. de Carvalho, Roberto D. Lins, Thereza A. Soares, Ronaldo Mohana-Borges, Jorge L. Neves, Adriane R. Todeschini
Carbohydrate Polymers, 2019
DOI

Rational Zika vaccine design via the modulation of antigen membrane anchors in chimpanzee adenoviral vectors
López-Camacho, César, Abbink, Peter, Larocca, Rafael A., Dejnirattisai, Wanwisa, Boyd, Michael, Badamchi-Zadeh, Alex, Wallace, Zoë R., Doig, Jennifer, Velazquez, Ricardo Sanchez, Neto, Roberto Dias Lins, Coelho, Danilo F., Kim, Young Chan, Donald, Claire L., Owsianka, Ania, De Lorenzo, Giuditta, Kohl, Alain, Gilbert, Sarah C., Dorrell, Lucy, Mongkolsapaya, Juthathip, Patel, Arvind H., Screaton, Gavin R., Barouch, Dan H., Hill, Adrian V. S., Reyes-Sandoval, Arturo
Nature Communications, 2018
DOI

Aromatic Rings Commonly Used in Medicinal Chemistry: Force Fields Comparison and Interactions With Water Toward the Design of New Chemical Entities
Marcelo D. Pol{\^{e}}to, Victor H. Rusu, Bruno I. Grisci, Marcio Dorn, Roberto D. Lins, Hugo Verli
Frontiers in Pharmacology, 2018
DOI

Significant Performance Enhancement of Polymer Resins by Bioinspired Dynamic Bonding
Sungbaek Seo, Dong Woog Lee, Jin Soo Ahn, Keila Cunha, Emmanouela Filippidi, Sung Won Ju, Eeseul Shin, Byeong-Su Kim, Zachary A. Levine, Roberto D. Lins, Jacob N. Israelachvili, J. Herbert Waite, Megan T. Valentine, Joan Emma Shea, B. Kollbe Ahn
Advanced Materials, 2017
DOI

Polymyxin Binding to the Bacterial Outer Membrane Reveals Cation Displacement and Increasing Membrane Curvature in Susceptible but Not in Resistant Lipopolysaccharide Chemotypes
Denys E. S. Santos, La{\'{e}}rcio Pol-Fachin, Roberto D. Lins, Thereza A. Soares
Journal of Chemical Information and Modeling, 2017
DOI

Mapping Putative B-Cell Zika Virus {NS}1 Epitopes Provides Molecular Basis for Anti-{NS}1 Antibody Discrimination between Zika and Dengue Viruses
Marjorie C. L. C. Freire, La{\'{e}}rcio Pol-Fachin, Danilo F. Co{\^{e}}lho, Isabelle F. T. Viana, Tereza Magalh{\~{a}}es, Marli T. Cordeiro, Nico Fischer, Felix F. Loeffler, Thomas Jaenisch, Rafael F. Franca, Ernesto T. A. Marques, Roberto D. Lins
{ACS} Omega, 2017
DOI

Conformational stability of the epidermal growth factor ({EGF}) receptor as influenced by glycosylation, dimerization and {EGF} hormone binding
Eric S. Taylor, Laercio Pol-Fachin, Roberto D. Lins, Steven K. Lower
Proteins: Structure, Function, and Bioinformatics, 2017
DOI

Molecularly Smooth Self-Assembled Monolayer for High-Mobility Organic Field-Effect Transistors
Saurabh Das, Byoung Hoon Lee, Roscoe T. H. Linstadt, Keila Cunha, Youli Li, Yair Kaufman, Zachary A. Levine, Bruce H. Lipshutz, Roberto D. Lins, Joan-Emma Shea, Alan J. Heeger, B. Kollbe Ahn
Nano Letters, 2016
DOI

De Novo Design and Biophysical Characterization of an Affinity-Enhanced Protein Displaying the Structure of the Broadly Neutralizing {HIV}-1 2F5 Antibody Epitope
Isabelle Freire Tabosa Viana, Eduardo Nascimento, Jodi Craigo, Marco Krieger, Robbie Mailliard, Rafael Dhalia, Roberto Lins, Ernesto T.A. Marques
Biophysical Journal, 2016
DOI

Endovascular Infections Caused by Methicillin-Resistant Staphylococcus aureus Are Linked to Clonal Complex-Specific Alterations in Binding and Invasion Domains of Fibronectin-Binding Protein A as Well as the Occurrence of {fnbB
Yan Q. Xiong, Batu K. Sharma-Kuinkel, Nadia N. Casillas-Ituarte, Vance G. Fowler, Thomas Rude, Alex C. DiBartola, Roberto D. Lins, Wessam Abdel-Hady, Steven K. Lower, Arnold S. Bayer
Infection and Immunity, 2015
DOI

Assessing protein conformational sampling and structural stability via de novo design and molecular dynamics simulations
Keila C. Cunha, Victor H. Rusu, Isabelle F. T. Viana, Ernesto T. A. Marques, Rafael Dhalia, Roberto D. Lins
Biopolymers, 2015
DOI

Comparative hazard analysis and toxicological modeling of diverse nanomaterials using the embryonic zebrafish (EZ) metric of toxicity
Harper, Bryan, Thomas, Dennis, Chikkagoudar, Satish, Baker, Nathan, Tang, Kaizhi, Heredia-Langner, Alejandro, Lins, Roberto, Harper, Stacey
Journal of Nanoparticle Research, 2015
DOI

Extension and validation of the {GROMOS} 53A6glycparameter set for glycoproteins
Laercio Pol-Fachin, Hugo Verli, Roberto D. Lins
Journal of Computational Chemistry, 2014
DOI

Anionic Form of Usnic Acid Promotes Lamellar to Nonlamellar Transition in DPPC and DOPC Membranes
Nadvorny, Daniela, da Silva, Joao Bosco P., Lins, Roberto D.
Journal of Physical Chemistry B, 2014
DOI

Desorption/ionization efficiencies of triacylglycerols and phospholipids via EASI-MS
Fernandes, Anna Maria A. P., Fernandes, Gabriel D., Barrera-Arellano, Daniel, de Sa, Gilberto F., Lins, Roberto D., Eberlin, Marcos N., Alberici, Rosana M.
Journal of Mass Spectrometry, 2014
DOI

Development of fine- and coarse-grained carbohydrate force fields: When one size fits all
Lins, Roberto D.
Abstracts of Papers of the American Chemical Society, 2014
DOI

GROMOS 53A6(GLYC) force field for aldohexopyranoses and glycoproteins
Pol-Fachin, Laercio, Verli, Hugo, Lins, Roberto Dias
Abstracts of Papers of the American Chemical Society, 2014
DOI

Hydration, ionic valence and cross-linking propensities of cations determine the stability of lipopolysaccharide (LPS) membranes
Nascimento, Agrinaldo, Jr., Pontes, Frederico J. S., Lins, Roberto D., Soares, Thereza A.
Chemical Communications, 2014
DOI

MDWiZ: A platform for the automated translation of molecular dynamics simulations
Rusu, Victor H., Horta, Vitor A. C., Horta, Bruno A. C., Lins, Roberto D., Baron, Riccardo
Journal of Molecular Graphics & Modelling, 2014
DOI

PITOMBA: Parameter Interface for Oligosaccharide Molecules Based on Atoms
Rusu, Victor H., Baron, Riccardo, Lins, Roberto D.
Journal of Chemical Theory and Computation, 2014
DOI

De novo design of immunoreactive conformation-specific HIV-1 epitopes based on Top7 scaffold
Viana, Isabelle F. T., Soares, Thereza A., Lima, Lucianna F. O., Marques, Ernesto T. A., Krieger, Marco A., Dhalia, Rafael, Lins, Roberto D.
Rsc Advances, 2013
DOI

IMSPeptider: A computational peptide collision cross-section area calculator based on a novel molecular dynamics simulation protocol
de Carvalho, Ranieri V., Lopez-Ferrer, Daniel, Guimaraes, Katia S., Lins, Roberto D.
Journal of Computational Chemistry, 2013
DOI

Influence of Scaffold Stability and Electrostatics on Top7-Based Engineered Helical HIV-1 Epitopes
Viana, Isabelle F. T., Dhalia, Rafael, Krieger, Marco A., Marques, Ernesto T. A., Lins, Roberto D., Setubal, JC, Almeida, NF
Advances in Bioinformatics and Computational Biology, 2013
DOI

Novel coarse-grained force field for carbohydrates
Rusu, Victor H., Baron, Riccardo, Lins, Roberto D.
Abstracts of Papers of the American Chemical Society, 2013
DOI

A Glycam-Based Force Field for Simulations of Lipopolysaccharide Membranes: Parametrization and Validation
Kirschner, Karl N., Lins, Roberto D., Maass, Astrid, Soares, Thereza A.
Journal of Chemical Theory and Computation, 2012
DOI

GROMOS 53A6(GLYC), an Improved GROMOS Force Field for Hexopyranose-Based Carbohydrates
Pol-Fachin, Laercio, Rusu, Victor H., Verli, Hugo, Lins, Roberto D.
Journal of Chemical Theory and Computation, 2012
DOI

The Effect of Temperature, Cations, and Number of Acyl Chains on the Lamellar to Non-Lamellar Transition in Lipid-A Membranes: A Microscopic View
Pontes, Frederico J. S., Rusu, Victor H., Soares, Thereza A., Lins, Roberto D.
Journal of Chemical Theory and Computation, 2012
DOI

Chitosan Molecular Structure as a Function of N-Acetylation
Franca, Eduardo F., Freitas, Luiz C. G., Lins, Roberto D.
Biopolymers, 2011
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Conformational Variability of Organophosphorus Hydrolase upon Soman and Paraoxon Binding
Gomes, Diego E. B., Lins, Roberto D., Pascutti, Pedro G., Lei, Chenghong, Soares, Thereza A.
Journal of Physical Chemistry B, 2011
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Modeling the Nanophase Structural Dynamics of Phenylated Sulfonated Poly Ether Ether Ketone Ketone (Ph-SPEEKK) Membranes As a Function of Hydration
Lins, Roberto D., Devanathan, Ram, Dupuis, Michel
Journal of Physical Chemistry B, 2011
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Molecular modeling of ion transport and water percolation in Nafion and Ph-SPEEKK membranes
Devanathan, Ram, Lins, Roberto, Idupulapati, Nagesh, Venkatnathan, Arun, Dupuis, Michel
Abstracts of Papers of the American Chemical Society, 2011
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Polymorphisms in fibronectin binding protein A of Staphylococcus aureus are associated with infection of cardiovascular devices
Lower, Steven K., Lamlertthon, Supaporn, Casillas-Ituarte, Nadia N., Lins, Roberto D., Yongsunthon, Ruchirej, Taylor, Eric S., DiBartola, Alex C., Edmonson, Catherine, McIntyre, Lauren M., Reller, L. Barth, Que, Yok-Ai, Ros, Robert, Lower, Brian H., Fowler, Vance G., Jr.
Proceedings of the National Academy of Sciences of the United States of America, 2011
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Prebiotic Chemical Kinetics Imprint on Positional Codon Usage
Ferreira, Ricardo, Lai, Kevin, Lins, Roberto D.
Journal of the Brazilian Chemical Society, 2010
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The Role of Nonbonded Interactions in the Conformational Dynamics of Organophosphorous Hydrolase Adsorbed onto Functionalized Mesoporous Silica Surfaces
Gomes, Diego E. B., Lins, Roberto D., Pascutti, Pedro G., Lei, Chenghong, Soares, Thereza A.
Journal of Physical Chemistry B, 2010
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Electrostatic Cooperativity of Hydroxyl Groups at Metal Oxide Surfaces
Boily, Jean-Francois, Lins, Roberto D.
Journal of Physical Chemistry C, 2009
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Interaction between the CBM of Cel9A from Thermobifida fusca and cellulose fibers
Oliveira, Osmair V., Freitas, Luiz C. G., Straatsma, T. P., Lins, Roberto D.
Journal of Molecular Recognition, 2009
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Molecular structure of chitosan nanoparticles in solution
Lins, Roberto D., Franca, Eduardo F., Freitas, Luiz C. G.
Abstracts of Papers of the American Chemical Society, 2009
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Characterization of Chitin and Chitosan Molecular Structure in Aqueous Solution
Franca, Eduardo F., Lins, Roberto D., Freitas, Luiz C. G., Straatsma, T. P.
Journal of Chemical Theory and Computation, 2008
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Computer simulation of uranyl uptake by the rough lipopolysaccharide membrane of pseudomonas aeruginosa
Lins, Roberto D., Vorpagel, Erich R., Guglielmi, Matteo, Straatsma, T. P.
Biomacromolecules, 2008
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In vitro evolution of a peptide with a hematite binding motif that may constitute a natural metal-oxide binding archetype
Lower, Brian H., Lins, Roberto D., Oestreicher, Zachery, Straatsma, Tjerk P., Hochella, Michael F., Jr., Shi, Liang, Lower, Steven K.
Environmental Science & Technology, 2008
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Influence of the B-band O-antigen chain in the structure and electrostatics of the lipopolysaccharide membrane of Pseudomonas aeruginosa
Soares, Thereza A., Straatsma, T. P., Lins, Roberto D.
Journal of the Brazilian Chemical Society, 2008
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Molecular models to emulate confinement effects on the internal dynamics of organophosphorous hydrolase
Gomes, Diego E. B., Lins, Roberto D., Pascutti, Pedro G., Straatsma, Tjerk P., Soares, Thereza A., Bazzan, ALC, Craven, M, Martins, NF
, 2008
DOI

Revisiting the internal conformational dynamics and solvation properties of cyclodextrins
Pereira, Cristina S., de Moura, Andre F., Freitas, Lutz Carlos G., Lins, Roberto A.
Journal of the Brazilian Chemical Society, 2007
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Influence of long-range electrostatic treatments on the folding of the N-terminal H4 histone tail peptide
Lins, RD, Rothlisberger, U
Journal of Chemical Theory and Computation, 2006
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Protein under pressure: Molecular dynamics simulation of the arc repressor
Trzesniak, Daniel, Lins, Roberto D., van Gunsteren, Wilfred F.
Proteins-Structure Function and Bioinformatics, 2006
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The stability of right- and left-handed alpra-helices as a function of monomer chirality
Lins, Roberto Dias, Ferreira, Ricardo
Quimica Nova, 2006
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A new GROMOS force field for hexopyranose-based carbohydrates
Lins, RD, Hunenberger, PH
Journal of Computational Chemistry, 2005
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An improved nucleic acid parameter set for the GROMOS force field
Soares, TA, Hunenberger, PH, Kastenholz, MA, Krautler, V, Lenz, T, Lins, RD, Oostenbrink, C, Van Gunsteren, WF
Journal of Computational Chemistry, 2005
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Variational particle number approach for rational compound design
von Lilienfeld, OA, Lins, RD, Rothlisberger, U
Physical Review Letters, 2005
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Interaction of the disaccharide trehalose with a phospholipid bilayer: A molecular dynamics study
Pereira, CS, Lins, RD, Chandrasekhar, I, Freitas, LCG, Hunenberger, PH
Biophysical Journal, 2004
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Prediction of HIV-1 integrase/viral DNA interactions in the catalytic domain by fast molecular docking
Adesokan, AA, Roberts, VA, Lee, KW, Lins, RD, Briggs, JM
Journal of Medicinal Chemistry, 2004
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Trehalose-protein interaction in aqueous solution
Lins, RD, Pereira, CS, Hunenberger, PH
Proteins-Structure Function and Bioinformatics, 2004
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A consistent potential energy parameter set for lipids: dipalmitoylphosphatidylcholine as a benchmark of the GROMOS96 45A3 force field
Chandrasekhar, I, Kastenholz, M, Lins, RD, Oostenbrink, C, Schuler, LD, Tieleman, DP, van Gunsteren, WF
European Biophysics Journal With Biophysics Letters, 2003
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Internal dynamics and ionization states of the macrophage migration inhibitory factor: Comparison between wild-type and mutant forms
Soares, TA, Lins, RD, Straatsma, TP, Briggs, JM
Biopolymers, 2002
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Computer simulation of the rough lipopolysaccharide membrane of Pseudomonas aeruginosa
Lins, RD, Straatsma, TP
Biophysical Journal, 2001
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Electrostatic interactions in biomolecular systems
Hunenberger, PH, Borjesson, U, Lins, RD
Chimia, 2001
DOI

Developing a dynamic pharmacophore model for HIV-1 integrase
Carlson, HA, Masukawa, KM, Rubins, K, Bushman, FD, Jorgensen, WL, Lins, RD, Briggs, JM, McCammon, JA
Journal of Medicinal Chemistry, 2000
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Investigations on human immunodeficiency virus type 1 integrase/DNA binding interactions via molecular dynamics and electrostatics calculations
Lins, RD, Adesokan, A, Soares, TA, Briggs, JM
Pharmacology & Therapeutics, 2000
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Similarities in the HIV-1 and ASV integrase active sites upon metal cofactor binding
Lins, RD, Straatsma, TP, Briggs, JM
Biopolymers, 2000
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A dynamic pharmacophore model for HIV-1 integrase.
Carlson, HA, Masukawa, KM, Lins, RD, Briggs, JM, Jorgensen, WL, McCammon, JA
Abstracts of Papers of the American Chemical Society, 1999
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Molecular dynamics studies on the HIV-1 integrase catalytic domain
Lins, RD, Briggs, JM, Straatsma, TP, Carlson, HA, Greenwald, J, Choe, S, McCammon, JA
Biophysical Journal, 1999
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Solvent accessibility to aspartyl and succinimidyl residues at positions 7 and 23 in the amyloid beta 1-28 peptide
Lins, RD, Soares, TA, Ferreira, R, Longo, RL
Zeitschrift Fur Naturforschung C-a Journal of Biosciences, 1999
DOI

Brownian and essential dynamics studies of the HIV-1 integrase catalytic domain
Weber, W, Demirdjian, H, Lins, RD, Briggs, JM, Ferreira, R, McCammon, JA
Journal of Biomolecular Structure & Dynamics, 1998
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Plural origins of molecular homochirality in our biota .2. The relative stabilities of homochiral and mixed oligoribotides and peptides
Soares, TA, Lins, RD, Longo, R, Garratt, R, Ferreira, R
Zeitschrift Fur Naturforschung C-a Journal of Biosciences, 1997
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Plural origins of the molecular homochirality in our biota
Lins, RD, Soares, TA, Ferreira, R
Zeitschrift Fur Naturforschung C-a Journal of Biosciences, 1996
DOI

RIBOZYMES - NOT EVERY ENZYME IS A PROTEIN
SOARES, TA, LINS, RD
Quimica Nova, 1995
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