Fernando Luis Barroso da Silva

Works (9)

Updated: August 4th, 2025 15:10

2025 article

Biophysics of SARS-CoV-2 spike protein’s receptor-binding domain interaction with ACE2 and neutralizing antibodies: from computation to functional insights

Silva, F. L. B., Paco, K., Laaksonen, A., & Ray, A. (2025, March 8). Biophysical Reviews.

By: F. Silva n, K. Paco *, A. Laaksonen * & A. Ray *

author keywords: Electrostatic interactions; pH effects; Molecular simulation; Complexation; Antibodies; Virus; Transmissibility
topics (OpenAlex): SARS-CoV-2 and COVID-19 Research; Computational Drug Discovery Methods; thermodynamics and calorimetric analyses
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Source: Web Of Science
Added: March 17, 2025

2022 article

Differences between Omicron SARS-CoV-2 RBD and other variants in their ability to interact with cell receptors and monoclonal antibodies

Giron, C. C., Laaksonen, A., & Silva, F. L. B. (2022, July 9). Journal of Biomolecular Structure and Dynamics.

By: C. Giron *, A. Laaksonen * & F. Silva n

author keywords: Protein-protein interactions; host-pathogen interaction; ACE2 polymorphism; molecular recognition; antibody; development; binding affinities; Covid-19; Monte Carlo
topics (OpenAlex): SARS-CoV-2 and COVID-19 Research; Monoclonal and Polyclonal Antibodies Research; Computational Drug Discovery Methods; COVID-19 Clinical Research Studies; SARS-CoV-2 detection and testing
TL;DR: This work aims to expand the knowledge about the SARS-CoV-2 receptor-binding domain (RBD) interactions with cell receptors and monoclonal antibodies (mAbs) and found these mAbs and especially their combination are amenable to experimentation and clinical trials because of their high binding affinities and neutralization potential for current known virus mutations and a universal coronavirus. (via Semantic Scholar)
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Source: Web Of Science
Added: July 18, 2022

2022 article

Self-association features of NS1 proteins from different flaviviruses

Poveda-Cuevas, S. A., Etchebest, C., & Silva, F. L. B. (2022, May 31). Virus Research.

By: S. Poveda-Cuevas *, C. Etchebest & F. Silva*

author keywords: Protein -protein interaction; Free energy; Non-structural protein 1; pH; Monte Carlo simulations
MeSH headings : Flavivirus; Humans; Viral Nonstructural Proteins / metabolism; Virus Replication; West Nile virus; Zika Virus / metabolism; Zika Virus Infection
topics (OpenAlex): Mosquito-borne diseases and control; HIV Research and Treatment; Vibrio bacteria research studies
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Source: Web Of Science
Added: July 26, 2022

2022 article

Towards an optimal monoclonal antibody with higher binding affinity to the receptor-binding domain of SARS-CoV-2 spike proteins from different variants

Neamtu, A., Mocci, F., Laaksonen, A., & Silva, F. L. B. (2022, October 29). Colloids and Surfaces B Biointerfaces.

By: A. Neamtu *, F. Mocci *, A. Laaksonen * & F. Silva n

author keywords: COVID-19; Molecular dynamics; Coarse -grain simulation; Constant -pH Monte Carlo; Multiscale protocol; Electrostatic interactions
MeSH headings : Humans; Spike Glycoprotein, Coronavirus / genetics; SARS-CoV-2; COVID-19; Antibodies, Monoclonal; Edible Grain
topics (OpenAlex): SARS-CoV-2 and COVID-19 Research; Bacteriophages and microbial interactions; Monoclonal and Polyclonal Antibodies Research
TL;DR: Although the SARS-CoV-2 was specifically targeted in this work, the approach is generally suitable for many diseases and viral and bacterial pathogens, leukemia, cancer, multiple sclerosis, rheumatoid, arthritis, lupus, and more. (via Semantic Scholar)
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Source: Web Of Science
Added: December 19, 2022

2021 article

How the Strain Origin of Zika Virus NS1 Protein Impacts Its Dynamics and Implications to Their Differential Virulence

Poveda-Cuevas, S. A., Silva, F. L. B., & Etchebest, C. (2021, March 2). Journal of Chemical Information and Modeling.

By: S. Poveda-Cuevas *, F. Silva n & C. Etchebest

MeSH headings : Humans; Viral Nonstructural Proteins; Virulence; Zika Virus; Zika Virus Infection
topics (OpenAlex): Mosquito-borne diseases and control; COVID-19 epidemiological studies; Virology and Viral Diseases
TL;DR: This work has used a computational approach to explore the dynamical properties of the nonstructural protein 1 from two strains of Zika virus and shows that despite a high sequence similarity, the two viral proteins from different origins can exhibit significant dissimilar structural dynamics, which complement their reported differential virulence. (via Semantic Scholar)
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Source: Web Of Science
Added: May 10, 2021

2020 journal article

Exploring the physicochemical and morphological properties of peptide‐hybridized dendrimers ( DendriPeps ) and their aggregates

Journal of Polymer Science, 58(16), 2234–2247.

By: R. Smith n, T. Fabiani n, S. Wang n, S. Ramesh n, S. Khan n , E. Santiso n , F. Silva*, C. Gorman n , S. Menegatti n 

author keywords: dendrimets; DendriPeps; molecular dynamics; PAMAM; reversible aggregation
topics (OpenAlex): Dendrimers and Hyperbranched Polymers; Chemical Synthesis and Analysis; Advanced Polymer Synthesis and Characterization
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Sources: Web Of Science, NC State University Libraries, Crossref
Added: July 27, 2020

2020 article

On the interactions of the receptor-binding domain of SARS-CoV-1 and SARS-CoV-2 spike proteins with monoclonal antibodies and the receptor ACE2

Giron, C. C., Laaksonen, A., & Silva, F. L. B. (2020, May 15). Virus Research.

By: C. Giron *, A. Laaksonen * & F. Silva n

author keywords: Epitopes; Binding affinity; Antibody development; Host-pathogen interaction; Electrostatic interactions; Antigenic analysis; Computer simulation; pH effect; Coronavirus; SARS-CoV-2; ACE2; Protein-protein interaction
MeSH headings : Angiotensin-Converting Enzyme 2; Antibodies, Monoclonal / immunology; Antibodies, Monoclonal / metabolism; Antibodies, Viral / immunology; Antibodies, Viral / metabolism; Betacoronavirus / chemistry; Betacoronavirus / immunology; Computer Simulation; Epitope Mapping; Humans; Models, Molecular; Monte Carlo Method; Peptidyl-Dipeptidase A / chemistry; Peptidyl-Dipeptidase A / metabolism; Protein Binding; Protein Conformation; Protein Interaction Domains and Motifs; Protein Interaction Mapping; Receptors, Virus / chemistry; Receptors, Virus / metabolism; Severe acute respiratory syndrome-related coronavirus / chemistry; Severe acute respiratory syndrome-related coronavirus / immunology; SARS-CoV-2; Spike Glycoprotein, Coronavirus / chemistry; Spike Glycoprotein, Coronavirus / immunology; Spike Glycoprotein, Coronavirus / metabolism; Thermodynamics
topics (OpenAlex): SARS-CoV-2 and COVID-19 Research; Viral gastroenteritis research and epidemiology; Monoclonal and Polyclonal Antibodies Research
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Source: Web Of Science
Added: July 6, 2020

2019 article

Coarse-grained dynamic RNA titration simulations

Pasquali, S., Frezza, E., & Silva, F. L. B. (2019, April 19). Interface Focus.

By: S. Pasquali *, E. Frezza * & F. Silva n

author keywords: RNA; titration; pH; coarse-grained model
topics (OpenAlex): RNA and protein synthesis mechanisms; RNA modifications and cancer; RNA Research and Splicing
TL;DR: Molecular dynamic simulations of RNA molecules at constant pH enable us to explore the RNA conformational plasticity at different pH values as well as to compute electrostatic properties as local pKa values for each nucleotide. (via Semantic Scholar)
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Added: May 13, 2019

2019 article

Identification of Electrostatic Epitopes in Flavivirus by Computer Simulations: The PROCEEDpKa Method

Poveda-Cuevas, S. A., Etchebest, C., & Silva, F. L. B. (2019, November 27). Journal of Chemical Information and Modeling.

By: S. Poveda-Cuevas *, C. Etchebest * & F. Silva n

MeSH headings : Antibodies, Viral / chemistry; Antibodies, Viral / immunology; Epitopes / chemistry; Epitopes / immunology; Flavivirus / immunology; Models, Molecular; Monte Carlo Method; Protein Conformation; Static Electricity
topics (OpenAlex): HIV Research and Treatment; Mosquito-borne diseases and control; vaccines and immunoinformatics approaches
TL;DR: It is found that it is possible to predict antigenic epitopes reproducing the interfaces as defined by the X-ray structure, and this opens up an important discussion about what are termed here "electrostatic epitopes" and how they work as an important reference in the paratope-epitope interaction for viral systems. (via Semantic Scholar)
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Source: Web Of Science
Added: April 20, 2020

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