Lucianna Helene Santos
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View article: Unraveling Common Patterns and Differences among Cruzipains through Molecular Dynamics Simulations and Structural Analyses
Unraveling Common Patterns and Differences among Cruzipains through Molecular Dynamics Simulations and Structural Analyses Open
Chagas disease (CD) is a neglected tropical disease for which novel and improved treatments are needed. The cysteine protease Cruzipain is one of the main targets for the development of novel drugs for the treatment of CD. Recent bioinform…
View article: Pragmatic Coarse-Graining of Proteins: Models and Applications
Pragmatic Coarse-Graining of Proteins: Models and Applications Open
The molecular details involved in the folding, dynamics, organization, and interaction of proteins with other molecules are often difficult to assess by experimental techniques. Consequently, computational models play an ever-increasing ro…
View article: Evaluating Known Zika Virus NS2B-NS3 Protease Inhibitor Scaffolds via In Silico Screening and Biochemical Assays
Evaluating Known Zika Virus NS2B-NS3 Protease Inhibitor Scaffolds via In Silico Screening and Biochemical Assays Open
The NS2B-NS3 protease (NS2B-NS3pro) is regarded as an interesting molecular target for drug design, discovery, and development because of its essential role in the Zika virus (ZIKV) cycle. Although no NS2B-NS3pro inhibitors have reached cl…
View article: BIOINFO #03 - Revista Brasileira de Bioinformática e Biologia Computacional
BIOINFO #03 - Revista Brasileira de Bioinformática e Biologia Computacional Open
A Revista BIOINFO é a primeira revista brasileira voltada a publicação de trabalhos de divulgação científica em bioinformática e biologia computacional, publicada em língua portuguesa e voltada ao público universitário. De setembro de 2022…
View article: Editorial: Bioinformatics in the age of data science: algorithms, methods, and tools applied from Omics to structural data
Editorial: Bioinformatics in the age of data science: algorithms, methods, and tools applied from Omics to structural data Open
In recent years, researchers have been confronted with an overwhelming influx of data, resulting 13 from novel technologies utilized for sequencing data and acquiring three-dimensional structures of 14 macromolecules. The increasing demand…
View article: The SIRAH force field: A suite for simulations of complex biological systems at the coarse-grained and multiscale levels
The SIRAH force field: A suite for simulations of complex biological systems at the coarse-grained and multiscale levels Open
View article: Structure-based discovery of novel cruzain inhibitors with distinct trypanocidal activity profiles
Structure-based discovery of novel cruzain inhibitors with distinct trypanocidal activity profiles Open
View article: Substrate Recognition Properties from an Intermediate Structural State of the UreA Transporter
Substrate Recognition Properties from an Intermediate Structural State of the UreA Transporter Open
Through a combination of comparative modeling, site-directed and classical random mutagenesis approaches, we previously identified critical residues for binding, recognition, and translocation of urea, and its inhibition by 2-thiourea and …
View article: BIOINFO #02 - Revista Brasileira de Bioinformática e Biologia Computacional
BIOINFO #02 - Revista Brasileira de Bioinformática e Biologia Computacional Open
Aqui apresentamos a segunda edição da Revista BIOINFO. Nesta nova edição, disponibilizamos 10 novos artigos relacionados a bioinformática e a biologia computacional. BIOINFO é um projeto amplo que engloba um portal (disponível em https://w…
View article: Using Computers to Improve Biofuel Production
Using Computers to Improve Biofuel Production Open
Petroleum is the most-used energy source in the world. However, as you probably know, petroleum is a fossil fuel that is very harmful to the environment, in addition to not being renewable. Biofuels are a type of fuel produced from plant m…
View article: Rad5 HIRAN domain: Structural insights into its interaction with ssDNA through molecular modeling approaches
Rad5 HIRAN domain: Structural insights into its interaction with ssDNA through molecular modeling approaches Open
The Rad5 protein is an SWI/SNF family ubiquitin ligase that contains an N-terminal HIRAN domain and a RING C3HC4 motif. The HIRAN domain is critical for recognition of the stalled replication fork during the replication process and acts as…
View article: Bacterial 2′-Deoxyguanosine Riboswitch Classes as Potential Targets for Antibiotics: A Structure and Dynamics Study
Bacterial 2′-Deoxyguanosine Riboswitch Classes as Potential Targets for Antibiotics: A Structure and Dynamics Study Open
The spread of antibiotic-resistant bacteria represents a substantial health threat. Current antibiotics act on a few metabolic pathways, facilitating resistance. Consequently, novel regulatory inhibition mechanisms are necessary. Riboswitc…
View article: Structure-based identification of naphthoquinones and derivatives as novel inhibitors of main protease Mpro and papain-like protease PLpro of SARS-CoV-2
Structure-based identification of naphthoquinones and derivatives as novel inhibitors of main protease Mpro and papain-like protease PLpro of SARS-CoV-2 Open
The worldwide COVID-19 pandemic caused by the coronavirus SARS-CoV-2 urgently demands novel direct antiviral treatments. The main protease (Mpro) and papain-like protease (PLpro) are attractive drug targets among coronaviruses due to their…
View article: An Alphafold2 Intermediate Conformational State Provides Insights on Urea Transporter Function
An Alphafold2 Intermediate Conformational State Provides Insights on Urea Transporter Function Open
View article: Rad5 HIRAN domain: Structural insights into its interaction with ssDNA through molecular modeling approaches
Rad5 HIRAN domain: Structural insights into its interaction with ssDNA through molecular modeling approaches Open
The Rad5 protein is an SWI/SNF family ubiquitin ligase that contains an N-terminal HIRAN domain and a RING C3HC4 motif. The HIRAN domain is critical for recognition of the stalled replication fork during the replication process and acts as…
View article: Structure-based identification of naphthoquinones and derivatives as novel inhibitors of main protease (Mpro) and papain-like protease (PLpro) of SARS-CoV-2
Structure-based identification of naphthoquinones and derivatives as novel inhibitors of main protease (Mpro) and papain-like protease (PLpro) of SARS-CoV-2 Open
Mmolecular dynamics simulation data of Mpro and PLpro proteases with the screened and tested inhibitors, in explicit solvent systems, description regarding execution is provided in the respective manuscript. Simulation systems are coded as…
View article: Structure-based identification of naphthoquinones and derivatives as novel inhibitors of main protease (Mpro) and papain-like protease (PLpro) of SARS-CoV-2
Structure-based identification of naphthoquinones and derivatives as novel inhibitors of main protease (Mpro) and papain-like protease (PLpro) of SARS-CoV-2 Open
Mmolecular dynamics simulation data of Mpro and PLpro proteases with the screened and tested inhibitors, in explicit solvent systems, description regarding execution is provided in the respective manuscript. Simulation systems are coded as…
View article: Docagem molecular: em busca do encaixe perfeito e acessível
Docagem molecular: em busca do encaixe perfeito e acessível Open
ocagem molecular é um dos métodos mais populares da modelagem molecular.Essa técnica computacional visa buscar "o encaixe perfeito" entre duas moléculas simulando assim o processo de reconhecimento molecular.A partir da predição de orienta…
View article: Modelagem computacional de proteínas
Modelagem computacional de proteínas Open
modelos, com níveis variáveis entre dados experimentais e predição computacional [2].Geralmente, para se obter as coordenadas atômicas de átomos pesados
View article: Propedia: a database for protein–peptide identification based on a hybrid clustering algorithm
Propedia: a database for protein–peptide identification based on a hybrid clustering algorithm Open
View article: Antigenic and Substrate Preference Differences between Scorpion and Spider Dermonecrotic Toxins, a Comparative Investigation
Antigenic and Substrate Preference Differences between Scorpion and Spider Dermonecrotic Toxins, a Comparative Investigation Open
The Hemiscorpius lepturus scorpion and brown spider Loxosceles intermedia represent a public health problem in Asia and America, respectively. Although distinct, these organisms contain similar toxins responsible for the principal clinical…
View article: Milk-Way algorithm for ligand-based virtual screening: CDK2 case study
Milk-Way algorithm for ligand-based virtual screening: CDK2 case study Open
Ligand-based screening of large molecular databases can help reduce costs with experiments by filtering and ranking promising compounds in an initial stage of the drug developing process.However, some ligand-based methods can be ineffectiv…
View article: Profiling selectivity of chagasin mutants towards cysteine proteases cruzain or cathepsin L through molecular dynamics simulations
Profiling selectivity of chagasin mutants towards cysteine proteases cruzain or cathepsin L through molecular dynamics simulations Open
Chagasin, an endogenous cysteine protease inhibitor from Trypanosoma cruzi, can control the activity of the parasitic cruzain and its homologous human cathepsin L. While chagasin inhibits both enzymes with similar potency, mutations…
View article: Proteus: An algorithm for proposing stabilizing mutation pairs based on interactions observed in known protein 3D structures
Proteus: An algorithm for proposing stabilizing mutation pairs based on interactions observed in known protein 3D structures Open
View article: Glutantβase: a database for improving the rational design of glucose-tolerant β-glucosidases
Glutantβase: a database for improving the rational design of glucose-tolerant β-glucosidases Open
Β-glucosidases are key enzymes used in second-generation biofuel production. They act in the last step of the lignocellulose saccharification, converting cellobiose in glucose. However, most of the β-glucosidases are inhibited by high gluc…
View article: Insights into the Mechanism of Ethionamide Resistance in Mycobacterium tuberculosis through an in silico Structural Evaluation of EthA and Mutants Identified in Clinical Isolates
Insights into the Mechanism of Ethionamide Resistance in Mycobacterium tuberculosis through an in silico Structural Evaluation of EthA and Mutants Identified in Clinical Isolates Open
Mutation in the ethionamide (ETH) activating enzyme, EthA, is the main factor determining resistance to this drug, used to treat TB patients infected with MDR and XDR Mycobacterium tuberculosis isolates. Many mutations in EthA of ETH resis…
View article: A Brief View of Molecular Modeling Approaches to P2 Receptors
A Brief View of Molecular Modeling Approaches to P2 Receptors Open
Purinergic receptors are a class of receptors distributed into two groups, P1 and P2. P1 receptors are activated by nucleosides, like adenosine, while nucleotides active P2 receptors. In turn, P2 receptors comprise two families, metabotrop…
View article: Benzimidazole Inhibitors of the Major Cysteine Protease of <i>Trypanosoma Brucei</i>
Benzimidazole Inhibitors of the Major Cysteine Protease of <i>Trypanosoma Brucei</i> Open
Aim: Limitations in available therapies for trypanosomiases indicate the need for improved medicines. Cysteine proteases cruzain and rhodesain are validated targets for treatment of Chagas disease and human African trypanosomiasis. …
View article: Introducing Programming Skills for Life Science Students
Introducing Programming Skills for Life Science Students Open
The advent of the high‐throughput next‐generation sequencing produced a large number of biological data. Knowledge discovery from the huge amount of available biological data requires researchers to develop solid skills in biology and comp…
View article: A Computational Method to Propose Mutations in Enzymes Based on Structural Signature Variation (SSV)
A Computational Method to Propose Mutations in Enzymes Based on Structural Signature Variation (SSV) Open
With the use of genetic engineering, modified and sometimes more efficient enzymes can be created for different purposes, including industrial applications. However, building modified enzymes depends on several in vitro experiments, which …