A5078237425- Scientific Computing and Data Management
- Genetics, Bioinformatics, and Biomedical Research
- Gene expression and cancer classification
- Distributed and Parallel Computing Systems
- Computational Drug Discovery Methods
- Genomics and Phylogenetic Studies
- Cloud Computing and Resource Management
- Protein Structure and Dynamics
- SARS-CoV-2 and COVID-19 Research
- Evolutionary Algorithms and Applications
- Click Chemistry and Applications
- Data Mining Algorithms and Applications
- CRISPR and Genetic Engineering
- Algorithms and Data Compression
- COVID-19 Clinical Research Studies
- Spectroscopy and Quantum Chemical Studies
- Advanced Chemical Physics Studies
Laboratório Nacional de Computação Científica
2016-2024
Abstract The COVID-19 caused by the SARS-CoV-2 virus was declared a pandemic disease in March 2020 World Health Organization (WHO). Structure-Based Drug Design strategies based on docking methodologies have been widely used for both new drug development and repurposing to find effective treatments against this disease. In work, we present developments implemented DockThor-VS web server provide virtual screening (VS) platform with curated structures of potential therapeutic targets from...
Rotational Profiler provides an analytical algorithm to compute sets of classical torsional dihedral parameters by fitting empirical energy profile a reference one that can be obtained experimentally or quantum-mechanical methods. The resulting profiles are compatible with the functional forms in most widely used biomolecular force fields (e.g., GROMOS, AMBER, OPLS, and CHARMM). linear least-squares regression method is generate best satisfy fitting. free use, analytical, field/package...
Abstract The COVID-19 caused by the SARS-CoV-2 virus was declared as a pandemic disease in March 2020 World Health Organization (WHO). Structure-Based Drug Design strategies based on docking methodologies have been widely used for both new drug development and repurposing to find effective treatments against this disease. In work, we present developments implemented DockThor-VS web server provide virtual screening (VS) platform with curated structures of potential therapeutic targets from...
Science gateways bring out the possibility of reproducible science as they are integrated into reusable techniques, data and workflow management systems, security mechanisms, high performance computing (HPC). We introduce BioinfoPortal, a gateway that integrates suite different bioinformatics applications using HPC resources provided by Brazilian National System (SINAPAD). BioinfoPortal follows Software Service (SaaS) model web server is freely available for academic use. The goal this paper...
Gateways científicos trazem enormes benefícios para usuários finais, simplificando o acesso e ocultando a complexidade da infraestrutura de computação distribuída subjacente. O gateway científico bioinformática, BioinfoPortal, por meio do seu middleware CSGrid, usufrui dos recursos heterogêneos Santos Dumont. No entanto, submissão tarefas ainda exige um esforço significativo, no que tange à decisão melhor configuração leve uma execução eficiente. framework aprendizado máquina, em...
Transcriptomics experiments are often expressed as scientific workflows and benefit from high-performance computing environments. In these environments, workflow management systems can allow handling independent or communicating tasks across nodes, which may be heterogeneous. Specifically, transcriptomics treat large volumes of data. ParslRNA-Seq is a for analyzing RNA-Seq experiments, efficiently manages the estimation differential gene expression levels raw sequencing reads executed in...
Bioinformatics experiments are rapidly and constantly evolving due improvements in sequencing technologies. These usually demand high performance computation produce huge quantities of data. They also require different programs to be executed a certain order, allowing the modeled as workflows. However, users do not always have infrastructure needed perform these experiments. Our contribution is integration scientific workflow management systems grid-enabled gateways, providing user with...
Bioinformatics, especially the areas of phylogeny and evolution organisms, requires high performance computing (HPC) environments. The present work presents a behavioral analysis RAxML tool in HPC implements parallelism task distribution by using threads MPI libraries. Executions were performed Santos Dumont (SDumont) supercomputer. Efficiency results show impact is generated variation configuration, coupling use SDumont. This information will allow better understanding efficient these specialized
Bioinformatics experiments are rapidly and constantly evolving due improvements in sequencing technologies. These usually demand high performance computation produce huge quantities of data. They also require different programs to be executed a certain order, allowing the modeled as workflows. However, users do not always have infrastructure needed perform these experiments. Our contribution is integration scientific workflow management systems grid-enabled gateways, providing user with...