A5057489258- Bioinformatics and Genomic Networks
- Protein Structure and Dynamics
- Enzyme Structure and Function
- Genomics and Phylogenetic Studies
- Machine Learning in Bioinformatics
- Biomedical Text Mining and Ontologies
- Microbial Metabolic Engineering and Bioproduction
- Advanced Proteomics Techniques and Applications
- Computational Drug Discovery Methods
- Metabolomics and Mass Spectrometry Studies
- Fluid Dynamics and Turbulent Flows
- Microfluidic and Bio-sensing Technologies
- Insect symbiosis and bacterial influences
- Mosquito-borne diseases and control
- Blood properties and coagulation
- RNA and protein synthesis mechanisms
- Studies on Chitinases and Chitosanases
- Biochemical and Structural Characterization
- Scientific Computing and Data Management
- DNA and Nucleic Acid Chemistry
- Lipid Membrane Structure and Behavior
- Invertebrate Immune Response Mechanisms
- Neuroendocrine regulation and behavior
- Neuroscience and Neuropharmacology Research
- Cardiac electrophysiology and arrhythmias
European Bioinformatics Institute
2022-2025
Universidade Federal de Minas Gerais
2013-2022
Abstract The Protein Data Bank (PDB) is the primary global repository for experimentally determined 3D structures of biological macromolecules and their complexes with ligands, proteins, nucleic acids. PDB contains over 47,000 unique small molecules bound to macromolecules. Despite extensive data available, complexity small‐molecule in necessitates specialized tools effective analysis visualization. PDBe has developed a number tools, including CCDUtils ( https://github.com/PDBeurope/ccdutils...
Abstract The archiving and dissemination of protein nucleic acid structures as well their structural, functional biophysical annotations is an essential task that enables the broader scientific community to conduct impactful research in multiple fields life sciences. Protein Data Bank Europe (PDBe; pdbe.org ) team develops maintains several databases web services address this fundamental need. From data a member Worldwide PDB consortium (wwPDB; wwpdb.org ), PDBe Knowledge Base (PDBe‐KB;...
Cell membrane deformation is an important feature that occurs during many physiological processes, and its study has been put to good use investigate cardiomyocyte function. Several methods have developed extract information on contractility. However, no existing computational framework provided, in a single platform, straightforward approach acquire, process, quantify this type of cellular dynamics. For reason, we develop CONTRACTIONWAVE, high-performance software written Python programming...
Flaviviruses are responsible for serious diseases such as dengue, yellow fever, and zika fever. Their genomes encode a polyprotein which, after cleavage, results in three structural seven non-structural proteins. Homologous proteins can be studied by conservation coevolution analysis detected multiple sequence alignments, usually reporting positions which strictly necessary the structure and/or function of all members protein family or involved specific sub-class feature requiring residue...
Trypsin-like serine proteases are a group of homologous enzymes which exert multiple roles in both vertebrate and invertebrate organisms. Key properties these include their activation from an inactive zymogen form to active by cleavage residues N-terminus, the presence conserved catalytic triad residues, existence different patterns substrate selectivity for residue between various members this protein family. In article, we apply decomposition coevolution networks computational method find...
PFstats is a software developed for the extraction of useful information from protein multiple sequence alignments. By analyzing positional conservation and residue coevolution networks, allows identification structurally functionally important groups discovery probable functional subclasses. Furthermore, it contains tools possible biological significance these findings. methods maximizing alignments through filtering weighting, analysis, automatic UniprotKb queries residue-position...
Nuclear receptors (NRs) are transcription factors which bind small hormones, whose evolutionary history and the presence of different functional surfaces makes them an interesting target for a correlation based analysis. Correlation analysis ligand binding domains shows that correlated residue subsets arise from differences between sites in nuclear receptor subfamilies. For DNA domain, particularly, main source comes residues regulate hormone response element specificity, one conserved...
Abstract Summary CONAN is a web application developed to detect specificity determinants and function-related sites by amino acids co-variation networks analysis, emphasizing local coevolutionary constraints. The software allows the characterization of structurally functionally relevant groups residues their relationship with subsets sequences automatic cross-referencing GO terms, UniprotKb annotations INTERPRO. Availability implementation free open-source, being distributed in terms GPLV3...
Computational studies of molecular evolution are usually performed from a multiple alignment homologous sequences, on which sequences resulting common ancestor aligned so that equivalent residues placed in the same position. Residues frequency patterns full or subset its can be highly useful for suggesting positions under selection. Most methods mapping co-evolving specificity determinant sites focused positions, however, they do not consider case determinants one subclass, but variable...
Voltage-gated sodium channels (Nav) are membrane proteins essential to initiating and propagating action potential in neurons other excitable cells. For a given organism there often multiple, specialized found different tissues, whose mutations can cause deleterious effects observed numerous diseases. Consequently, is high medical pharmacological interest these proteins. Scientific literature uses diagrams depict important patterns including the six transmembrane segments (S1–S6) present...
We present a novel system that leverages curators in the loop to develop dataset and model for detecting residue-level functional annotations other protein structure features from standard publication text. Our approach involves integration of data multiple resources, including PDBe, EuropePMC, PubMedCentral, PubMed, combined with annotation guidelines UniProt, while employing LitSuggest Huggingface models as tools process. A team seven annotators manually curated ten articles named...
Abstract The Protein Data Bank (PDB) is the primary global repository for experimentally determined 3D structures of biological macromolecules and their complexes with ligands, proteins, nucleic acids. PDB contains over 47,000 unique small molecules bound to macromolecules. Despite extensive data available, complexity molecule in necessitates specialised tools effective analysis visualisation. PDBe has developed a number tools, including CCDUtils ( https://github.com/PDBeurope/ccdutils )...