A5090468327- Pneumocystis jirovecii pneumonia detection and treatment
- Protein Structure and Dynamics
- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
- Computational Drug Discovery Methods
- Enzyme Structure and Function
- Thermal and Kinetic Analysis
- Microbial Metabolic Engineering and Bioproduction
- Trace Elements in Health
- HIV/AIDS drug development and treatment
- Pharmacogenetics and Drug Metabolism
- Energetic Materials and Combustion
- Eosinophilic Esophagitis
- Peptidase Inhibition and Analysis
- RNA and protein synthesis mechanisms
- Tuberculosis Research and Epidemiology
- Machine Learning in Bioinformatics
- Gut microbiota and health
- Chemical Thermodynamics and Molecular Structure
- Bacterial Identification and Susceptibility Testing
- Advanced Materials Characterization Techniques
- Microbial bioremediation and biosurfactants
- Viral-associated cancers and disorders
- Neonatal Respiratory Health Research
- Electron and X-Ray Spectroscopy Techniques
University of Cincinnati
2013-2024
Cincinnati Children's Hospital Medical Center
2015-2024
University of Cincinnati Medical Center
2013-2024
Autoimmune Technologies (United States)
2019
Children's Hospital & Medical Center
2018
N.D. Zelinsky Institute of Organic Chemistry
2010
Mari State University
1997-1999
Abstract The recognition of protein interaction sites is an important intermediate step toward identification functionally relevant residues and understanding function, facilitating experimental efforts in that regard. Toward goal, the authors propose a novel representation for protein–protein integrates enhanced relative solvent accessibility (RSA) predictions with high resolution structural data. An observation RSA are biased level surface exposure consistent complexes led to investigate...
Owing to the use of evolutionary information and advanced machine learning protocols, secondary structures amino acid residues in proteins can be predicted from primary sequence with more than 75% per-residue accuracy for 3-state (i.e., helix, beta-strand, coil) classification problem. In this work we investigate whether further progress may achieved by incorporating relative solvent accessibility (RSA) an residue as a fingerprint overall topology protein. Toward that goal, developed novel...
Abstract Accurate prediction of relative solvent accessibilities (RSAs) amino acid residues in proteins may be used to facilitate protein structure and functional annotation. Toward that goal we developed a novel method for improved RSAs. Contrary other machine learning–based methods from the literature, do not impose classification problem with arbitrary boundaries between classes. Instead, seek continuous approximation real‐value RSA using nonlinear regression, several feed forward...
Parabens are a group of alkyl esters p-hydroxybenzoic acid that include methylparaben, ethylparaben, propylparaben, butylparaben, and benzylparaben. Paraben their salts widely used as preservatives in cosmetics, toiletries, food, pharmaceuticals. Humans exposed to parabens through the use such products from dermal contact, ingestion, inhalation. However, research on effects health is limited, adipogenesis have not been systematically studied. Here, we report (1) promote (or adipocyte...
Abstract Summary: The POLYVIEW visualization server can be used to generate protein sequence annotations, including secondary structures, relative solvent accessibilities, functional motifs and polymorphic sites. Two-dimensional graphical representations in a customizable format may generated for both known structures predictions obtained using structure prediction servers. automated generation of pictures with structural annotations publications proteomic on-line resources. Availability:...
Macromolecular visualization as well automated structural and functional annotation tools play an increasingly important role in the post-genomic era, contributing significantly towards understanding of molecular systems processes. For example, three dimensional (3D) models help exploring protein active sites hot spots that can be targeted drug design. Automated pipelines also reveal other functionally attributes macromolecules. These goals are dependent on availability advanced integrate...
Cytochrome P450 monooxygenases (P450s) are known to oxidize hydrocarbons, albeit with limited substrate specificity across classes of these compounds. Here we report a monooxygenase (CYP63A2) from the model ligninolytic white rot fungus Phanerochaete chrysosporium that was found possess broad oxidizing capability toward structurally diverse hydrocarbons belonging mutagenic/carcinogenic fused-ring higher-molecular-weight polycyclic aromatic (HMW-PAHs), endocrine-disrupting long-chain...
We report the first pediatric specific Phenome-Wide Association Study (PheWAS) using electronic medical records (EMRs). Given early success of PheWAS in adult populations, we investigated feasibility this approach cohorts which associations between a previously known genetic variant and wide range clinical or physiological traits were evaluated. Although computationally intensive, has potential to reveal disease mechanistic relationships network phenotypes.Data on 5049 samples European...
Severe short stature can be caused by defects in numerous biological processes including IGF-1 signaling, centromere function, cell cycle control, and DNA damage repair. Many syndromic causes of are associated with medical comorbidities hypogonadism microcephaly.To identify an underlying genetic etiology two siblings severe gonadal failure.Clinical phenotyping, analysis, complemented vitro functional studies the candidate gene.An academic pediatric endocrinology clinic.Two adult (male...
Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) is a lethal congenital disorder causing respiratory failure and hypertension shortly after birth. There are no effective treatments for ACDMPV other than lung transplant, new therapeutic approaches urgently needed. Although linked to mutations in the
Early detection of antimicrobial resistance in pathogens and prescription more effective antibiotics is a fast-emerging need clinical practice. High-throughput sequencing technology, such as whole genome (WGS), may have the capacity to rapidly guide decision-making process. The prediction Gram-negative bacteria, often cause serious systemic infections, challenging genotype-to-phenotype (drug resistance) relationship complex than for most Gram-positive organisms.We used NCBI BioSample...
The relative solvent accessibility (RSA) of an amino acid residue in a protein structure is real number that represents the exposed surface area this terms. problem predicting RSA from primary sequence can therefore be cast as regression problem. Nevertheless, prediction has so far typically been classification Consequently, various machine learning techniques have used within framework to predict whether given exceeds some (arbitrary) threshold and would thus predicted "exposed," opposed...
Membrane domain prediction has recently been re-evaluated by several groups, suggesting that the accuracy of existing methods is still rather limited. In this work, we revisit problem and propose novel for alpha-helical as well beta-sheet transmembrane (TM) domains. The new approach based on a compact representation an amino acid residue its environment, which consists predicted solvent accessibility secondary structure each acid. A introduced method trained set soluble proteins used here to...
We previously reported that preconditioning of stem cells with insulin-like growth factor-1 (IGF-1) translocated connexin-43 (Cx-43) into mitochondria, causing cytoprotection. posit these effects could be simulated by mitochondria-specific overexpression Cx-43.During IGF-1-induced C57black/6 mouse bone marrow cell antigen-1(+) (Sca-1(+)) cells, Cx-43 was mainly onto the mitochondrial inner membrane, which abrogated an extracellular signal-regulated kinases 1 and 2 (ERK1/2) blocker PD98059....
Abstract Background Proteins generally perform their function in a folded state. Residues forming an active site, whether it is catalytic center or interaction interface, are frequently distant protein sequence. Hence, traditional sequence-based prediction methods focusing on single residue (or short window of residues) at time may have difficulties identifying and clustering the residues constituting functional especially when has multiple functions. Evolutionary information encoded...
Alternative activation of macrophages promotes wound healing but weakens antimicrobial defenses against intracellular pathogens. The mechanisms that suppress macrophage function to create a favorable environment for pathogen growth remain elusive. We show interleukin (IL)-4 triggers metallothionein 3 (MT3)- and Zn exporter SLC30A4-dependent increase in the labile Zn(2+) stores pathogens can exploit this survive. IL-4 regulates pathway by shuttling extracellular into activating cathepsins act...
Derived from the natural language processing (NLP) algorithms, protein models enable encoding of sequences, which are widely diverse in length and amino acid composition, fixed-size numerical vectors (embeddings). We surveyed representative embedding such as Esm, Esm1b, ProtT5, SeqVec, along with their derivatives (GoPredSim PLAST), to conduct following tasks computational biology: Saccharomyces cerevisiae proteome, gene ontology (GO) annotation uncharacterized proteins this organism,...