A5100387325- Advanced Biosensing Techniques and Applications
- Immunotherapy and Immune Responses
- CAR-T cell therapy research
- Protein Structure and Dynamics
- Advanced MRI Techniques and Applications
- Histone Deacetylase Inhibitors Research
- Computational Drug Discovery Methods
- Microbial Metabolic Engineering and Bioproduction
- Monoclonal and Polyclonal Antibodies Research
- Cardiac Imaging and Diagnostics
- Enzyme Structure and Function
- RNA and protein synthesis mechanisms
- Ubiquitin and proteasome pathways
- Bioinformatics and Genomic Networks
- Medical Imaging Techniques and Applications
- HIV/AIDS drug development and treatment
- Photoacoustic and Ultrasonic Imaging
- Genomic variations and chromosomal abnormalities
- Receptor Mechanisms and Signaling
- Machine Learning in Bioinformatics
- Mechanisms of cancer metastasis
- Celiac Disease Research and Management
- HIV Research and Treatment
- ATP Synthase and ATPases Research
- Galectins and Cancer Biology
The University of Queensland
2021-2025
University of Utah
2025
Baker Heart and Diabetes Institute
2021-2024
Agency for Science, Technology and Research
2013-2024
Pham Ngoc Thach University of Medicine
2024
Ho Chi Minh City Medicine and Pharmacy University
2024
Bình Dương University
2024
Thu Dau Mot University
2024
Bioinformatics Institute
2013-2024
The University of Melbourne
2020-2023
Residue depth accurately measures burial and parameterizes local protein environment. Depth is the distance of any atom/residue to closest bulk water. We consider non-bulk waters occupy cavities, whose volumes are determined using a Voronoi procedure. Our estimation cavity sizes statistically superior estimates made by CASTp VOIDOO, on par with McVol over data set 40 cavities. calculated correlated best experimentally destabilization 34 mutants from five proteins. Some cavities identified...
Abstract Proteins are intricate, dynamic structures, and small changes in their amino acid sequences can lead to large effects on folding, stability dynamics. To facilitate the further development evaluation of methods predict these changes, we have developed ThermoMutDB, a manually curated database containing >14,669 experimental data thermodynamic parameters for wild type mutant proteins. This represents an increase 83% unique mutations over previous databases includes information...
This research explored the potential of artificial intelligence (AI)-assisted learning using ChatGPT in an engineering course at a university South-east Asia. The study investigated benefits and challenges that students may encounter when utilising ChatGPT-3.5 as tool. developed AI-assisted flow empowers learners lecturers to integrate into their teaching processes. was subsequently used validate assess variety exercises, tutorial tasks assessment-like questions for under study. Introducing...
Abstract Changes in protein sequence can have dramatic effects on how proteins fold, their stability and dynamics. Over the last 20 years, pioneering methods been developed to try estimate of missense mutations stability, leveraging growing availability 3D structures. These, however, validated using experimentally derived structures biophysical measurements. A large proportion remain be elucidated and, while many studies based conclusions predictions made homology models, there has no...
Abstract Little is known about how interactions between the uveal melanoma (UM) and host cells in tumor microenvironment (TME) drive progression of liver metastases. Single cell RNA-seq analysis UM samples identified marked differences cell-cell communication primary metastatic characterized by increased signaling strength numbers emanating from hepatic stellate (HSCs) endothelial samples. In co-culture, HSCs modulated transcriptional heterogeneity cells, enriching for states that expressed...
Uveal melanoma (UM) results in fatal liver metastasis, yet little is known about the interactions between UM and host cells tumor microenvironment that promote this distinctive proclivity. Here, we used single cell (sc)-RNA-Seq analysis of UM-hepatic stellate (HSC) co-cultures to demonstrate HSCs enriched for states expressed genes implicated survival, metabolic reprogramming angiogenesis. A lead candidate driver HSC was TGF-B family member GDF15, which associated with a metastatic...
The neuropeptide relaxin-3 is composed of an A chain and a B held together by disulfide bonds, it modulates functions such as anxiety food intake binding to activating its cognate receptor RXFP3, mainly through the chain. Biased ligands RXFP3 would help determine molecular mechanisms underlying activation G proteins β-arrestins downstream that lead diverse functions. We showed i, i+4 stapled chains, 14s18 d(1-7)14s18, were Gα i/o -biased agonists RXFP3. These peptides did not induce...
Continued advances in variant effect prediction are necessary to demonstrate the ability of machine learning methods accurately determine clinical impact variants unknown significance (VUS). Towards this goal, ARSA Critical Assessment Genome Interpretation (CAGI) challenge was designed characterize progress by utilizing 219 experimentally assayed missense VUS
Nonhomologous end joining (NHEJ) is a DNA repair mechanism that religates double-strand breaks to maintain genomic integrity during the entire cell cycle. The Ku70/80 complex recognizes and serves as an essential hub for recruitment of NHEJ components. Here, we describe intramolecular interactions Ku70 C-terminal domain, known SAP domain. Using single-particle cryo-electron microscopy, mass spectrometric analysis intermolecular cross-linking molecular modelling simulations, captured variable...
Kinases play crucial roles in cellular signalling and biological processes with their dysregulation associated diseases, including cancers. Kinase inhibitors, most notably those targeting ABeLson 1 (ABL1) kinase chronic myeloid leukemia, have had a significant impact on cancer survival, yet emergence of resistance mutations can reduce effectiveness, leading to therapeutic failure. Limited effort, however, has been devoted developing tools accurately identify ABL1 mutations, as well providing...
Rabies virus phosphoprotein (P protein) is a multifunctional protein that plays key roles in replication as the polymerase cofactor binds to complex of viral genomic RNA and nucleoprotein (N protein), evading innate immune response by binding STAT transcription factors. These interactions are mediated C-terminal domain P CTD ). The colocation these sites small globular raises question how underlying evasion, central infection, coordinated and, potentially, coregulated. While direct data on...
Abstract While protein–nucleic acid interactions are pivotal for many crucial biological processes, limited experimental data has made the development of computational approaches to characterise these a challenge. Consequently, most understand effects missense mutations on protein-nucleic affinity have focused single-point and presented performance independent sets. To overcome this, we curated largest dataset experimentally measured nucleic binding date, encompassing 856 141 multiple-point...
The ubiquitin–proteasome system is essential to all eukaryotes and has been shown be critical parasite survival as well, including Plasmodium falciparum , the causative agent of deadliest form malarial disease. Despite central role pathway viability across its entire life-cycle, specific inhibitors targeting individual enzymes mediating ubiquitin attachment removal do not currently exist. ability disrupt P. growth at multiple developmental stages particularly attractive this could...
Abstract Protein phosphorylation acts as an essential on/off switch in many cellular signaling pathways. This has led to ongoing interest targeting kinases for therapeutic intervention. Computer‐aided drug discovery been proven a useful and cost‐effective approach facilitating prioritization enrichment of screening libraries, but limited effort devoted providing insights on what makes potent kinase inhibitor. To fill this gap, here we developed kinCSM, integrative computational tool capable...
Introduction COVID-19 pandemic has been threatening public health and economic development worldwide for over two years. Compared with the original SARS-CoV-2 strain reported in 2019, Omicron variant (B.1.1.529.1) is more transmissible. This 34 mutations its Spike protein, 15 of which are present Receptor Binding Domain (RBD), facilitating viral internalization via binding to angiotensin-converting enzyme 2 (ACE2) receptor on endothelial cells as well promoting increased immune evasion...
Diabetes has always been a matter of concern to health experts as well the community due increasing number patients with diabetes and severe consequences it may cause. Many attempts have made discover new treatment options for diabetes, herbal medicines are currently considered great potential. This study was conducted evaluate effect Camellia flava flower extract on degeneration islets Langerhans insulin resistance in an alloxan-induced hyperglycemia model Swiss albino mice. Hyperglycemic...
Abstract Alzheimer's disease (AD) is one of the most common forms dementia and neurodegenerative diseases, characterized by formation neuritic plaques neurofibrillary tangles. Many different proteins participate in this complicated pathogenic mechanism, missense mutations can alter folding functions these proteins, significantly increasing risk AD. However, many methods to identify AD‐causing variants did not consider effect from perspective a protein three‐dimensional environment. Here, we...
Abstract Protein-carbohydrate interactions are crucial for many cellular processes but can be challenging to biologically characterise. To improve our understanding and ability model these molecular interactions, we used a carefully curated set of 370 protein-carbohydrate complexes with experimental structural biophysical data in order train validate new tool, cutoff scanning matrix (CSM)-carbohydrate, using machine learning algorithms accurately predict their binding affinity rank docking...