Biomolecules
Deep generative models are rapidly advancing structure-based drug design, offering substantial promise for generating small molecule ligands that bind to specific protein targets. However, most current approaches assume a rigid protein…
The single nucleotide polymorphism (SNP) rs7903146 in the TCF7L2 gene has been determined as one of the strongest common genetic risk factors for Type 2 Diabetes (T2D). The location of the SNP in a non-coding region suggests a regulatory…
Protein-protein docking is crucial for understanding how proteins interact. Numerous docking tools have been developed to discover possible conformations of two interacting proteins. However, the reliability and success of these docking…
This study introduces a novel iron-based gas diffusion electrode-photocatalytic system aimed at enhancing the degradation of phenolic compounds in wastewater. Phenolic compounds are toxic environmental pollutants with significant resistance…
The PTPN11 gene encodes the Src homology 2 domain-containing protein tyrosine phosphatase (SHP2), a key regulator of cell growth, differentiation, and apoptosis through its modulation of various signaling pathways, including the RAS/MAPK…
"How to evaluate the de novo designs proposed by a generative model?" Despite the transformative potential of generative deep learning in drug discovery, this seemingly simple question has no clear answer. The absence of standardized…
Large Artificial Neural Network (ANN) models have demonstrated success in various domains, including general text and image generation, drug discovery, and protein-RNA (ribonucleic acid) binding tasks. However, these models typically demand…
Deep generative models have recently been proposed for sampling protein conformations from the Boltzmann distribution, as an alternative to often prohibitively expensive Molecular Dynamics simulations. However, current state-of-the-art…
Food polysaccharides have emerged as suitable carriers of active substances and as additives to food and nutraceutical formulations, showing potential to stabilize bioactive compounds during the storage of microencapsulate preparations,…
Alzheimers disease (AD), a progressive neuro-degenerative disorder, currently lacks effective therapeutic strategies that can modify disease progression. Recent studies have highlighted the circadian rhythm critical role in AD…
The convergence of statistical learning and molecular physics is transforming our approach to modeling biomolecular systems. Physics-informed machine learning (PIML) offers a systematic framework that integrates data-driven inference with…
Structurally nanoengineered antimicrobial peptide polymers (SNAPPs) are emerging as promising selective agents against bacterial membranes. In this study, we used all atom molecular dynamics simulation techniques to investigate the…
Understanding the dynamic behavior of proteins is critical to elucidating their functional mechanisms, yet generating realistic, temporally coherent trajectories of protein ensembles remains a significant challenge. In this work, we…
The presence of an expanded polyglutamine produces a toxic gain of function in huntingtin. Protein aggregation resulting from this gain of function is likely to be the cause of neuronal death. Two main mechanisms of aggregation have been…
Computational methods for predicting and designing biomolecular structures are increasingly powerful. While previous approaches relied on physics-based modeling, modern tools, such as AlphaFold2 in CASP14, leverage artificial intelligence…
Template-based molecular generation offers a promising avenue for drug design by ensuring generated compounds are synthetically accessible through predefined reaction templates and building blocks. In this work, we tackle three core…
Molecular discovery has brought great benefits to the chemical industry. Various molecule design techniques are developed to identify molecules with desirable properties. Traditional optimization methods, such as genetic algorithms,…
How proteins fold remains a central unsolved problem in biology. While the idea of a folding code embedded in the amino acid sequence was introduced more than 6 decades ago, this code remains undefined. While we now have powerful predictive…
DNA helicases undergo conformational changes; however, their structural dynamics are poorly understood. Here, we study single molecules of superfamily 1A DNA helicase Rep, which undergo conformational transitions during bacterial DNA…
By stabilizing weak and transient protein-protein interactions (PPIs), molecular glues address the challenge of targeting proteins previously considered undruggable. Rapamycin and WDB002 are molecular glues that bind to FK506-binding…