Biomolecules
Escherichia coli bacterium is a rod-shaped organism composed of a complex double membrane structure. Knowledge of electric field driven ion transport through both membranes and the evolution of their induced permeabilization has important…
Scope: Biomarkers of food intake (BFIs) are useful tools for objective assessment of food intake and compliance. The aim of this study was to discover and identify urinary BFIs for onion. Methods and results: In a randomized controlled…
The binding between proteins and ligands plays a crucial role in the realm of drug discovery. Previous deep learning approaches have shown promising results over traditional computationally intensive methods, but resulting in poor…
RNA protein Interactions (RPIs) play an important role in biological systems. Recently, we have enumerated the RPIs at the residue level and have elucidated the minimum structural unit (MSU) in these interactions to be a stretch of five…
Therapeutic antibodies are an essential and rapidly expanding drug modality. The binding specificity between antibodies and antigens is decided by complementarity-determining regions (CDRs) at the tips of these Y-shaped proteins. In this…
Accurately modeling protein 3D structure is essential for the design of functional proteins. An important sub-task of structure modeling is protein side-chain packing: predicting the conformation of side-chains (rotamers) given the…
The epidermis is a specialized epithelium that constitutes the outermost layer of the skin, and it provides a protective barrier against environmental assaults. Primarily consisting of multilayered keratinocytes, the epidermis is…
Despite recent advancement in 3D molecule conformation generation driven by diffusion models, its high computational cost in iterative diffusion/denoising process limits its application. In this paper, an equivariant consistency model…
Inverse protein folding, the process of designing sequences that fold into a specific 3D structure, is crucial in bio-engineering and drug discovery. Traditional methods rely on experimentally resolved structures, but these cover only a…
We propose HydraScreen, a deep-learning approach that aims to provide a framework for more robust machine-learning-accelerated drug discovery. HydraScreen utilizes a state-of-the-art 3D convolutional neural network, designed for the…
Post-transcriptional modifications are crucial for RNA function, with roles ranging from the stabilization of functional RNA structures to modulation of RNA--protein interactions. Additionally, artificially modified RNAs have been suggested…
Current protein language models (pLMs) predominantly focus on single-chain protein sequences and often have not accounted for constraints on generative design imposed by protein-protein interactions. To address this gap, we present paired…
On August 9-10, 2023, a workshop was convened at the Pacific Northwest National Laboratory (PNNL) in Richland, WA that brought together a group of internationally recognized experts in metabolomics, natural products discovery, chemical…
In this study, we present a novel molecular fingerprint generation method based on multiparameter persistent homology. This approach reveals the latent structures and relationships within molecular geometry, and detects topological features…
Recent advances in applying Graph Neural Networks (GNNs) to molecular science have showcased the power of learning three-dimensional (3D) structure representations with GNNs. However, most existing GNNs suffer from the limitations of…
The drug development pipeline for a new compound can last 10-20 years and cost over 10 billion. Drug repurposing offers a more time- and cost-effective alternative. Computational approaches based on biomedical knowledge graph…
In recent years, the development of Artificial Intelligence (AI) has offered the possibility to tackle many interdisciplinary problems, and the field of chemistry is not an exception. Drug analysis is crucial in drug discovery, playing an…
Contraction assay based on surface measurement have been widely used to evaluate cell contractility in 3D models. This method is straightforward and requires no specific equipment, but it does not provide quantitative data about contraction…
Viruses and their hosts are involved in an 'arms race' where they continually evolve mechanisms to overcome each other. It has long been proposed that intrinsic disorder provides a substrate for the evolution of viral hijack functions and…
Background: the stability of serum specimen during time storage is importance in clinical and medical science researches in addition of diagnosis. Lipids are organic molecules that classified into 8 classes: fatty acids, phospholipids,…