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The structure of DNA Binding Proteins enables a strong interaction with their specific target site on DNA. However, recent single molecule experiment reported that proteins can diffuse on DNA. This suggests that the interactions between…
Multisite protein phosphorylation plays a pivotal role in regulating cellular signaling and decision-making processes. In this study, we focus on the mathematical underpinnings and informational aspects of sequential, distributive…
The conjugation of high-affinity cRGD-containing peptides is a promising approach in nanomedicine to efficiently reduce off-targeting effects and enhance the cellular uptake by integrin-overexpressing tumor cells. Herein we utilize…
Genome-wide association studies (GWAS) have successfully identified over two hundred thousand genotype-trait associations. Yet some challenges remain. First, complex traits are often associated with many single nucleotide polymorphisms…
We exploit the widening margin in tensor-core performance between [FP64/FP32/FP16/INT8,FP64/FP32/FP16/FP8/INT8] on NVIDIA [Ampere,Hopper] GPUs to boost the performance of output accuracy-preserving mixed-precision computation of Genome-Wide…
Geometric deep learning has recently achieved great success in non-Euclidean domains, and learning on 3D structures of large biomolecules is emerging as a distinct research area. However, its efficacy is largely constrained due to the…
The spatio-temporal organization of proteins and the associated morphological changes in membranes are of importance in cell signaling. Several mechanisms that promote the aggregation of proteins at low cell surface concentrations have been…
We report the results of our first-principles investigation on the interaction of the nucleobases adenine (A), cytosine (C), guanine (G), thymine (T), and uracil (U) with graphene, carried out within the density functional theory framework,…
Phase separation in biomolecular mixtures can result from multiple physical interactions, which may act either complementarily or antagonistically. In the case of protein-nucleic acid mixtures, charge plays a key role but can have…
Activity cliff prediction is a critical task in drug discovery and material design. Existing computational methods are limited to handling single binding targets, which restricts the applicability of these prediction models. In this paper,…
G-Protein Coupled Receptors (GPCRs) are integral to numerous physiological processes and are the target of approximately one-third of FDA-approved therapeutics. Despite their significance, only a limited subset of GPCRs has been…
Pulsar timing arrays (PTAs) seek to detect a nano-Hz stochastic gravitational-wave background (GWB) by searching for the characteristic Hellings and Downs angular pattern of timing residual correlations. So far, the evidence remains below…
Adenosine 5'-triphosphate (ATP) is the nearly ubiquitous "energy currency" of living organisms, and thus is a crucial participant in the majority of enzymatic reactions. The standard models in enzyme kinetics generally ignore the temporal…
In order to realise the potential of graphene nanocomposites it is vital to control the degree of dispersion and achieve a strong graphene polymer interface. Herein, we developed a facile grafting to functionalisation approach for graphene…
Electrostatic interactions play a fundamental role in the structure and function of proteins. Due to ionizable amino acid residues present on the solvent-exposed surfaces of proteins, the protein charge is not constant but varies with the…
In the course of evolution, proteins show a remarkable conservation of their three-dimensional structure and their biological function, leading to strong evolutionary constraints on the sequence variability between homologous proteins. Our…
The 70 kDa Heat Shock Proteins Hsp70 have several essential functions in living systems, such as protecting cells against protein aggregation, assisting protein folding, remodeling protein complexes and driving the translocation into…
Retrieving the biological impacts of protein-protein interactions (PPIs) is essential for target identification (Target ID) in drug development. Given the vast number of proteins involved, this process remains time-consuming and…
Graph Neural Networks (GNNs) excel in node classification tasks but often assume homophily, where connected nodes share similar labels. This assumption does not hold in many real-world heterophilic graphs. Existing models for heterophilic…
Protein crystal production is a major bottleneck for the structural characterisation of proteins. To advance beyond large-scale screening, rational strategies for protein crystallization are crucial. Understanding how chemical anisotropy…