Related papers: HLA class I binding prediction via convolutional n…

This study proposes an efficient neural network with convolutional layers to classify significantly class-imbalanced clinical data. The data are curated from the National Health and Nutritional Examination Survey (NHANES) with the goal of…

Computational approaches to drug discovery can reduce the time and cost associated with experimental assays and enable the screening of novel chemotypes. Structure-based drug design methods rely on scoring functions to rank and predict…

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…

The Gene or DNA sequence in every cell does not control genetic properties on its own; Rather, this is done through translation of DNA into protein and subsequent formation of a certain 3D structure. The biological function of a protein is…

Artificial intelligence (AI) is reshaping computational and network biology by enabling new approaches to decode cellular communication networks. We introduce Hierarchical Molecular Language Models (HMLMs), a novel framework that models…

Due to the lack of a method to efficiently represent the multimodal information of a protein, including its structure and sequence information, predicting compound-protein binding affinity (CPA) still suffers from low accuracy when applying…

While deep learning methods are increasingly being applied to tasks such as computer-aided diagnosis, these models are difficult to interpret, do not incorporate prior domain knowledge, and are often considered as a "black-box." The lack of…

The prediction of amyloidogenicity in peptides and proteins remains a focal point of ongoing bioinformatics. The crucial step in this field is to apply advanced computational methodologies. Many recent approaches to predicting…

Computational drug discovery provides an efficient tool helping large scale lead molecules screening. One of the major tasks of lead discovery is identifying molecules with promising binding affinities towards a target, a protein in…

Peptides play a pivotal role in a wide range of biological activities through participating in up to 40% protein-protein interactions in cellular processes. They also demonstrate remarkable specificity and efficacy, making them promising…

How humans understand and recognize the actions of others is a complex neuroscientific problem that involves a combination of cognitive mechanisms and neural networks. Research has shown that humans have brain areas that recognize actions…

The 21st century is presenting humankind with unprecedented environmental and medical challenges. The ability to design novel proteins tailored for specific purposes could transform our ability to respond timely to these issues. Recent…

Heterogeneous graph convolutional networks have gained great popularity in tackling various network analytical tasks on heterogeneous network data, ranging from link prediction to node classification. However, most existing works ignore the…

The binding affinity between the T-cell receptors (TCRs) and antigenic peptides mainly determines immunological recognition. It is not a trivial task that T cells identify the digital sequences of peptide amino acids by simply relying on…

Leukemia, the cancer of blood cells, originates in the blood-forming cells of the bone marrow. In Chronic Myeloid Leukemia (CML) conditions, the cells partially become mature that look like normal white blood cells but do not resist…

Protein-protein bindings play a key role in a variety of fundamental biological processes, and thus predicting the effects of amino acid mutations on protein-protein binding is crucial. To tackle the scarcity of annotated mutation data,…

Protein-ligand interactions are one of the fundamental types of molecular interactions in living systems. Ligands are small molecules that interact with protein molecules at specific regions on their surfaces called binding sites. Tasks…

Protein language models (PLMs) learn contextual representations from protein sequences and are profoundly impacting various scientific disciplines spanning protein design, drug discovery, and structural predictions. One particular research…

Publicly available collections of drug-like molecules have grown to comprise 10s of billions of possibilities in recent history due to advances in chemical synthesis. Traditional methods for identifying "hit" molecules from a large…

As a natural extension of link prediction on graphs, hyperlink prediction aims for the inference of missing hyperlinks in hypergraphs, where a hyperlink can connect more than two nodes. Hyperlink prediction has applications in a wide range…