相关论文: Assigning function to protein-protein interactions…
Decoding protein-protein interactions (PPIs) at the residue level is crucial for understanding cellular mechanisms and developing targeted therapeutics. We present Seq2Bind Webserver, a computational framework that leverages fine-tuned…
Aligning protein interaction networks (PPI) of two or more organisms consists of finding a mapping of the nodes (proteins) of the networks that captures important structural and functional associations (similarity). It is a well studied but…
The availability of biomedical text data and advances in natural language processing (NLP) have made new applications in biomedical NLP possible. Language models trained or fine tuned using domain specific corpora can outperform general…
Understanding protein-protein interactions is central to our understanding of almost all complex biological processes. Computational tools exploiting rapidly growing genomic databases to characterize protein-protein interactions are…
The ongoing opioid crisis highlights the urgent need for novel therapeutic strategies that can be rapidly deployed. This study presents a novel approach to identify potential repurposable drugs for the treatment of opioid addiction, aiming…
Protein function is driven by cohesive substructures, such as catalytic triads, binding pockets, and structural motifs, that occupy only a small fraction of a protein's residues. Yet existing pipelines built on protein encoders do not model…
Scientific literature contains a considerable amount of information that provides an excellent opportunity for developing text mining methods to extract biomedical relationships. An important type of information is the relationship between…
Living systems rely on coordinated molecular interactions, especially those related to gene expression and protein activity. The Unfolded Protein Response is a crucial mechanism in eukaryotic cells, activated when unfolded proteins exceed a…
Accurate identification of bioactive peptides (BPs) and protein post-translational modifications (PTMs) is essential for understanding protein function and advancing therapeutic discovery. However, most computational methods remain limited…
Genomic duplication-divergence events, which are the primary source of new protein functions, occur stochastically at a wide range of genomic scales, from single gene to whole genome duplications. Clearly, this fundamental evolutionary…
Exploring the functions of genes and gene products is crucial to a wide range of fields, including medical research, evolutionary biology, and environmental science. However, discovering new functions largely relies on expensive and…
Structural assessment of biomolecular complexes is vital for translating molecular models into functional insights, shaping our understanding of biology and aiding drug discovery. However, current structure-based scoring functions often…
Protein-protein interaction (PPI) represents a central challenge within the biology field, and accurately predicting the consequences of mutations in this context is crucial for drug design and protein engineering. Deep learning (DL) has…
Bioinformatics workflows are essential for complex biological data analyses and are often described in scientific articles with source code in public repositories. Extracting detailed workflow information from articles can improve…
The widespread of Coronavirus has led to a worldwide pandemic with a high mortality rate. Currently, the knowledge accumulated from different studies about this virus is very limited. Leveraging a wide-range of biological knowledge, such as…
Accurate identification of interactions between protein residues and ligand functional groups is essential to understand molecular recognition and guide rational drug design. Existing deep learning approaches for protein-ligand…
In Track-1 of the BioCreative VII Challenge participants are asked to identify interactions between drugs/chemicals and proteins. In-context named entity annotations for each drug/chemical and protein are provided and one of fourteen…
We study the correlation between the codon usage bias of genetic sequences and the network features of protein-protein interaction (PPI) in bacterial species. We use PCA techniques in the space of codon bias indices to show that genes with…
Clinical notes contain an abundance of important but not-readily accessible information about patients. Systems to automatically extract this information rely on large amounts of training data for which their exists limited resources to…
Protein-ligand bioactivity data published in the literature are essential for drug discovery, yet manual curation struggles to keep pace with rapidly growing literature. Automated bioactivity extraction remains challenging because it…