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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…
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…
Detecting protein-protein interactions (PPIs) is crucial for understanding genetic mechanisms, disease pathogenesis, and drug design. However, with the fast-paced growth of biomedical literature, there is a growing need for automated and…
Biological networks provide insight into the complex organization of biological processes in a cell at the system level. They are an effective tool for understanding the comprehensive map of functional interactions, finding the functional…
Identifying the interaction targets of bioactive compounds is a foundational element for deciphering their pharmacological effects. Target prediction algorithms equip researchers with an effective tool to rapidly scope and explore potential…
In silico drug-target interaction (DTI) prediction is an important and challenging problem in biomedical research with a huge potential benefit to the pharmaceutical industry and patients. Most existing methods for DTI prediction including…
MicroRNAs play critical roles in many physiological processes. Their dysregulations are also closely related to the development and progression of various human diseases, including cancer. Therefore, identifying new microRNAs that are…
The study of multi-type Protein-Protein Interaction (PPI) is fundamental for understanding biological processes from a systematic perspective and revealing disease mechanisms. Existing methods suffer from significant performance degradation…
Proteins are macromolecules which hardly act alone; they need to make interactions with some other proteins to do so. Numerous factors are there which can regulate the interactions between proteins [4]. Here in this present study we aim to…
Structural biology has made significant progress in determining membrane proteins, leading to a remarkable increase in the number of available structures in dedicated databases. The inherent complexity of membrane protein structures,…
Functional protein-protein interactions are crucial in most cellular processes. They enable multi-protein complexes to assemble and to remain stable, and they allow signal transduction in various pathways. Functional interactions between…
Cocaine addiction accounts for a large portion of substance use disorders and threatens millions of lives worldwide. There is an urgent need to come up with efficient anti-cocaine addiction drugs. Unfortunately, no medications have been…
Genetic interactions and protein co-dependencies shape cellular fitness, buffering capacity, and disease vulnerability. However, systematic integration of co-dependency relationships across heterogeneous datasets remains limited. Here, we…
Proteins are the main workhorses of biological functions in a cell, a tissue, or an organism. Identification and quantification of proteins in a given sample, e.g. a cell type under normal/disease conditions, are fundamental tasks for the…
Infections depend on interactions between pathogen and host proteins, but comprehensively mapping these interactions is challenging and labor intensive. Many biological networks have hierarchical, scale-free structure, so we developed a…
High-resolution connectomics data allows for the identification of dysfunctional mitochondria which are linked to a variety of diseases such as autism or bipolar. However, manual analysis is not feasible since datasets can be petabytes in…
A major part of membrane function is conducted by proteins, both integral and peripheral. Peripheral membrane proteins temporarily adhere to biological membranes, either to the lipid bilayer or to integral membrane proteins with…
Understanding the 3D structures of protein multimers is crucial, as they play a vital role in regulating various cellular processes. It has been empirically confirmed that the multimer structure prediction~(MSP) can be well handled in a…
The accurate screening of candidate drug ligands against target proteins through computational approaches is of prime interest to drug development efforts. Such virtual screening depends in part on methods to predict the binding affinity…
Comprehensive knowledge of protein-ligand interactions should provide a useful basis for annotating protein functions, studying protein evolution, engineering enzymatic activity, and designing drugs. To investigate the diversity and…