Identification of small-molecule binding sites in proteins is of great significance in analysis of protein function and drug design. Modified sites can be recognized via proteolytic cleavage followed by liquid chromatography-mass spectrometry (LC-MS)...
Computational identification of human-virus protein-protein interactions (PHIs) is a worthwhile step towards understanding infection mechanisms. Analysis of the PHI networks is important for the determination of pathogenic diseases. Prediction of the...
Journal of computational biology : a journal of computational molecular cell biology
Aug 10, 2022
The scientific community is rapidly generating protein sequence information, but only a fraction of these proteins can be experimentally characterized. While promising deep learning approaches for protein prediction tasks have emerged, they have comp...
Journal of chemical theory and computation
Aug 8, 2022
The traditional approach of computational biology consists of calculating molecule properties by using approximate classical potentials. Interactions between atoms are described by an energy function derived from physical principles or fitted to expe...
IEEE/ACM transactions on computational biology and bioinformatics
Aug 8, 2022
The identification of compound-protein relations (CPRs), which includes compound-protein interactions (CPIs) and compound-protein affinities (CPAs), is critical to drug development. A common method for compound-protein relation identification is the ...
IEEE/ACM transactions on computational biology and bioinformatics
Aug 8, 2022
Computational strategies for identifying new drug-target interactions (DTIs) can guide the process of drug discovery, reduce the cost and time of drug development, and thus promote drug development. Most recently proposed methods predict DTIs via int...
Most proteins in cells are composed of multiple folding units (or domains) to perform complex functions in a cooperative manner. Relative to the rapid progress in single-domain structure prediction, there are few effective tools available for multi-d...
This paper describes ppdx, a python workflow tool that combines protein sequence alignment, homology modeling, and structural refinement, to compute a broad array of descriptors for characterizing protein-protein interactions. The descriptors can be ...
BACKGROUND: Essential Proteins are demonstrated to exert vital functions on cellular processes and are indispensable for the survival and reproduction of the organism. Traditional centrality methods perform poorly on complex protein-protein interacti...
BACKGROUND: Protein-protein interaction (PPI) is very important for many biochemical processes. Therefore, accurate prediction of PPI can help us better understand the role of proteins in biochemical processes. Although there are many methods to pred...
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