Bagchi, AngshumanJohn Wiley & Sons, Inc.Bagchi A. Prediction of Protein-Protein Interactions. Computational Intelligence and Pattern Analysis in Biological Informatics [Internet]. 2010. p. 325-47. Available from: http: //doi.wiley.com/10.1002/ 9780470872352.ch15...
Cellular responses to environmental conditions are governed by the fine tuning of functional and physical interactions in the proteome. A number of methods have been proposed for the prediction of these protein鈥損rotein interactions (PPI), which are based on genomic contexts (includes co-evolution,...
If a gene does not participate in a protein–protein interaction, then this gene can be eliminated from the informative gene list. Algorithm 2 describes the process of finding the PPI interaction of every cellular component. Algorithm 2. PPI interactions...
PPI Protein–Protein Interactions NN Neural Networks GCN Graph Convolutional Neural Networks GAT Graph Attention Networks HNN Hyperbolic Neural Networks HGCN Hyperbolic Graph Convolutions References Berggård, T.; Linse, S.; James, P. Methods for the detection and analysis of protein–protein interac...
In-depth knowledge of PPIs and their intricate network is the key to the understanding of interactions that are the foundation of cellular processes behind disease mechanisms. Of the ten intermediate genes discovered through PPI analysis, six genes show a possible link to RP, supported by previous...
However, the quantitative analysis of protein–protein interactions (PPIs) in cells is also important since these interactions are the bases of many processes, such as the cell cycle and signaling pathways. This paper describes the application of Skyline software for the identification and ...
The modulation of protein–protein interactions (PPIs) by small chemical compounds is challenging. PPIs play a critical role in most cellular processes and are involved in numerous disease pathways. As such, novel strategies that assist the design of PPI inhibitors are of major importance. We previ...
The water solubility of protein increases during the protein–protein interaction process, based on the higher activity of electrostatic repulsion more than hydrophobic interactions between the polymers of proteins. Hydrophobic interactions in an aqueous solution can also enhance PPI. Different types of pro...
For example, the binding site is chosen based on the information of co-crystallized ligand/substrate binding site, such as ATP binding site or protein–protein interactions (PPI) interface. However, when the binding site information is missing or a novel binding pocket needs to be explored, ...
The existence of a small-molecule binding site at the LsrK/HPr PPI site and the key residues involved in the interactions between HPr and LsrK were determined by MD simulation and binding site analysis. Virtual screening was processed with the constraint of forming at least one hydrogen bond ...