Patel, S., Tripathi, R., Kumari, V., and Varadwaj, P. (2017). DeepInteract: deep neural network based protein-protein interaction prediction tool. Curr. Bioinform. 12, 551-557. doi: 10.2174/1574893611666160815 150746Deep neural network based protein-protein interaction extraction from biomedical...
5. What is a computer-aided tool? 6. What is a protein-protein interface? 7. Give an account of binding site prediction in protein complexes. 8. What are protein-protein interaction networks? 9. Give an account of proteome-scale analysis of PPI in model organism. 10. Name some structure...
In a Fold and Dock approach, two proteins are folded and docked simultaneously. We recently developed a Fold and Dock pipeline using another distance prediction method focused on protein folding (trRosetta23). In this pipeline, the interaction between two chains from a heterodimeric protein complex ...
To date, there have been a plethora of works that employed traditional machine learning (ML) techniques to solve several problems in the computational biology domain, such as protein classification, structure prediction, protein interaction prediction, etc. Support vector machines (SVMs), Random forest...
This chapter focuses on the considerations involved in applying deep learning methods to protein structure data for the prediction of protein–protein interaction sites. The main steps in developing such a project, from data collection and preparation, featurization and representation, through to model ...
detailed gene functions and prediction of biological pathways (81). In summary, protein–protein interaction networks in various organisms are increasingly becoming the focus of understanding the functional organization of the proteome. Although only the yeast genome is demonstrated in this study, our ...
Figure 7.7.Protein-protein interaction sites prediction using 3D structure with cons-PPISP: (a) input parameters, atomic coordinates, and chain information of the protein and (b) predicted binding sites; P: positive and N: negative. 7.1.6Energy-based approach for understanding the recognition mech...
(Spiwoket al., 2005).Molecular dockingof proteins and their interacting carbohydrates is still a challenge, due to the inaccuracy of scoring functions for accurate prediction of their interaction. At present, very limited number of carbohydrate specific scoring functions have been developed and ...
2.3.1. Structure-Based Prediction Approaches The idea behind the structure-based method is to predict protein-protein interaction if two proteins have a similar structure. Therefore, if two proteins A and B can interact with each other, then there may be two other proteins A′and B′whose str...
protein interaction prediction based on a majority voting method. The model uses four well-established machine learning methods: support vector machines, random forests, decision trees, and naive Bayes. In the cross-validation experiment, the ensemble learning method achieved over 80% sensitivity and ...