Are there any open software for protein-protein interaction analysis?
Hello everybody,
I work on plant science, more specificlly in plant pathogen interaction. In my project I need to analyse an interaction of some proteins related to host and virus interaction, but before I'd like to do this analyses in silico.
Do you have any idea of a good software/program, online or not?
For your issue, I believe you have to use machine learning solutions. For the PPI, Neural Networks (NNs) are a popular alternative, you can find several open source NNs toolboxes.
This is my article on the interaction of HIV-1 and human protein-protein, which might be useful:
I have been using STRING database for PPI, but it appears not working since few days... Either the species (e.g., equus caballus) are not recognized while being selected from the provided list, or the search stop without results.
If your goal is just a surface analysis of the interaction, the UCSF Chimera is appropriate, but if your analysis contains details of the interaction , the BIOVIA Discovery Studio Visualizer is very useful.
Les interactions protéine–protéine jouent un rôle essentiel dans le fonctionnement cellulaire et sont impliquées dans diverses pathologies. L’étude de ces interactions est donc primordiale. Nous avons entrepris de développer une méthode de « footprinting » basée sur la différence d’accessibilité à l’eau des acides aminés d’une protéine selon qu’ell...
The Cover Feature shows three chipmunks involved in the creation, analysis, and clustering of the synthesizable virtual molecule library CHIPMUNK. Nearly 100 million compounds were generated with in silico reactions on accessible building blocks, and their descriptor profile was analysed. The library was clustered together with molecules from other...