Question
Asked 30th Jun, 2016

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?

Most recent answer

3rd Feb, 2021
Priyadarshini Chakrabarti Basu
Mississippi State University
I have been using String and Panther.

All Answers (15)

30th Jun, 2016
Amir Atashin
Eindhoven University of Technology
Hi,
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:
1 Recommendation
4th Jul, 2016
Mrityunjay Kumar Singh
Indian Institute of Technology Madras
There are lot of software to do protein protein interaction. Some of them are, PIC (http://pic.mbu.iisc.ernet.in/). 2P2I (http://2p2idb.cnrs-mrs.fr/2p2i_inspector.html) pr PISA. there are lot of options in these servers. Hope this will help you.
1 Recommendation
7th Jul, 2016
Kirill E Medvedev
University of Texas Southwestern Medical Center
13th Jun, 2018
Rajesh Kumar
CSIR - Institute of Microbial Technology
String is an open source server for predicting protein protein interaction
1 Recommendation
29th Nov, 2018
Li Guo
Peking University
STRING database is a very good one.
2 Recommendations
5th Mar, 2019
Jean M Feugang
Mississippi State University
Hop someone can help.
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.
1 Recommendation
13th Mar, 2019
Debanjan Mitra
Raiganj University
For protein ligand interaction use Autodock or VEGA ZZ
14th Mar, 2019
Jean M Feugang
Mississippi State University
Thank you Mitra. The problem is now resolved and the software is working just fine.
31st May, 2019
Md Abu Sufian
Temple University
Patchdock, Firedock, Pydock, Cluspro
2 Recommendations
25th Dec, 2019
Poorani Rajendran
Bannari Amman Institute of Technology
Is comsol used for protein protein interaction similation??
26th Jun, 2020
Athithan Velan
Pondicherry University
Dear All,
I want to analysis, final Protein-Protein Interaction result. Can any one help me, which software i can go/use.
29th Aug, 2020
Md. Nazim Uddin
Bangladesh Council of Scientific and Industrial Research
https://string-db.org/ and then use cytoscape
1 Recommendation
3rd Sep, 2020
Antonio Moretta
Claude Bernard University Lyon 1
Dear Athithan,
you can use PDBsum. I think it is very useful and intuitive.
2 Recommendations
29th Sep, 2020
Hossein Aghazadeh
Pasteur Institute of Iran
Dear Guilherme,
Dear Athithan,
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.
3rd Feb, 2021
Priyadarshini Chakrabarti Basu
Mississippi State University
I have been using String and Panther.

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