use String or BIND database....

You can use gramm (also available as a web server gamma-X) or patchdock web server

You can use "SCHRODINGER"

I use psicquic view. It allows us to check multiple protein-protein interaction databases simultaneously. http://www.ebi.ac.uk/Tools/webservices/psicquic/view/main.xhtml?conversationContext=2

STRING is an online free web tool..try that...its common for proteion interaction maps

Thanks you all for your kind help

Do want to know about protein - protein interactions of known/published interactions or do you want to predict whether a specific protein can have any sort of interaction with another specific protein?

Dear Pruthvi: Its about the prediction of protein-protein interaction.

@Debasish: You can use the PSICQUIC database where you can get the best reliable information from STRINGS (Functional characteristic binding predictions), You can get the entire network predictions from Reactome. we can obtain Just a normal motif - motif binding prediction from BIND database.

If your query protein has any experimentally observed binding partners then you can get that data from best protein - protein Interaction curated databases like InAct and MINT databases.

P.S. When you are using any of these tools and databases make sure the leads obtained from them have a proper literature support. (Sometimes these tools might give certain genes and proteins which does not have a proper information about them in literature) and don't choose any gene or protein which is not curated properly in NCBI Gene or Uniprot database

@Pruthvi: I would like to know the tools that can be used to address the second part of your question, i.e, to predict whether a specific protein can have any sort of interaction with another specific protein?

Schrodinger

Hex Tol

Cytoscape is the best tool for PPIs studies,go for it.

Dear Debasish Paul

Welcome to PSOPIA ( https://mizuguchilab.org/PSOPIA/ ).

PSOPIA is an AODE for predicting protein-protein interactions using three seqeucne based features; (I) sequence similarities to a known interacting protein pair, (II) statistical propensities of domain pairs observed in interacting proteins and (III) a sum of edge weights along the shortest path between homologous proteins in a PPI network.

You can use ClusPro server.

https://cluspro.bu.edu/login.php

Coev2Net http://groups.csail.mit.edu/cb/coev2net/ TSEMA http://tsema.bioinfo.cnio.es/

InterPreTS http://www.russell.embl.de/interprets Struct2Net http://groups.csail.mit.edu/cb/struct2net/webserver/ PoiNet http://poinet.bioinformatics.tw/

PrePPI http://bhapp.c2b2.columbia.edu/PrePPI/ iWARP http://groups.csail.mit.edu/cb/iwrap/ PIPE2 http://cgmlab.carleton.ca/PIPE2

PreSPI http://code.google.com/p/prespi/

SPPS http://mdl.shsmu.edu.cn/SPPS/

HomoMINT http://mint.bio.uniroma2.it/HomoMINT

P-POD http://ppod.princeton.edu/

BLASTO http://oxytricha.princeton.edu/BlastO/

PHOG http://phylogenomics.berkeley.edu/phog/

COG http://www.ncbi.nlm.nih.gov/COG/

OrthoMCL-DB http://orthomcl.org/orthomcl/

STRING http://string.embl.de

MirrorTree http://csbg.cnb.csic.es/mtserver/

G-NEST https://github.com/dglemay/G-NEST

InPrePPI http://inpreppi.biosino.org/InPrePPI/index.jsp

PRISM PROTOCOL http://prism.ccbb.ku.edu.tr/prismprotocol/

https://string-db.org/ and then cytoscape

BioGRID, HPIDB, STRING.....etc