Dear Abhishek
you may check the following online software and servers for your work
1. Patchdock
2. Firedock
3. ZDock
4. Autodock
5. Molegro
and many more
Dear Abhishek,
You may please be in touch with Kannan Muthu who would certainly be helpful for your future studies along the notions and objectives you are planning to consider for.
ROSETTA is a software suite for predicting and designing protein structures,
protein folding mechanisms, and protein-protein interactions.
@Shahin Gavanji: Great. It will certainly be aiding to our ongoing research projects.
1. 3Dock Suits
2. BIGGER
3. ClusPro
4. Hex and
5. HADDOCK.
But i personally believes that HADDOCK is best for Protein-Protein Docking. Moreover its free!!
The Biological General Repository for Interaction Datasets (BioGRID) database was developed to house and distribute collections of protein and genetic interactions from major model organism species. BioGRID currently contains over 198 000 interactions from six different species, as derived from both high-throughput studies and conventional focused studies.
http://www.thebiogrid.org/
Biomolecular INteraction Network Database
http://bond.unleashedinformatics.com/
IntAct provides a freely available, open source database system and analysis tools for protein interaction data. All interactions are derived from literature curation or direct user submissions and are freely available.
http://www.ebi.ac.uk/intact/main.xhtml
The DIP database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions.
http://dip.doe-mbi.ucla.edu/dip/Main.cgi
The Molecular INTeraction database (MINT) focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators. The curated data can be analyzed in the context of the high throughput data and viewed graphically with the 'MINT Viewer'.
http://mint.bio.uniroma2.it/mint/Welcome.do
To faciliate experimentation and integrated computational analysis with model organism PPI networks, we have integrated known, experimental and predicted PPIs for five model organisms and human in the I2D database.
http://ophid.utoronto.ca/ophidv2.201/index.jsp
Homomint is a web available tool extending protein-protein interactions experimentally verified in models organisms, to the orthologous proteins in Homo sapiens.
http://mint.bio.uniroma2.it/HomoMINT/Welcome.do
The Unified Human Interactome is a comperehensive database of the computational and experimental based human protein interaction networks. This database is aimed to integrate diverge maps, which offers the research a flexible and direct entry gate into the human interactome.
http://www.unihi.org
APID (Agile Protein Interaction DataAnalyzer) is an interactive bioinformatic web-tool that has been developed to allow exploration and analysis of main currently known information about protein-protein interactions integrated and unified in a common and comparative platform.
http://bioinfow.dep.usal.es/apid/index.htm
The Human Protein Reference Database represents a centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.
http://www.hprd.org/
The Human Protein Interaction Database (HPID, http://www.hpid.org) was designed 1) to provide human protein interaction information pre-computed by a statistical method from existing structural and experimental data, 2) to provide integrated human protein interactions derived from BIND, DIP and HPRD, and 3) to find proteins from the databases that potentially interact with proteins submitted by users.
http://wilab.inha.ac.kr/hpid/
The MIPS Mammalian Protein-Protein Interaction Database is a collection of manually curated high-quality PPI data collected from the scientific literature by expert curators. We took great care to include only data from individually performed experiments since they usually provide the most reliable evidence for physical interactions.
http://mips.helmholtz-muenchen.de/proj/ppi/
A database of protein-protein interactions between large proteins
http://www.kazusa.or.jp/huge/ppi/
PPI section of the Comprehensive Yeast Genome Database.
http://mips.gsf.de/proj/yeast/CYGD/interaction/
Interactions between HIV and host proteins at the NCBI
http://www.ncbi.nlm.nih.gov/RefSeq/HIVInteractions/
A database of protein-protein interactions mediated by interchain
http://www.igb.uci.edu/servers/icbs/
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