All the options mentioned above are great, especially HPRD and STRING. Cytoscape is a wonderful software to analyse a network. I would also add several other useful databases:

BOND is good for PPI, along with references (http://bond.unleashedinformatics.com/Action?pg=1001).

Usually all the general website like UniProt, Ensembl, Genecards, iHOP give you a pretty good overview of a given protein.

NextProt is a very good website with an interesting search engine for proteins (http://www.nextprot.org/db/).

I like VirHostNet (http://pbildb1.univ-lyon1.fr/virhostnet/login.php). It's specifically made for viruses but you can definitely search for human PPI or virus-human PPI. For each PPI, you have a direct link to references in PubMed.

Finally, you can use HomoMINT (http://mint.bio.uniroma2.it/HomoMINT/Welcome.do).

The most official if you want to get all the known resources of a gene is HGNC (http://www.genenames.org/).

Godd luck

Maybe this helps:

http://string-db.org/

This site has reasonable information on subcellular localization: http://www.hprd.org

Check this: http://www.nature.com/nmeth/journal/v10/n8/full/nmeth.2561.html

You could go to SignalPep which predicts the sequence of the signal peptide to which that protein is targeted. For example, the proteins which are targeted to membranes (plasma membrane and endosomal membrane) contain a membrane localisation sequence which targets it to the organelle.Hope this helps.Here is the link:

http://www.cbs.dtu.dk/services/SignalP/

http://www.cbs.dtu.dk/services/TargetP/ try this i hope you find what you are looking for.

Try This

Database for intracellular location of proteins DBSubLoc (Guo et al, 2004).

http://www.bioinfo.tsinghua.edu.cn/dbsubloc.html

Use UniProtKB annotation reviewed proteins

I would suggest :

http://www.ncbi.nlm.nih.gov/CBBresearch/Lu/subcellular/

It has several prediction tools.

UniProt (http://www.uniprot.org) also has a reasonable prediction capability. Good luck

All the options mentioned above are great, especially HPRD and STRING. Cytoscape is a wonderful software to analyse a network. I would also add several other useful databases:

BOND is good for PPI, along with references (http://bond.unleashedinformatics.com/Action?pg=1001).

Usually all the general website like UniProt, Ensembl, Genecards, iHOP give you a pretty good overview of a given protein.

NextProt is a very good website with an interesting search engine for proteins (http://www.nextprot.org/db/).

I like VirHostNet (http://pbildb1.univ-lyon1.fr/virhostnet/login.php). It's specifically made for viruses but you can definitely search for human PPI or virus-human PPI. For each PPI, you have a direct link to references in PubMed.

Finally, you can use HomoMINT (http://mint.bio.uniroma2.it/HomoMINT/Welcome.do).

The most official if you want to get all the known resources of a gene is HGNC (http://www.genenames.org/).

Godd luck

http://www.proteinatlas.org/ can be quite useful. They basically stain 3 different cell lines for a protein of interest. If you hit the "subcellular location" tab in the left menu on a gene page you can expand images and toggle channels etc. Sometimes the staining works, sometimes it doesn't, but you can see the pictures for yourself.

Most of the protein databases like SWISSPROT also has these facilities.

Aldolase A is present in smooth muscle cell nuclei.

Mamczur P, Dzugaj A.

Acta Biochim Pol. 2008;55(4):799-805. Epub 2008 Dec 16.

Subcellular localization of muscle FBPase in carp (Cyprinus carpio) tissues.

Adamowicz A, Gizak A, Dzugaj A.

Comp Biochem Physiol B Biochem Mol Biol. 2006 Jun;144(2):223-8. Epub 2006 Feb 28.

Nuclear localization of fructose 1,6-bisphosphatase in smooth muscle cells.

Gizak A, Rakus D, Dzugaj A.

J Mol Histol. 2005 May;36(4):243-8.

The effect of calcium ions on subcellular localization of aldolase-FBPase complex in skeletal muscle.

Mamczur P, Rakus D, Gizak A, Dus D, Dzugaj A.

FEBS Lett. 2005 Mar 14;579(7):1607-12.

Calcium inhibits muscle FBPase and affects its intracellular localization in cardiomyocytes.

Gizak A, Majkowski M, Dus D, Dzugaj A.

FEBS Lett. 2004 Oct 22;576(3):445-8.

As Tom said, http://www.proteinatlas.org/ is quite extensive. Check it out.

You may find number of software packages for predicting function of proteins in OSDDlinux, try http://osddlinux.osdd.net/