This has been done to make the molecules more accessible and organized. It is true that it might not be very precise in every case, but our goal with the molecular class categories is to find proteins easily. Molecular class should be thought of as: "What is this molecule most commonly considered to be (democratic consensus)" instead of "What all can this molecule possibly be?". We have done our best to make the categories as independent as we could. Because we cannot be experts in all molecules, we are looking for better ways to classify, so if you find something misclassified, please inform us because we will change it if a majority of scientists in that field agree.

We know, from our own experience, that most bioinformaticists do not want a fancy graphical display. Nevertheless, this database is intended for biologists rather than computer scientists. If you are interested in global analysis and the graphical display disturbs you, please download the XML and FLAT files and manipulate them yourself.

We consider two proteins to be interacting in vivo when, through the experiment performed, it can be assured that the proteins interacting are truly interacting in a mammalian cell. An interaction occurs in vitro when the experiment was performed in such a way that one cannot conclude it is happening in the context of a mammalian cell. Because Yeast 2-hybrid and similar experiments test interactions in the context of a yeast cell, they are technically in vivo, but we have annotated them specifically as Yeast 2-hybrid because of the greater degree of false positive interactions seen with this method.

The existing 3D structure databases are excellent and it does not make sense for us to duplicate the effort. We are providing a link to the corresponding entry in PDB.

The pathway diagrams have been drawn based on the protein-protein interaction data contained in HPRD. The pages show static JPEG images by default. If you click 'view SVG format' button at the bottom of the diagrams, you might be prompted to download a plug-in for SVG. You should accept and download the plug-in as it will allow you to visualize the data in SVG format in a new pop up window. In this window, you will be able to link directly to any molecule page by clicking on the name of any molecule in the interaction network. You will also be able to search for a protein by name by 'right clicking' and using the 'Find' command on the SVG page.

If you want the interactions of Protein X, query by name Protein X and then go to the interactions.