Antibody design is an important part of many proteomic experiments. However, exactly which antibody you should use will depend on the question you are asking, the type of experiment you intend to do, the location of your target, the state of the targeted protein and many other factors. While there are a number of searchable databases that contain vital protein information such as protein function, domains structure, post-translational modifications etc (see for example Swissprot ) and others databases that will help you identify antibodies for a variety of different research applications (for example Antibody/Epitope Registry Database ), there are not many tools for designing new antibodies based on both the protein target and the experiment you intend to carry out.
Based on this need, a European group has created the ProteomeBinders Epitope Choice Resource (EpiC) which collates and presents a structure-function summary and antigenicity prediction of your protein to help you design antibodies that are appropriate to your planned experiments. EpiC utilizes information on both the protein target and the various experiments that you plan to carry out and helps in the prediction of antigenicity and therefore epitopes. In order to best design the antibody, EpiC asks you for a plethora of information. This includes:
-protein information such as the Uniprot ID, the subcellular localization you are interested in, the state of the protein you are studying (i.e. native, denatured, folded etc)
-information on the intended experimental conditions such as the experiment type (i.e. pull-down, Western Blot, ELISA etc), the antibody type (monoclonal, polyclonal), the membrane topology, target conditions and epitope type
EpiC then takes all of this information and queries a set of 26 databases (such as BLAST, Protein Atlas, EMBOSS , immune epitope database) and returns the number of antibodies that will be needed for you experiment and where to target the epitopes.
The database is currently in its beta version and the authors welcome user feedback. Ideally the resource should be used in a Firefox browser but may be stable in other browsers as well.
Below are some screenshots from the EpiC website:
Below are the 26 Servers that EpiC integrates into its search: