Nucleic Acids Research, 2012, Vol. 40, Web Server issue W529 Figure 2. Screenshots of the homology modeling tool. (A) The input page. (B) The output page: a pair-wise sequence alignment of the source protein and one of the PDB hits. Epitope residues are shown in orange. Solvent exposed residues (with a relative solvent accessibility of side chain atoms, RSA, above 40%) are shown in red and buried (RSA below 7%), in blue (these cut-offs can be changed as shown in C). In the annotation for secondary structures (34), ‘H’ denotes an alpha-helix; ‘G’, a 3-10 helix; ‘E’, a beta-strand; ‘T’, a turn; ‘X’, no structure. (C) The output page: a fragment of a multiple sequence alignment of the source protein and all PDB hits (at the Blast E-value < 1.0E-3). (D) Default view of the protein source and epitope (colored in blue) in EpitopeViewer. The view can be changed using the EpitopeViewer’s tools and shortcuts accessible on the right top panel. server, which in turn generates a page with the prediction results. Such programmatic calls can be integrated into external applications, and they not only allow the user to run prediction jobs in batch mode but also ensure that the most up-to-date predictions will continue to be used. Finally, these calls do not require any local installa- tion. Details on the use of IEDB-API as well as examples are provided at the IEDB-AR website (http://tools.iedb. org/main/html/iedb_api.html). SOFTWARE DISTRIBUTION PACKAGES OF PREDICTIVE TOOLS In addition to the web services described above, down- loadable versions of the predictive tools are available freely for educational use, and with a licensing fee for commercial use. The MHC class I and class II binding prediction tools are available as a standalone package in compressed tarball and Ubuntu packages. These packages consist of Python scripts that are directly callable from the command line, making it convenient for batch processing. Additionally, a virtual machine image of the IEDB Tools server is available for download and includes all tools on the website, with the user-friendly web interface to which users are accustomed. The image can be easily imported into an existing VMware ESX/ESXi deployment for site-wide access and should also run on a local installation of any virtualization software that supports OVF format. Both versions are updated on a 6-month cycle with the release of the website. SUMMARY A comprehensive set of immune epitope prediction and analysis tools are provided in the IEDB-AR. All compo- nents of the resource have been updated since the last publication in 2008, including retraining of prediction methods and addition of new methods. Furthermore, with the ability to use the IEDB-AR tools through a web-based API, it is becoming easier to integrate the tools into external applications. In the future, we plan to continue to make improvements to existing tools and add new ones. In addition to these efforts, we very much en- courage people to notify us of predictive tools they are willing to contribute to the IEDB. FUNDING The IEDB is funded by National Institutes of Health [contract number HHSN272201200010C]. Funding for open access charge: National Institutes of Health. Conﬂict of interest statement. None declared.