title: Software tools for simultaneous data visualization and T cell epitopes and disorder prediction in proteins.
abstract: We have developed EpDis and MassPred, extendable open source software tools that support bioinformatic research and enable parallel use of different methods for the prediction of T cell epitopes, disorder and disordered binding regions and hydropathy calculation. These tools offer a semi-automated installation of chosen sets of external predictors and an interface allowing for easy application of the prediction methods, which can be applied either to individual proteins or to datasets of a large number of proteins. In addition to access to prediction methods, the tools also provide visualization of the obtained results, calculation of consensus from results of different methods, as well as import of experimental data and their comparison with results obtained with different predictors. The tools also offer a graphical user interface and the possibility to store data and the results obtained using all of the integrated methods in the relational database or flat file for further analysis. The MassPred part enables a massive parallel application of all integrated predictors to the set of proteins. Both tools can be downloaded from http://bioinfo.matf.bg.ac.rs/home/downloads.wafl?cat=Software. Appendix A includes the technical description of the created tools and a list of supported predictors.
authors: University of Belgrade, Faculty of Mechanical Engineering, Kraljice Marije 16, Belgrade, Serbia. Electronic address: djandrlic@mas.bg.ac.rs.
authors: Davorka R
authors: DR
authors: Jandrlić
authors: University of Belgrade, Faculty of Mathematics, P.O.B. 550, Studentski trg 16/IV, Belgrade, Serbia. Electronic address: chupcko@alas.matf.bg.ac.rs.
authors: Goran M
authors: GM
authors: Lazić
authors: University of Belgrade, Faculty of Mathematics, P.O.B. 550, Studentski trg 16/IV, Belgrade, Serbia. Electronic address: nenad@matf.bg.ac.rs.
authors: Nenad S
authors: NS
authors: Mitić
authors: University of Belgrade, Institute of General and Physical Chemistry, Studentski trg 12/V, Belgrade, Serbia. Electronic address: mpavlovic@iofh.bg.ac.rs.
authors: Mirjana D
authors: MD
authors: Pavlović
mesh_terms: D019295:Computational Biology; D030562:Databases, Protein; D018984:Epitopes, T-Lymphocyte / Q000737:chemistry*; D006801:Humans; D011487:Protein Conformation; D012984:Software; D014584:User-Computer Interface
chemical_list: D018984:Epitopes, T-Lymphocyte
keywords: Disorder prediction; Massive parallel prediction; T cell epitope prediction; Visualization