The MS2DB ++ webserver: disulfide bond determination through evidence combination

MS2DB++ is a web server for computationally determining disulfide connectivity in proteins by combining evidence from multiple methods. The constituent methods implemented as part of the MS2DB++ webserver include a mass spectrometry-based method and two protein sequence-based predictive methods. The software also allows users to incorporate results from up to two other external methods of choice. The results from all these methods are combined using Dempster-Shafer theory through the use of four different formulations for evidence combination. In practice, MS2DB++ can be especially helpful in obtaining the disulfide topology in cases where no single method performs consistently across a set of molecules due to complexity of the bonding topology, specificities of the fragmentation pattern, or limitations of computational models.