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As one of the most self-centred and ubiquitous post-translational modifications (PTMs) of proteins, S-nitrosylation plays important roles in a variety of biological processes, including the decree of cellular dynamics and plasticity. Verification of S-nitrosylated substrates with their fastidious sites is important for apperception the molecular mechanisms of S-nitrosylation. In discriminate with labor-intensive and time-consuming speculative approaches, hint of S-nitrosylation sites using computational methods could provide convenience and increased velocity. In this work, we developed a unconventional software of GPS-SNO 1.0 for the intimation of S-nitrosylation sites. We greatly improved our time past developed algorithm and released the GPS 3.0 algorithm for GPS-SNO. By comparison, the suggestion accomplishment of GPS 3.0 algorithm was advantage than other methods, with an preciseness of 75.80%, a sensitivity of 53.57% and a specificity of 80.14%. As an devotion of GPS-SNO 1.0, we predicted putative S-nitrosylation sites for hundreds of potentially S-nitrosylated substrates for which the consummate S-nitrosylation sites had not been experimentally determined. In this regard, GPS-SNO 1.0 should show to be a fruitful way for experimentalists. The online service and nearby packages of GPS-SNO were implemented in JAVA and are cleanly ready at: .