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Zeus
Zeus 1.5   
... very high quality molecular graphics. Zeus incorporates Sequence Search/Highlighting within the molecular structure with Wildcard capability. A ... be applied to sections of the molecular structure. Peptide/Nucleic structure can be "cartoonised" using 3d Ribbon based ...
Freeware

SearchGUI
SearchGUI 4.3.11   
SearchGUI, developed by the PeptideShaker Team, is a versatile and powerful open-source software ... proteomics data analysis. Tailored for researchers and bioinformaticians, SearchGUI serves as an intuitive graphical user interface that integrates multiple search engines, enabling comprehensive and efficient peptide and protein ...
Open Source
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