aminoXpress

aminoXpress is an advanced CAD application whose purpose is to help biochemists input sequences using a conventional protocol or building blocks and corresponding counts. Plus, it is able to deal with complicated, branched, cyclic and lengthy sequences.

User interface

The tool reveals a clean feature lineup but there are a lot of configuration settings that you can experiment with, so you need to invest some extra time in order to understand how it works.
You can check out a help manual that includes details about the program’s capabilities. There are several important steps that you can follow for processing data: load sequences into the workspace, study sequences in single-entry module (like molecular weight), switch loaded sequences in the working environment, as well as analyze sequences in multi-entry module.

Analysis modes that can be used in the biochemistry field

aminoXpress gives you the possibility to enter the amino acid analysis results for those residues that you want to be included in optimization procedure and choose the preferred method (least square, least difference, difference/count).
In addition, you can build block composition and choose the method for sorting data using the combinatorial scan or Monte Carlo, submit protein or peptide sequence for digestion, enable the elemental analysis, and enter a sequence to be fragmented.
The program helps you calculate molecular weights of a library, their distributions and their random section combinations, find out those common motifs automatically and sort them by occurring frequencies, as well as calculate molecular weights of a compound by using amino acids, fragments and elements as building blocks.
Last but not least, you are allowed to automatically toggle amino acid from one letter code to three letter code for all entry fields, manage information stored in all databases (you may add, change or delete the selected database), back up the database, and print the information.

Bottom line

All in all, aminoXpress comes with several powerful features that can be used in the field of biochemistry. On the downside, the GUI cannot be described as highly intuitive.