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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.
Modules :
AAA :Amino Acid Analysis: This module calculates optimized residue ratio for amino acid analysis result. By entering residues easy to be oxidized in hydrolysis into Residues Not To Be Optimized section its influence to the optimization result can be minimized.
Comp :Building Block Composition: This module discerns identity of unexpected product based on the fact that building blocks: amino acids, fragments, possess discrete weight values. Upon scanning their combinations, the ones with least deviations will more likely be the derivatized product.
Digest
igestion Pattern: This module predicts digestion products through user defined enzymatic or chemical pattern.E A : Elemental Analysis: This module calculates the theoretical percentage of different elements in a sequence. By further entering experimental percent composition for each element, its empirical formula and/or its aggregates can be identified.
Frag :Fragmentation: This module predicts fragments generated in mass spectrometor by three types of bond cleavage: CH/CO, CO/NH, and NH/CH. The resultant fragments can be directly imported into Mass module for a simulated mass distribution pattern.
Helix :Helix Wheel/Net: This module displays and manipulates sequence wheel/net presentation of helix structure.
Iso : Isotopic Profile: This module predicts isotopic profile of a input formula or sequence, in either + or - mode with charges varying from 1 to 3
Lib : Combinatorial Library: This module predicts mass spectra for combinatorial libraries, such as peptide libraries, in either + or - mode with charges varying from 1 to 3. No mass round-up is performed until last step to assure accuracy. What is more, the module extends its prediction power to organic libraries: The random variants could be either amino acids, fragments or both. The result also includes random section residue combinations
Motif : Motif Discovery: This module predicts potential drug active sites in sequences via pattern recognition. It facilitates the scanning of pre-set patterns or random repeating patterns, potential pharmacophores, among loaded sequences that demonstrate same biological activity.
M W : Molecular Weight: This module calculates molecular weight of peptides and proteins. The input could be performed either through conventional sequence protocol, or with building blocks such as amino acids and fragments. The alternative enables the module to calculate molecular weight of complicate molecules such as peptide with protection groups, peptido mimetics, lengthy and branchy molecules, etc. Further use of atomic weights generally extends the module's power to calculate molecular weight of any compound.
Auxiliary : Description
Database : Database Management: This auxiliary module allows user to manage all databases utilized in this program, such as amino acid database, fragment add-on database ... etc. The open design allows user to customize databases according to their specific project.
Sequence : Sequence Loader: This auxiliary module allows user to load and parse sequence into the entry section of a corresponding module. The expert system automatically recognizes properties such as side chains, cyclic structures, pseudo replacements and additional adducts.
Code 3 1 : Code Base Switch: This auxiliary module allows user to automatically toggle between three letter code and one letter code for all the entry fields.
SYSTEM REQUIREMENTS :
Screen resolution: Microsoft standard font (small font), 1024 x 768 or above.
What's new
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http://www.angelsystems.net/Products/aminoXpress/aminoXpress_Information.aspxHOMEPAGE
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http://www.angelsystems.net/Angel.aspx?
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