Pavel Simakov - Protein Manager

 

 

 

 

by Pavel Simakov 2005-01-01

In 1997 I worked at ACDLabs in the position of a technical lead for new pilot software product tentatively called Protein/DNA Manager. ACDLabs always had an still has the finest chemistry software. The objective of this specific project was to build the core software tools for all aspects of proteomics & genomic research, to bundle them into a single product for increased productivity and to enter bioinformatics software market.

Product was built around around three-in-one functionality concept and provides all the features to Analyze, Manage and Publish protein and DNA sequence data in one application. The from-ground-up development of over dozen of scientific algorithms was successfully completed, resulting in the solid code-base for the future development in the area. Some of the features included:

  • instant access to SWISS-PROT, TREMBL, PROSITE and PFAM on your desktop with scheduled updates
  • protein secondary structure prediction
  • over 40 protein property profiles, including: transmembrane segments, antigenic regions, hydrophobicity, helix and turn preference, HPLC retention times, and many more
  • local BLAST search engine & multiple sequence alignment
  • protein restriction Maps; browse and search proprietary database of over 350 proteolytic enzymes; screen protein for digestion by all known proteases and predict potential restriction sites

From the software development perspective it featured a rich user interface, with embedded inter-user network messaging, multi-threaded processing, state of the art printing and export/import capabilities. The target platform was Intel 486 PC's on Windows 95 & NT operating system empowered by with the seamless integration with the web based tools. First version was built in Microsoft VC++ with MFC, but it was later abandoned and rebuilt in Borland Delphi.

As a result of dedicated sales and marketing efforts we were able to sell several copies, but also learned the specifics of bioinformatics software market and decided to pull out in late 1998. Couple of screen shots are shown below to get you a feel for the product design and functionality.

Protein secondary structure predictionOver 40 different protein profile charts2D-gel simulation and digestion analysisMultiple alignment HTML outputMultiple alignment (outlined)Multiple alignment (color coded)Protein isoelectric point (pI) calculationCircular/linear sequence editorEmbedded BLAST search engineApplication Main Window