Solutions White Papers
Download DocumentMeeting the challenges of representing large, modified biopolymers
Abstract
This white paper discusses the challenge of developing a chemically-aware method of representation for large, modified biopolymers that is meaningful for both biologists and chemists, reduces redundant information and enables the electronic searching of structural features. The paper compares the methods used by chemists to represent chemical structures with those used by biologists to depict biological structures, employing the synthetic erythropoiesis protein (SEP) to illustrate the extreme complexity encountered at the interface between chemical and biological research where biological entities are often modified to change their biological activity. The paper concludes by explaining the four methods for recording chemical structures supported by the Symyx Direct (previously MDL Direct) data cartridge and describes recommended approaches.
Symyx recognized the growing importance of bio-molecules in the pharmaceutical industry over a decade ago. To meet customer needs, the atom and bond limits in the early molfile format (V2000) were removed with the introduction of the V3000 molfile format. In addition, biopolymer drawing capabilities were included in the new and improved Symyx Draw (previously MDL Draw) structure editor, enabling scientists to draw, register, search and report on chemically modified peptide and nucleotide sequences. The Symyx Direct data cartridge imposes no arbitrary limits on the size or composition of the structures. The combined capabilities of Symyx Draw and Symyx Direct meet the challenges of registering large, modified biopolymers today.
To read the complete white paper, click the Download Document link near the top of the this article.
