the program for biopolymer structural analysis

BIOPSEL (BIOpolymers Primary Structure ELucidation) is the computer predictor of the structure of regular biopolymers built of residues linked by glycosidic, amidic and phospho-diester bridges.

  • monomeric composition
  • experimental 13C NMR spectrum
  • constraints (optional)

  • PC

  • repeating unit topology
  • sequence of residues
  • substitution pattern
  • absolute and anomeric configs
  • Click here for the general information and introduction to the problem.

    The input data are experimental 13C NMR spectrum of the regular polymer and its monomeric composition. Optional constraints on anomeric and absolute configurations and substitution positions may be specified, which means as soon as the researcher already knows something about the structure, he is able to improve the accuracy and performance by entering the data he knows. Output is the list of possible structures with repeating unit topology, residue sequence, complete substitution pattern and unknown configurations determined.

    The solution of an inverse problem, i.e. simulation of the assigned theoretical 13C NMR spectrum for the known structure, may be performed too.

      The proposed approach to the structure elucidation involves three steps:
    1. working out all the possible structures of the repeating unit for the given monomeric composition
    2. evaluation of the 13C NMR spectrum for each structure generated, basing on the spectra of mono-, di- and trimeric fragments and the average substitution effects.
    3. searching for the structures with the calculated spectrum closest to that observed for the polymer.

    4. (The detailed information on these steps is under highlighted links)
    monomeric residues (for structure generation),
    chemical shifts of di- and trimeric fragments (for NMR spectra simulation),
    average substitution effects (for NMR spectra simulation).

    The databases distributed with the program contain pyranose and furanose monosaccharides, sugar phosphates, alditols, aminoacids and other residues and can be easily updated by user., Databases for chemical shifts and substitution effects are presently being expanded on the basis of literature data for di- and trimeric fragments.

    BIOPSEL is tested on bacterial polysaccharides, mainly of the medically important genus Proteus. Running on a personal computer it made proper predictions in 70% cases for less than five minutes for hexameric repeating units and for several hours for hepta-, octa- and nonameric units (see structure generation for details). In the rest 30% cases satisfactory results were obtained after updating databases with data for specific residues or linkage types. The potential of BIOPSEL to predict structure of biopolymers, mainly polysaccharides, has been demonstrated on a variety of biopolymers with independently determined structure (click here for details).

    • repeating unit topology and residue sequence prediction

    • variable input: known substitution positions and residue configs are utilized, unknown are predicted

    • residues of any monosaccharides, alditols, aminoacids etc.

    • glycosidic, amidic or phosphodiester residue linking

    • all linear and branched topologies of up to 9 residues

    • databases are easily extendable by user

    NEW: Among advantages of the last version 3.0 (as compared to the previous version) are: knowledge of anomeric and absolute configuration is desirable but no longer required to perform an analisys; constraints for substitution positions are supported; database format is adapted to hold separate records for more than 10 types of residues; maximal size of repeating unit is expanded to 9 residues; up to 9 significant carbons per residue are supported; the code is now 32-bit to improve stability and performance.

    Abstract Publication data and abstract (v.2.0)
    Download the BIOPSEL user's manual in english (RTF,559K) or in russian (RTF,765K)
    Download the distribution of BIOPSEL 3.06 (332 Kb)

    Last update: 2002 Nov 26