|Chemical Database Management System
Databases that operate with chemical information
CheD was developed to store, view, and search chemical structures and infrared, nuclear magnetic resonance, and mass spectra.
For: chemical plants, universities, research centers.
The software is intended for engineers and scientists working in chemistry
CheD was developed to store, view, and search chemical structures and infrared, nuclear magnetic resonance, and mass spectra
The software runs on the personal computer for the storage, retrieval and processing of chemical information. The program can work both as stand-alone application and with especially written WWW server and some SQL servers such as Oracle, Interbase, MS SQL. New kinds of data fields are introduced: arrays for spectral information store, WWW and database links, and user-defined functions. CheD has an open architecture for customized types, controls, services to be added. WWW server for chemical data exposure is created as a distributive, which may be installed at Windows NT or 95 platform in some minutes
Some modifications were introduced into the previously described Centroid algorithm of diversity sorting, which uses cosine similarity metric. The modified algorithm is suitable for working with large databases on personal computers. For example, less than 9 hours are required (Pentium III, 800 MHz) for diversity sorting of the database with the size greater than million of records. The problem of selection of new compounds to the existing collection is examined to reach the maximum diversity of the collection. A new algorithm for the selection of heterocyclic compounds is described
The software was applied at Uniroyal Chemical, ChemDiv, TimTec, Chemical Block International, Harvard University; many institutes of the Russian Academy of Sciences, the Moscow University, and many research institutes.
CheD program package for chemistry
- Basic version
- CheD is 32-bit Windows program, used for creation and supporting of chemical databases.
- With a CheD's tools you are capable to create your own database using a variety of field types.
- You can arrange database for viewing and printing.
- Any record is easy to be found with CheD's search functions.
- CheD has many routines to arrange, sort, verify, compare, merge databases
- All search and comparison processes are very fast with CheD.
- CheD supports the interfacing with the SDF and JCAMP formats for Chemical and Spectral data exchange, which make CheD compatible with related programs.
- Original Structure Editor makes drawing of structure easy and pleasant
- CheD is capable to operate with large databases - up to 10,000,000 records.
- Due to standard Windows style it is easy to communicate with other applications.
- With prediction tools available your database can be learned to predict unknown data.
NMR-spectra processing includes:
- Element properties - list of nuclei magnetic properties
- Spectrum calculation - predict NMR peak table spectrum using database learned
- Check DB content - compare database spectra with predicted ones
- Standard recalculation - recalculate spectrum to another standard
HNMR processing and assignment - loads instrumental FID, processes FT, Phase correction, Integral calculation, peak peaking, manual assignment of peaks, print assigned spectrum.
- Prediction 1H, 13C and 31P chemical shift
- Databases of 4,000 13C and 4,000 31P assigned spectra
The screenshot of the Chemical and Spectral data appearance is shown here.
IR-spectra processing includes:
- Spectrum processing- loads instrumental spectrum, performs base line correction, spectrum normalization, spectra subtraction.
- Peaktable generation - calculates peak table from spectral curve
- Spectrum edit - edits spectrum by points
- Contour decomposition - decomposes spectral curve into Lorentz/Gauss contours
MASS-spectra processing includes:
- JCAMP(Wiley)->JCAMP-Link - execute files transformation
- Import Instrumental files - loads instrumental Finnigan *.pic and Vector *.txt files
- Intensities correction - correct spectrum intensities using calibration table
- Export in text exchange format - saves spectrum in simple text file
- Peak's isotopic structure - calculates intensities of isotopic components of mass peak
- Exact mass - calculate exact mass for given isotopic composition
- Element properties - isotopes exact mass table
- Composition of peak - proposes brutto-formulas for given mass
- Expert - analyses mass spectrum using possible fragmentation
- Calculator - calculates in real time masses and isotopic distribution of selected fragment in structure. Saves assigned fragments in spectrum into teaching database.
- Look assignment database - browser of database learned
- Spectrum analyzing - analyzes spectrum using database learned
Routines for synthesis planning:
- Material balance- to calculate amount and volume of compounds, including and obtained in a synthesis. Yields and excess are taken into consideration.
- Calculates brutto-formula from element composition.
- Units of concentrations re-calculation.
- Dilution of solvents
Diversity, chemical structures and combinatorial chemistry:
- Diversity sorting - sort a data set by diversity with very fast algorithm (full sorting of 1,000,000 compounds per 9 hours).
- Compound Selection - select compounds from external data set, the diversity being maximized
- Similarity calculations - for each compound in initial data set calculates similarities with selected data set.
- SDF file error analyzing - checks for possible errors in SDF file.
- SDF file processing - edition and search in a SDF file without its conversion to database.
- SDF file creation - converts *.mol files from a selected directory to a SDF file.
- SDF file sorting - sort records in SDF file accordingly to diversity.
- Heterocyclic fragments generation - generate a database with non-substituted heterocycles from a dataset. Occurrence of heterocycles in the dataset is calculated. Sorting by diversity with heterocyclic fragments.
- Virtual compound generation - create combinatorial data set by radical recombination and from scaffold structures.
- Interface with SQL servers - Oracle, MS SQL, Interbase
- Upload and download data for above-mentioned SQL servers.
WEB server extension
Enable to publish chemical data - structures, spectra, also as text and pictures over WWW. A client can select data with structure/substructure search and traditional text search. One may compare content of local SDF with remote database very fast - 5 minutes are required to compare 1,000,000 remote databases with 10,000 SDF chemical structures.
Here you can find the structural scheme of CheD components interaction.
Software and hardware required
CheD can run at any computer with installed Windows 95/NT/2000. But to achieve appropriate performance, computer requires:
- Processor Pentium 133 or better.
- 32Mb of RAM to run CheD itself. To manipulate with a database of 100,000 chemical structures, 24Mb of RAM should be added.
- 60Mb of free disk space for installation. To store 1,000,000 structures without additional data, one needs approximately 400Mb of free disk space.