Chemical Database Consulting

Research IT

A database is a collection of organized data, which enables safe storage and efficient retrieval of data. Wildcard Pharmaceutical Consulting works with databases related to chemical and biological information which are needed in industrial drug discovery setting.

Benefits of using a chemical database

Standard databases are good at handling numbers as well as texts. When chemical structures should be stored in a database additional features and attention are necessary. Storing the molecular structures in the correct way, enables substructure searching. Alternatively identity matching can be implemented by use of chemical fingerprints. When chemical structures are stored together with the  assay results obtained from these structures, it gets much more efficient to generate datasets for more advanced modeling and visualization. The effort and resources spent on making the database and storing the information saves time an money in the long run due to the higher efficiency in retrieval and formatting of the information. It also lowers the risk of loosing important information because of unstructured data handling. Excel sheets are often lost or overwritten accidentally, multiple versions with different content tend to emerge over time. Storing data in an organized way in a chemical and biological database prevents repeating previous work.

Wildcard Pharmaceutical Consulting is providing chemical database consultant services by developing new SQL functions, views, triggers and relational models. We have experience with Oracle and Postgres DBMS software, as well as  with PL/SQL, PlpgSQL and PlpythonU. PlpythonU enables the use of Python programming directly in the database functions. Database software solutions are very similar on the basic level and we are not restricted to work with only Oracle or Postgres solutions.

Peptide databases with covalent modifications are a special case, because one must both be able to handle the structures in sequence space (one letter amino acid codes) and in chemical space for handling the modification. Wildcard Pharmaceutical Consulting is collaborating with BioChemFusionto use their Proteax database cartridge, which can interconvert between the two formats and handle modifications in an organized manner.

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More about databases

A database is an organized collection of data that can be queried for data retrieval. The data is stored in a relational model, which relate to the inherent structure of the data. The model must also be created in a way that supports processes and queries. Chemical and biological databases need special approaches for handling the information.  The database must enable both chemical and biological queries such as substructure searching or sequence matching.

The way the model is defined sets limits on the database usability. An efficient database balances the generality and usability. It must be general enough that it enables future variations to be stored, while at the same time ensure that the data is organized in a way that suits the way of working. Wildcard Pharmaceutical Consulting has research based scientific insight into chemical and biological issues, which enables us to work more efficiently when providing chemical database consultant services. We can successfully develop or modify chemical and biological database models, that are perfectly suited for the research environment. We do not only focus on the current tasks and processes, but strive to make the models more future proof. Our aim is to minimize the risks of expensive future data migration projects which arise from the shifting demands in the scientific research processes.

Wildcard Pharmaceutical Consulting also has experience with Linux operating system. We can help as Linux Server Consultant to set up Linux servers as database platforms.  Contact us today for a free but confidential chat about your data storage needs for biological or chemical data.