Overview of the DFT Database for RNA Catalysis

This page contains general information about the DFT Database for RNA Catalysis.  Click on any of the following links:

What is the Database?

The DFT Database for RNA Catalysis is a large collection of high-level density-functional electronic structure calculations of molecules, complexes and reactions relevent to RNA Catalysis.  This is part of a 5-year project funded by the NIH to study the molecular mechanisms of RNA enzymes, or ribozymes.  A detailed understanding of RNA catalysis is fundamental to biology, and has important implications toward the design of new medical therapies that target genetic disorders as well as the development of new biotechnology.  The  DFT Database for RNA Catalysis can be used to derive information about molecular structure, compelxes and reactions.  Moreover, the design of the database with a careful and consistent theoretical level opens the door to the design of new, highly accurate and efficient quantum models able to be applied in large-scale hybrid quantum mechanical/molecular mechanical simulations of ribozyme reactions.

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What does the Database contain?

The database contains information derivable from electronic structure calculations including:
The technical details of the calculations are described elsewhere.

The Database contains a host of molecular structures and reactions relevent to RNA catalysis including:
The chemical reaction database includes:
In all reactions the effects of solvation and pH (protonation state) are considered.

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How do I to use the Database?

Basic use of the DFT Database for RNA Catalysis is very simple.  All you need to do to start out is go to the Database Search Page accessible from the main page.  From there you can perform searches for individual molecules, chemical reactions, hydrogen bonded complexes, etc... based on molecular formulas or a host of other chemical properties.  You can also choose to browse the contents of the entire database. 

Although the DFT Database for RNA Catalysis can be used alone to access property information, to take full advantage through visualization and animation, you will need to set up a special release of the MOLDEN program as a viewer for chemical MIME types (see the link off of the main page for further details).

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Further Information

For specialists wanting to know more information about how the files composing the Database were constructed, additional information regarding the Calculation Details and the Nomenclature and Conventions used for the Database are available.

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