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Biomolecular Modeling Database (BMOD)

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Description

Biomolecular Modeling Database (BMOD) is designed to archive and provide force field parameters of small molecules for different molecular modeling software packages.
The search engine in the left panel provides quick search on a large number of small molecules. These small molecules have been aggregated from different databases.
The current “release note” introduces the source databases and describes the utilized software packages for populating the data entries.

Data Access

To access data in the BMOD database, please use the search bar on the left of the page. You can also click here to view a random entry.

Release notes

  • Release 3 (24 Sept. 2018): The current version of the database contains 400,164 small molecules. The structure file of these compounds have been aggregated from different databases. The complete list of the databases can be found here.

  • Release 2 (24 April 2018): The current version of the database contains 124,343 small molecules. The structure file of these compounds have been aggregated from different databases. The complete list of the databases can be found here. Different software packages have been utilized to construct the current version of the database;
    • RUNER: To generate force field parameter files. This program utilizes the Antechamber and ALATIS to generate the parameters.
    • Open Babel: To generate 3D structure files from input 2D structures. In addition, Open Babel was used for adding explicit hydrogen atoms to the structures when needed.
    • ChemAxon Marvin: To generate 2D images of structure files, to be displayed on entry pages.
    • Computing platforms: NMRbox and HTCondor have been utilized to execute the underlying software programs.

  • Release 1 (12 Jan 2018): The current version of the database contains 10,684 small molecules. The structure file of these compounds have been aggregated from different databases. Different software packages have been utilized to construct the current version of the database;
    • RUNER: To generate force field parameter files. This program utilizes the Antechamber and ALATIS to generate the parameters.
    • Open Babel: To generate 3D structure files from input 2D structures. In addition, Open Babel was used for adding explicit hydrogen atoms to the structures when needed.
    • ChemAxon Marvin: To generate 2D images of structure files, to be displayed on entry pages.
    • Computing platforms: NMRbox and HTCondor have been utilized to execute the underlying software programs.
Disclaimer:
  • BMOD is available to the public as a web-service via our web server. This work is copyrighted under the terms of GPL. The data entries are provided on an "as is" basis without warranty of any kind, either expressed or implied. Any usage of BMOD data entries, or modification and application of the data are free for academic use when BMOD publications are cited.
  • The chemical compounds archived in this database are aggregated from several different databases and have been processed with different software packages. For appropriate citation of the data entries please check the PDF description files provided for every entry.
  • The majority of the aggregated compounds are provided in 2D structure and with implicit hydrogen atoms. We utilized the Open Babel (The Open Source Chemistry Toolbox) software package to add explicit hydrogen atoms and to generate 3D structure of the compounds; please comply with the Open Babel license agreements.
Contact:
    For any question or concern please contact Hesam Dashti (hdashti@bwh.harvard.edu).
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