Robust nomenclature and software for enhanced reproducibility in molecular modeling
1. Upload or paste input structure
2. Modifying structure
  • (using ALATIS)
  • (using OpenBabel)
  • (using OpenBabel)
3. Restraints files
4. Semi-empirical quantum mechanics

  • GAFF

  • Semi-empirical quantum chemistry; AM1-BCC (SQM-AMBER)

  • (will not be used for antechamber)

5. Submit

  • Hesam Dashti, Jonathan R. Wedell, Gabriel Cornilescu, Charles D. Schwieters, William M. Westler, John L. Markley, and Hamid R. Eghbalnia, "Robust nomenclature and software for enhanced reproducibility in molecular modeling",https://www.biorxiv.org/content/10.1101/429530v1
  • Hesam Dashti, William M. Westler, John L. Markley, Hamid R. Eghbalnia, "Unique identifiers for small molecules enable rigorous labeling of their atoms", Scientific Data 4, Article number: 170073 (2017), doi:10.1038/sdata.2017.73, https://www.nature.com/articles/sdata201773
  • RUNER is available to the public as a web-service via our web server, and also through the NMRBox virtual machine. The custom source code, developed using the academic license of MATLAB® in the Linux environment (MATLAB® 2016a for CentOS 6.5). This work is copyrighted under the terms of GPL. The web-service and the source codes are provided on an “as is” basis without warranty of any kind, either expressed or implied. Any usage of the web server, or modification and application of the source codes are free for academic use when RUNER publications are cited.
  • The input/output file formats to RUNER are Mol V2000 and its corresponding SDF. Other acceptable input/output file formats of this website are provided by utilizing the Open Babel (The Open Source Chemistry Toolbox) software package, please comply with the Open Babel license agreements.
    For any question or concern please contact Hesam Dashti (dashti@wisc.edu).
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