Robust nomenclature and software for enhanced reproducibility in molecular modeling
Home
GUI download
Biomolecular Modeling Database (BMOD)
NMRFAM Servers
Search:
1. Upload or paste input structure
upload a structure file (one compounds per submit):
or paste a structure:
(if a file has been uploaded we process the uploaded file)
Specify input format:
Mol v2000 (*.mol)
SDF MDL (*.sdf)
PDB (*.pdb)
CDX (*.cdx)
2. Modifying structure
Use unique atom labeling
(using
ALATIS
)
Project two-dimensional structure to 3D structure
(using
OpenBabel
)
Add explicit hydrogen atoms
(using
OpenBabel
)
3. Restraints files
*Optional
upload a NOE restraints file (
acceptable format; Xplor-NIH
):
upload a RDC restraints table (
acceptable format; NMRPipe
):
upload a Dihedral restraints table (
acceptable format; Xplor-NIH
):
4. Semi-empirical quantum mechanics
General AMBER force field:
GAFF
GAFF2
Charge calculation options:
Semi-empirical quantum chemistry; AM1-BCC (
SQM-AMBER
)
MOPAC; PM7 (
MOPAC
)
Molecules charge:
Multiplicity:
Singlet
Doublet
Triplet
Quartet
Quintet
(will not be used for antechamber)
Geometry optimization
5. Submit
Email address to receive the outputs:
Citation:
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
Disclaimer:
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.
Contact:
For any question or concern please contact
Hesam Dashti (dashti@wisc.edu)
.