Welcome

Welcome to the homepage of the ARMOR project. If you run into any problems, so please email me, Konstantin Berlin (kberlin at gmail.com). I will be very happy to work with you.

ARMOR (Accurate and Rapid computation of Molecular Optimization Restraints) is a package for rapidly computing several important long-range molecular restraints used in multi-domain structural refinement of complexes consisting of DNA, RNA, and/or proteins. The package consists of three major toolboxes: (i) a package for processing, prediction, and rigid-body docking based on nuclear spin-relaxation (ROTDIF); (ii) a package for processing, prediction, and rigid-body docking based on Residual Dipolar Couplings (PATI); (iii) a Sparse Ensemble Selection (SES) algorithm for selecting representative ensembles of dynamic molecular systems from experimental data.

ARMOR is written primarily in Java, can run on virtually any platform, including Linux, Windows, and Mac OS, and contains a highly scalable, thread-safe API that can be rapidly leveraged by advanced users for easy integration into their own software.

News

2014-06-30: New version (1.1) of all the software packages has been released!

2014-04-22: ROTDIF is under construction. A new version will be released soon that will fix several bugs.

Instructions

The instruction pages are currently under development. If you have questions about running the software, please email me (kberlin@umd.edu) directly.

Make sure Java 6 or above is installed.

Basic Instructions:

Download and unzip the lib.zip file, provided in the download link into a directory. Alternatively download the individual .jar files from the associated websites and put them in the ./lib directory. See Dependencies.
In the same directory please put any desired ARMOR "*.jar" files. These files are also provided in the download directory.
For GUI interface, simply double click the jar file.
For console interface, type "java -jar <jar file name>"

Currently ARMOR has 3 standalone components:

Click for instructions for how to use ROTDIF, a package for processing NMR relaxation data.
Click for instructions for how to use PATI, a package for processing NMR RDC data.
Click for instructions for how to use SES, a method for conformational ensemble selection.

If you experience any bugs or have feature suggestions, please submit a bug report using Bitbucket's issues tracker.

Dependencies

Publications

[1] K. Berlin, A. Longhini, T. K. Dayie, and D. Fushman, “Deriving quantitative dynamics information for proteins and RNAs using ROTDIF with a graphical user interface,” Journal of Biomolecular NMR, vol. 57, no. 4, pp. 333–352, 2013.

[2] K. Berlin, C. A. Castaneda, D. Schneidman-Duhovny, A. Sali, A. Nava-Tudela, and D. Fushman, “Recovering a representative conformational ensemble from underdetermined macromolecular structural data,” Journal of the American Chemical Society, vol. 135, no. 44, pp. 16595–16609, 2013.

[3] K. Berlin, D. P. O’Leary, and D. Fushman, “Fast approximations of the rotational diffusion tensor and their application to structural assembly of molecular complexes,” Proteins: Structure, Function, and Bioinformatics, vol. 79, no. 7, pp. 2268–2281, 2011.

[4] K. Berlin, D. P. O’Leary, and D. Fushman, “Structural assembly of molecular complexes based on residual dipolar couplings,” Journal of the American Chemical Society, vol. 132, no. 26, pp. 8961–8972, 2010.

[5] K. Berlin, D. P. O’Leary, and D. Fushman, “Improvement and analysis of computational methods for prediction of residual dipolar couplings,” Journal of Magnetic Resonance, vol. 201, no. 1, pp. 25–33, 2009.

Links

My website: http://sites.google.com/site/kberlin/

Fushman lab: http://http://gandalf.umd.edu/FushmanLab

License

LICENSE

Copyright

This software is distributed "as is", without any warranty, including any implied warranty of merchantability or fitness for a particular use. The authors assume no responsibility for, and shall not be liable for, any special, indirect, or consequential damages, or any damages whatsoever, arising out of or in connection with the use of this software.

Wiki

ARMOR / Home