Nanosecond chain dynamics of single-stranded nucleic acids

fragment_library.tar.gz: Fragment libraries used as input to grow dTab19, dA19, dC19, and dT19 with HCG. All folders contain the topology as pdb file and the processed 100 ns trajectory as xtc file without water molecules, and the mdp file used to run the library at 300 K. Please note that we performed temperature replica exchange to create the fragment library as described in the publication. We also provide custom force field parameters for the fragment with the abasic site.

HCG_models.tar.gz: rA19, rC19, rU19, dTab19, dA19, dC19, and dT19 with attached FRET fluorophores Alexa 594 and Alexa 488. For each model we provide a topology file as pdb and a xtc trajectory with 10000 frames.

Distributions.xlsx: columns - A = dye-distance in nm, B = weights from refinement.

BioEnMeanVarianceOneSigma.tgz: Fortran code to perform the BioEn reweighting; input, output files and csh script to run the code, and a README file describing the input and output.