Vivian A . Salazar , Marc Torrent

Molecular docking modelling was performed as previously described (Torrent et al., 2011). Briefl y, the docking simulations were performed using Autodock 4.2 (The Scripps Research Institute, La Jolla, CA, USA). The protein coordinates of the eight human RNases were taken from X-ray crystallography or NMR data. When no three-dimensional structure was available, the protein structures were predicted using the Swiss Modeller server ( http://swissmodel.expasy.org/ ). For protein coordinates, the following crystal structures were used: RNase 1 (2K11.pdb), RNase2 (1H1H.pdb), RNase3 (1DYT.pdb), RNase 5 (2ANG.pdb) and models from nuclear magnetic resonance of RNase 4 (1RNF.pdb) and RNase 7 (2HKY.pdb), the RNases 6 and 7 three dimensional models were designed using Swiss Model software. The ligands d(ApTpApA) and heparin tetramer fragment were taken from protein data bank coordinates 1RCN.pdb and 1BFB.pdb, respectively; CpA and heparin IdoA(2S) GlcNS (6S) (5S) were designed using PRODRG server. As fi rst step, all ribonucleases were superposed using Swiss-PdbViewer to the RNase A model (1RCN.pdb). In all crystal structures used, water molecules were removed from the structure. Hydrogen atoms were added using Autodock Tools. This software was also used to add atomic partial charges, using the Gasteiger method, and non-polar hydrogen merging. The protein was kept rigid during the docking simulation. The docking was accomplished using Supplemental data