PROSESS

[…] set to 10 with a step size of 0.02 å. the secondary structure of the modeled protein was validated using protein structure validation suite (psvs) and protein structure evaluation suite and server (prosess). the secondary structure elements of the 3d model were compared with those of the predicted ones in order to measure the structural reliability. the selected p4a model was subjected to md […]

[…] in our hybrid model was further ascertained by the structure analysis and verification server v4 (saves, see http://services.mbi.ucla.edu) and protein structure evaluation suite and server (prosess, see http://www.prosess.ca/) [], and details of the analysis are compiled in additional file : figure s5., the molecular dynamics simulations were performed using amber 03 force field [] […]

[…] in the center of a water box with 10 å layer from the structure and with periodic conditions. in order to stabilize the system nacl ions were added. correctness of the model was validated using prosess (). the structure was visualized with pymol (http://www.pymol.org/)., the xre binding site was found using the dbtbs database searching tool (http://dbtbs.hgc.jp/) (). when searching […]

[…] threading programs (fugue, hhsearch, muster, ppa, prospect2, sam-t02, sparksx, sp3, ffas, and prc)., all 3d models of baua structure were qualitatively estimated by 4 various independent servers (prosess,vadar, prosa, and qmean). prosess [] server at http://www.prosess.ca (protein structure evaluation suite & server) is a web server designed to evaluate and validate protein structures […]

[…] in the approach presented here. the conformers generated using concoord may be artificially produced but appeared realistic when assessed for geometry and packing by the structure validation server prosess . moreover, the range of cavity characteristics observed was consistent with the variation between crystal structures. although the conformational space of the protein is unlikely to be fully […]