project.rst: contains a table with the top 10000 conformations scored using the restraints applied.If any distance restraint has been chosen: They correspond with the first 100 rows in project_.ene file. project_*.pdb: One of the top 100 conformations in PDB file format.project_.ene: a table with a list of generated conformations scored and ranked by the energy scoring selected.project_setup.log: A log file of the pyDock setup process (PDB files parsing).project_lig.pdb: Ligand PDB file parsed pyDockDNA.project_rec.pdb: Receptor PDB file parsed pyDockDNA.project.rot: rotation angles for each of the poses generated by FTDock.project.ftdock: FTDock application output.Tar archive containing the following files ("" is a numeric identifier): Once the computation has ended, pyDockWeb prepares a gzip compressed This methodology dramatically improves the docking results when compared to the use of energy criteria alone,Īnd is able to find the correct orientation within the top 20 docking solutions in 80% of the cases. PyDockRST software package uses the percentage of satisfied distance restraints, together with theĮlectrostatics and desolvation binding energy, to identify correct docking orientations. Rodríguez-Lumbreras LA, Jiménez-García B, Giménez-Santamarina S and Fernández-Recio J (2022) pyDockDNA: A new web server for energy-based protein-DNA docking and scoring. We would like to thank the Dunbrack lab for granting us permission to use their software. PyDockDNA server makes use of the SCWRL software for rebuilding missing side-chains (if possible). Note that incomplete backbone atoms may incur in inaccurate results and/or software failure. In order to avoid invalid results for a given PDB structure, be encourage to follow the PDB file format. When the user selects this option, pyDockDNA polls the RCSB Protein Data Bank and download the PDB structure automatically (only if exists). This option is identified by the label ' Select PDB by RCSB code'. When this option is selected, the user is asked to upload two separate PDB files, receptor and ligand structures respectively. This option is identified by the label ' Upload PDB structures'. PyDockDNA server uses two different sources of input data:
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