| Description |
This file is part of the Supplementary material of Segura et al. "VORFFIP-driven dock: VD2OCK, a fast and accurate protein docking algorithm" It contains all the docking decoys generated for BENCHMARK v.4.0[1] using VD2OCK algorithm After bunzip2 and untar the file, there is tree of directories, each containing the data foreach of the protein complexes in BENCHMARK v.4.0[1]. The directory's name is same of the PDB code represented in BENCHMARK v.4.0 ==== Contents of each directory Inside each directory there are different files: site1_X.txt: interface protein A. X start with 0 if only 1 interface, 1 second interface, etc. site2_X.txt: same as protein A, but interface protein B settings.txt: VORFFIP[2] parameter file. This is the input file to execute VORFFIP. Shown paths relate to computer where this predictions were ex ecuted protA.pdb: PDB file receptor protB.pdb: PDB file ligand params.txt new_params.txt: PatchDock[3] input files out_rot_00: PatchDock output file patch_dock.log: PatchDock log file PDBCODE_00_cluster_200.log: Output file GROMACS[4] clustering PDBCODE_00_centroids_200: Centroids of the top 200 clusters (same id number as the 'middle' member in previous file) out_rot_00.XXXX.pdb: PDB coordinades centroid XXXX References: [1] Hwang H et al (2010) Protein-protein docking benchmark version 4.0, Proteins, 78, 3111-3114 [2] Segura J et al (2011) Improving the prediction of protein binding sites by combining heterogeneous data and Voronoi diagrams, BMC Bioinformat ics 12, 352 [3] Schneidman-Duhovny D et al (2005) PatchDock and SymmDock: servers for rigid and symmetric docking. Nucleic Acids Research,33, W363-367 [4] Van Der Spoel D et al (2005) GROMACS: fast, flexible and free, J Comput Chem, 216, 1701-1718
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