{"data":{"id":"10.7910/dvn/28610","type":"dois","attributes":{"doi":"10.7910/dvn/28610","prefix":"10.7910","suffix":"dvn/28610","identifiers":[],"alternateIdentifiers":[],"creators":[{"name":"Fernandez-Fuentes, Narcis","nameType":"Personal","givenName":"Narcis","familyName":"Fernandez-Fuentes","affiliation":["Aberystywyth University"],"nameIdentifiers":[]}],"titles":[{"title":"VORFFIP-driven dock: VD2OCK, a fast and accurate protein docking algorithm"}],"publisher":"Harvard Dataverse","container":{},"publicationYear":2021,"subjects":[{"subject":"Bioinformatics","schemeUri":"http://www.bioinsilico.org/VD2OCK"},{"subject":"FOS: Computer and information sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"}],"contributors":[{"name":"Harvard Dataverse Network","nameType":"Organizational","affiliation":[],"contributorType":"Distributor","nameIdentifiers":[]}],"dates":[{"date":"2015","dateType":"Issued"},{"date":"2015-01-07","dateType":"Submitted"},{"date":"2021-10-25","dateType":"Available"}],"language":null,"types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":["104857600","104857600","104857600","104857600","104857600","104857600","104857600","104857600","104857600","44082426","104857600","104857600","104857600","104857600","104857600","104857600"],"formats":["application/octet-stream","application/octet-stream","application/octet-stream","application/octet-stream","application/octet-stream","application/octet-stream","application/octet-stream","application/octet-stream","application/octet-stream","application/octet-stream","application/octet-stream","application/octet-stream","application/octet-stream","application/octet-stream","application/octet-stream","application/octet-stream"],"version":"1.0","rightsList":[{"rightsUri":"info:eu-repo/semantics/openAccess"},{"lang":"en","rights":"Creative Commons Zero v1.0 Universal","rightsUri":"https://creativecommons.org/publicdomain/zero/1.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc0-1.0","rightsIdentifierScheme":"SPDX"}],"descriptions":[{"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","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"xml":"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