{"data":{"id":"10.6084/m9.figshare.662163","type":"dois","attributes":{"doi":"10.6084/m9.figshare.662163","prefix":"10.6084","suffix":"m9.figshare.662163","identifiers":[],"alternateIdentifiers":[],"creators":[{"name":"REGAD, Leslie","nameType":"Personal","givenName":"Leslie","familyName":"REGAD","affiliation":[],"nameIdentifiers":[]}],"titles":[{"title":"Regad et al. dataset"}],"publisher":"figshare","container":{},"publicationYear":2013,"subjects":[{"subject":"Computational Biology"},{"subject":"60102 Bioinformatics","subjectScheme":"FOR"},{"subject":"FOS: Computer and information sciences","schemeUri":"http://www.oecd.org/science/inno/38235147.pdf","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"FOS: Computer and information sciences","subjectScheme":"Fields of Science and Technology (FOS)"},{"subject":"Cheminformatics"},{"subject":"Applied Computer Science"},{"subject":"Pharmacology"}],"contributors":[],"dates":[{"date":"2013-03-29","dateType":"Created"},{"date":"2013-03-29","dateType":"Updated"},{"date":"2013","dateType":"Issued"}],"language":null,"types":{"ris":"DATA","bibtex":"misc","citeproc":"dataset","schemaOrg":"Dataset","resourceType":"Dataset","resourceTypeGeneral":"Dataset"},"relatedIdentifiers":[],"relatedItems":[],"sizes":["281218 Bytes"],"formats":[],"version":null,"rightsList":[{"rights":"Creative Commons Attribution 4.0 International","rightsUri":"https://creativecommons.org/licenses/by/4.0/legalcode","schemeUri":"https://spdx.org/licenses/","rightsIdentifier":"cc-by-4.0","rightsIdentifierScheme":"SPDX"}],"descriptions":[{"description":"\u003cstrong\u003eDescription of the file DataDescription.csv\u003c/strong\u003e \u003cbr\u003eThis study is based on a dataset composed of 483 pocket-ligand pairs. To create a large training set of pocket-ligand pairs, we initially gathered the refined set from the PDBbind database (Wang et al., 2004; 2005) and the Astex test set (Hartshorn et al., 2007) and selected complexes that contained drug-like ligands (i.e. small chemical compounds). Two protein-ligand complex datasets were compiled for the training set. The first one is composed of 560 non-redundant protein-ligand structures, with a resolution better than 2.5 Å retrieved from the refined set of the PDBbind database. From these structures, we removed those containing metal ions or cofactors next to the co-crystallized ligand resulting in a selection of 432 structures. The second one is composed of 85 manually curated protein-ligand complexes from the Astex test set. As for the previous set, we removed the structures with some ions or cofactors next to the ligand, resulting in a selection of 51 structures. The resulting dataset corresponds at the end to 483 protein-ligand structures. The id and information about each pair are available in the following table DataDescription.csv\u003cbr\u003eThis table contains: * PDB code of the complex * Protein chains containing in the PDB files. If the complex contains several protein chains, their chain Id are separated by \"/\" * Amino acid (AA) sequence of each chain. AA sequences correspond to sequence of the crystallized proteins. If the complex contains several protein chains, their AA sequences are separated by \"/\" * UniProt Id of each chain. If the complex contains several protein chains, their UniProt Id are separated by \"/\". NoId means no UniProt Id was find for a given chainSmile code of the interested ligandPDB code of the interested ligandObtained cluster of the pocket-ligand pairs","descriptionType":"Abstract"}],"geoLocations":[],"fundingReferences":[],"xml":"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","url":"https://figshare.com/articles/dataset/Regad_et_al_dataset/662163","contentUrl":null,"metadataVersion":2,"schemaVersion":"http://datacite.org/schema/kernel-4","source":"mds","isActive":true,"state":"findable","reason":null,"viewCount":0,"viewsOverTime":[],"downloadCount":0,"downloadsOverTime":[],"referenceCount":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