Enlarged representative set of protein structures

By Uwe Hobohm, Christopher Sander. 1994

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Citations in the corpus

• LOMETS: A local meta-threading-server for protein structure prediction (2007, methodology): “For the testing of the LOMETS server, we select 620 non-homologous proteins ( 5 25% sequence identity with lengths from 50 to 600) from PDBSELECT (2006 March) (30).”
• PDB-REPRDB: A Database of Representative Protein Chains in PDB (Protein Data Bank) (1997, result): “To clarify the difference between our representative chain set and PDB_SELECT (Hobohm et al. 1992; Hobohm & Sander 1994; Hobohm & Sander), we compared the number of selected chains of ours and PDB_SELECT as shown in Table 1. Both representative sets are based on PDB release 78. When the threshold ”
• A critical view on conservative mutations. (2001, methodology): “The sequences used are a subset of the 25% sequence identity set of non-homologous structures (Hobohm et al., 1992; Hobohm and Sander, 1994) derived from the protein structure databank PDB (Bernstein et al., 1977).”
• Aromatic-aromatic interactions in and around α-helices (2002, background): “The proteins selected were based on the January 2000 release of the representative list of structures (Hobohm and Sander, 1994) determined at a resolution of 2.0 Å or better and R-factor 20%; the maximum sequence identity between any two of the polypeptide chains was 25%.”
• Discovering common stem-loop motifs in unaligned RNA sequences. (2001, background): “We further reduced the set to eliminate sequences that are >90% identical (35).”
• DATA MINING TECHNIQUES (2003, methodology): “This test set is derived from the 10% of the 691 proteins from PDBselect [39] not used in the training of the HMM and association rules.”
• Recognition of Structure Classification of Protein Folding by NN and SVM Hierarchical Learning Architecture (2003, methodology): “This training data set was built for the prediction of 128 protein folds based on the PDB select sets [7].”
• Intrinsic Disorder Is a Common Feature of Hub Proteins from Four Eukaryotic Interactomes (2006, methodology): “The composition of each dataset is plotted relative to the composition of a subset of well-ordered globular proteins extracted from the PDB Select 25 database [28].”
• UniqueProt: creating representative protein sequence sets (2003, methodology): “In order to find the largest sub-set of proteins that fulfil the constraint that no pair in that set has an HSSPvalue> u (u1⁄4 user defined threshold), we applied a simple greedy algorithm similar to that employed toward this end by Hobohm and Sander (17): for each protein P in the submitted set, th”
• Statistical potentials extracted from protein structures: how accurate are they? (1996, methodology): “We sorted a group of 346 non-homologous protein chains (Hobohm & Sander, 1994) from the PDB by the partition propensity of each protein, labeling each residue type as H (hydrophobic) or P (others).”
• Multi-class protein fold recognition using support vector machines and neural networks (2001, methodology): “This database was based on the PDB select sets (Hobohm et al., 1992; Hobohm and Sander, 1994) where two proteins have no more than 35% of the sequence identity for the aligned subsequences longer than 80 residues.”