Using known substructures in protein model building and crystallography.

By T. Jones, S. Thirup. 1986

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Citations in the corpus

• Features and development of Coot (2010, positive): “Hexapeptide and pentapeptide fragments are chosen to match the C positions of each successive pentapeptide of the C (cid:2) trace in turn, following the method of Esnouf (1997), which is similar to that of Jones & Thirup (1986).”
• A position-specific distance-dependent statistical potential for protein structure and functional study (2012, background): “…Case et al., 2005; Dill, 1985, 1997; Dobson et al., 1998; Schuler et al., 2001; Shakhnovich, 2006) in many applications including ab initio folding (Jones and Thirup, 1986; Kihara et al., 2001; Levitt, 1992; Simons et al., 1997; Wu et al., 2007a; Zhao et al., 2008, 2010), docking (Zhang et al.,…”
• Exploiting evolutionary relationships for predicting protein structures (2003, background): “At about the same time, Jones and Thirup (1986) suggested that the database of solved protein structures could be used to extract fragments for use in molecular modeling, both for the interpretation of electron density maps and for modeling homologous protein.”
• Comparative Protein Structure Modeling Using MODELLER (2016, methodology): “…basis of modeling by coordinate reconstruction is the finding that most hexapeptide segments of protein structure can be clustered into only 100 structurally different classes (Jones and Thirup, 1986; Claessens et al., 1989; Unger et al., 1989; Levitt, 1992; Bystroff and Baker, 1998).”
• Comparative Protein Structure Modeling Using Modeller (2006, methodology): “The basis of modeling by coordinate reconstruction is the finding that most hexapeptide segments of protein structure can be clustered into only 100 structurally different classes (Jones and Thirup, 1986; Claessens et al., 1989; Unger et al., 1989; Levitt, 1992; Bystroff and Baker, 1998).”
• Small libraries of protein fragments model native protein structures accurately. (2002, methodology): “In 1986, Jones & Thirup discovered that almost all regions of the protein backbone are comprised of repeating canonical structures.(3) These regions, up to ten residues long, provided an efficient method for interpreting electron density maps.”
• Local Protein Structures (2007, unknown): “In 1986, Jones and Thirup reconstructed a retinol-binding protein (RBP) using fragments of the main chain from three unrelated proteins leading to a model with a Cα rmsd of 1.0 Å from the known structure [295].”
• Comparative protein structure modeling of genes and genomes. (2000, methodology): “Some side chain modeling methods (195) and loop construction methods based on finding suitable fragments in the database of known structures (85) can be seen as segment matching or coordinate reconstruction methods.”