Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes.

By Jay W. Ponder, F. Richards. 1987

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Citations in the corpus

Scientific Benchmarks for Guiding Macromolecular Energy Function Improvement (2013, methodology): “…energy—has been used to justify creating knowledge-based potentials from distribution of features from crystal structures (Miyazawa & Jernigan, 1985; Sippl, 1990); for example, rotamer libraries are often based on feature distributions (Dunbrack & Karplus, 1993; Ponder & Richards, 1987).”
Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules (2011, positive): “At each residue, i , the algorithm considers a set of rotamers (Ponder and Richards, 1987), S i , which represent one or more amino acid types.”
Modeling Symmetric Macromolecular Structures in Rosetta3 (2011, background): “In asymmetric sidechain optimization, the packer builds a discrete set of rotamers [5] at n positions on the structure, and attempts to solve Figure 3.”
A graph‐theory algorithm for rapid protein side‐chain prediction (2003, unknown): “Nearly all of these are based on using a rotamer library of discrete side-chain conformations (McGregor et al. 1987; Ponder and Richards 1987; Tuffery et al. 1991; Dunbrack and Karplus 1993, 1994; De Maeyer et al. 1997; Dunbrack and Cohen 1997; Lovell et al. 2000; Xiang and Honig 2001; Dunbrack 2002”
The coming of age of de novo protein design (2016, background): “In side-chain sampling, discrete combinatorial optimization is used to identify amino acids and side-chain conformations (known as rotamers) that lead to low-energy, closely packed protein cores 19–22 .”
A New Generation of Crystallographic Validation Tools for the Protein Data Bank (2011, background): “Most H atoms can be placed by simple geometry with adequate accuracy, but the orientations of groups such as OH,”
Recent advances in de novo protein design: Principles, methods, and applications (2021, background): “Because side-chain conformations are clustered as rotamers (87, 88), the side-chain design can be formulated as a discrete optimization problem (89), that is, ﬁ nd a combination of rotamers that minimize the energy of a structure.”
Protein design: a perspective from simple tractable models (1998, result): “Although some original proposals gave affirmative answer to this question [84,85], more recent experimental studies indicated that chain flexibility needs to be taken into account so that many sidechain substitutions can be accommodated by slightly varying the backbone conformations [86,87].”