How to derive a protein folding potential? A new approach to an old problem.

By Leonid A. Mirny, Eugene I. Shakhnovich. 1996

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Citations in the corpus

Developing optimal non-linear scoring function for protein design (2004, background): “The objectives of optimization are often maximization of score gap between native protein and the average of decoys, or score gap between native and decoys with the lowest score, or the Z-score of the native protein (Goldstein et al., 1992; Koretke et al., 1996, 1998; Hao and Scheraga, 1996; Mirny a”
Pair potentials for protein folding: Choice of reference states and sensitivity of predicted native states to variations in the interaction schemes (2008, methodology): “The statistical potentials have now been used in many different contexts~Sun, 1993; Sippl, 1995; Jernigan & Bahar, 1996; Mirny & Shakhnovich, 1996; Moult, 1997!. Reprint requests to: D. Thirumalai, Institute for Physical Science and Technology, University of Maryland, College Park, Maryland 20742;…”
Structure‐based prediction of transcription factor binding sites using a protein‐DNA docking approach (2008, background): “…knowledge-based scoring function, which employs a corrected uniform density reference state and a parameterized Z -score optimization,20,21 and have demonstrated that this scoring function could accurately and quantitatively predict the binding affinities between TFs and their DNA…”
Protein design: a perspective from simple tractable models (1998, background): “The parameters U(σi,σj) determine the magnitude of the contact interaction between monomers of type σi and σj; several sets of such parameters have been published [22,23, 26,27].”
The scoring of poses in protein-protein docking: current capabilities and future directions (2013, unknown): “CP_MS [156] r”
All-atom ab initio folding of a diverse set of proteins. (2006, methodology): “Further analysis of the m-potential derivation used the approach (Mirny and Shakhnovich, 1996) where a toy database of lattice proteins was designed, and the m-potential prescription was used to derive potentials from the database and compare them with ‘‘true’’ input potentials.”