Statistical potentials extracted from protein structures: how accurate are they?

By Paul D. Thomas, Ken A. Dill. 1996

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Citations in the corpus

Ab initio protein structure prediction: progress and prospects. (2001, background): “The most significant problem with pair potentials is that they are dominated by hydrophobic/polar partitioning, which gives rise to anomalous effects such as a long-range repulsion between hydrophobic residues (89).”
Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions. (1997, methodology): “The problems with the assumption of independence of the pair distributions have been elegantly demonstrated by Thomas & Dill (1996).”
QMEAN: A comprehensive scoring function for model quality assessment (2008, background): “…functions are based on the inverse Boltzmann equation, although their physical basis has been questioned and is still not completely understood.28 –31 The Boltzmann equation describes a particular system in its thermodynamic equilibrium, whereas statistical potentials assume the system to be a…”
Advances and Challenges in Protein-Ligand Docking (2010, methodology): “As the ideal reference state is inaccessible for complicated systems like proteins [132], one major challenge for knowledge-based scoring functions is the calculation for the afore-mentioned reference state; based on the methods knowledge-based scoring functions can be classified into three categori”
Developing optimal non-linear scoring function for protein design (2004, background): “These include the neglect of chain connectivity in the reference state, and the problematic implicit assumption of Boltzmann distribution (Thomas and Dill, 1996b,a; Ben-Naim, 1997).”
How to derive a protein folding potential? A new approach to an old problem. (1996, background): “Unfortunately, there are no sequences in HP model which have energy gaps (Thomas & Dill, 1996), and one cannot even design such sequences in HP model.”
Potentials of Mean Force for Protein Structure Prediction Vindicated, Formalized and Generalized (2010, background): “Clearly, the assumption that the joint probability can be written as a product of pairwise probabilities is not justified [12,13,43], but in practice this assumption often provides useful results [22].”
Integrating statistical pair potentials into protein complex prediction (2007, background): “14,15 Most studies have used a variety of chemical, physical, and biological properties of amino acids and their functional groups to derive atom type schemes, while incorporating different investigators’ understanding of protein energetics.”