Theory of protein folding: the energy landscape perspective.

By José N. Onuchic, Zaida Luthey-Schulten, Peter G. Wolynes. 1997

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TANKBind: Trigonometry-Aware Neural NetworKs for Drug-Protein Binding Structure Prediction (2022, background): “By doing so, we create a funnel-shape energy landscape for the inter-molecular interaction, removing the need of extensive sampling Jumper et al. [2021], Jain [2006], Chen et al. [2020a], Onuchic et al. [1997].”
Ab initio protein structure prediction. (2002, background): “Energy landscape theory describes how the energy of the system changes with the geometry of the protein; its usefulness as a framework to analyze protein folding has been reviewed in many places [14,15].”
Generalized correlation for biomolecular dynamics (2005, background): “Evaluation of the right hand side of Eq. ( 4 ) relates MI to the more widely known measure of information content (entropy) H[x] p(x)ln p(x)dx, Ix1,x2 ,. .. ,xN”
Low-dimensional, free-energy landscapes of protein-folding reactions by nonlinear dimensionality reduction (2006, background): “This argument is not sufficient to ensure a perfect a priori correspondence between a given ensemble of structures experimentally detected [as, for instance, the transition-state ensemble, experimentally characterized by ⌽-value analysis (20, 21)] and the corresponding ensembles obtained on a…”
Computational approaches to structure-based ligand design. (1999, background): “In particular, many people are working on ways to try to predict the three-dimensional structure of a protein from its one-dimensional amino acid sequence (Dunbrack et al., 1997; Onuchic et al., 1997; Westhead & Thornton, 1998).”
The amyloid state and its association with protein misfolding diseases (2014, background): “Paired betasheet structure of an Aβ(1-40) amyloid fibril revealed by electron microscopy.”
Connecting the Sequence-Space of Bacterial Signaling Proteins to Phenotypes Using Coevolutionary Landscapes (2016, background): “The evolutionary constraint to fold into a particular, stable three-dimensional structure whereas minimizing the number of frustrated interactions greatly restricts the sequence-space of a protein (Leopold et al. 1992; Bryngelson et al. 1995; Onuchic et al. 1997).”
Matching Simulation and Experiment: A New Simplified Model for Simulating Protein Folding (2000, unknown): “…this process has stemmed from experimental folding studies on small proteins (Fersht, 1997; Eaton et al ., 1998; Capaldi and Radford, 1998) combined with new advances in theoretical perspectives (Dill and Chan, 1997; Onuchic et al ., 1997) and computational approaches (Dill et al ., 1995;…”