Binding energy landscape

L, et al. 2001. Hierarchy of simulation models in predicting molecular recognition mechanisms from the binding energy landscapes structural analysis of the peptide complexes with SH2 domains. Proteins 45(4) 456-470. 

K., Larson, V., Luty, B. A., Rose, P W., Verkhivker, G. M. (1999) Computer simulations of ligand-protein binding with ensembles of protein conformations a Monte Carlo study of HIV-1 protease binding energy landscapes. Inti J Quantum Chem 72, 73-84. 

Bouzida D, Rejto PA, Verkhivker GM(1999) Monte Carlo simulations of ligand-protein binding energy landscapes with the weighted histogram analysis method, Int I Quantum Chem, 73 113—121... 

Hydrophobic and aromatic residues constitute a majority of hot spot residues however, polar and charged residues are also significant contributors at interfaces (Fig. 9b) [90]. This analysis supports the common perception that PPIs are generally hydrophobic but also feature key polar interactions that appreciably influence the binding energy landscape [28]. This view is further supported by the evaluation of residues on the partner protein that are within 5 A of the helical hot spot residue (Fig. 11). Not surprisingly a majority of residues that are within the specified radius of a hydrophobic residue are themselves hydrophobic, which is consistent with the... 

Wei D et al (2010) Binding energy landscape analysis helps to discriminate true hits from high-scoring decoys in virtual screening. J Chem Inf Model 50(10) 1855-1864... 

Verkhivker GM, Bouzida D, Gehlhaar DK, Rejto PA, Freer ST, Rose PM (2002) Monte Carlo simulation of the peptide recognition at the consensus binding site of the constant fragment of the human immunoglobulin G the energy landscape analysis of a hot spot at the intermolecular interface, Proteins, 48 539-557... 

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