Protein-ligand recognition

Simonson, T. Archontis, G. Karplus, M., Free energy simulations come of age protein-ligand recognition, Acc. Chem. Res. 2002, 35, 430-437... 

Continuum models are being increasingly used to study protein-ligand recognition [115]. Most studies have considered series of similar ligands or protein mutants and focussed on binding free energy differences. This leads to partial cancelation of some troublesome contributions, especially rotational/translation/vibrational entropy... 

Surface Motifs by a Computer Vision Technique Searches, Detection and Implications for Protein-Ligand Recognition. 

Jain, A.N. (2000) Morphological similarity a 3D molecular similarity method correlated with protein—ligand recognition. /. Comput. Aid. Mol. Des., 14, 199-213. 

Fischer, D., Norel, R., Wolfson, H. Nussinov, R. (1993). Surface motifs by a computer vision technique searches, detection, and implications for protein-ligand recognition. Proteins Structure, Function, and Genetics 16, 278-292. 

Figure 7.9 Right X-ray structure of the Human serum albumin (HSA) protein and molecular structure ofthe used ligand HPMO. Left Schematic representation of a normal micelle structure (left top) X-ray structure of/ -cyclodextrin (left middle), and illustration of a protein-ligand recognition process (left bottom) [58].

Stayton PS, Shimoboji T, Long C, Chilkoti A, Chen G, Harris JM, Hoffman AS. Control of protein-ligand recognition using a stimuli-responsive polymer. Nature 1995 378 472-474. 

Jain AN. Morphological similarity A 3d molecular similarity method correlated with protein-ligand recognition. J Comput Aided Mol Des 2000 14(2) 199-213. 

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