Affinity fingerprinting

Predicting ligand binding to proteins by affinity fingerprinting. Chem. Biol. 1995,... 

Briem, H. and Lessel, U. F. (2000) In vitro and in silico affinity fingerprints finding similarities beyond structural classes. Perspect. Drug Discov. Design 20, 231-244. 

Kauver et al. [59] have developed a structural descriptor, called an affinity fingerprint, that is based on the binding affinities of a molecule for a... 

Bukar, R., Bauer, K.E., Dilley, H. and Rocke, D.M. Predicting Ligand-Binding to Proteins by Affinity Fingerprinting. Chem. Biol., 1995, 2, 107-1 18. 

Dickopf S, Prank M, Junker HD, Maier S, Metz G, Ottleben H, Rau H, Schellhaas N, Schmidt K, Sekul R, et al. Custom chemical microarray production and affinity fingerprinting for the SI pocket of factor Vila. Anal. Biochem. 2004 335 50-57. 

Dixon, J.S. and Villar, H.O. (1998). Bioactive Diversity and Screening Library Selection via Affinity Fingerprinting. J.Chem.Inf.Comput.ScL, 38,11%-1203. 

Weber A, Teckentrup A, Briem H. Flexsim-R a virtual affinity fingerprint descriptor to calculate similarities of functional groups. J Comput Aided Mol Des 2002 16(12) 903-916. 

Fig. 9.7 Affinity fingerprint of a target protein probed against a chemical microarray presenting 9216 immobilized binary compounds. The color range goes from red to orange to yellow to green to blue to code for decreasing SPR signal. Rows and columns each represent one of two monomers of the binary library...

In contrast to most other molecular descriptors, affinity fingerprints are not directly derived from molecular structures. 

Virtual affinity fingerprints (or in sUico affinity fingerprints) are derived by computational methods and, thus, are vectorial descriptors where experimentally determined binding affinities of molecules are replaced by some calculated scores with respect to the reference panel [Briem and Lessel, 2000]. 

Some virtual affinity fingerprints are explained below. 

Flexsim-R fingerprints are virtual affinity fingerprints specifically designed for similarity assessments of small fragments, such as R-groups of combinatorial libraries [Weber, Teckentrup et al, 2002]. 

This implies at least one rule to define a fixed number L of elements in each vector and one rule to fill in the vector elements when the values are missing (for example, filling in with zero values). Examples of uniform-length descriptors are EVA descriptors, topolcgical charge indices, atomic walk count sequence, —> SE-vectors, molecular profiles, spectra descriptors, 3D-MoRSE descriptors, autocorrelation descriptors, affinity fingerprints, and most of the string... 

Greenbaum, D.C., Arnold, W.D., Lu, K, et al. (2002) Small molecule affinity fingerprinting a tool for enzyme family subclassification, target identification, and inhibitor design. Chem. Biol. 9, 1085-1094. 

Custom chemical microarray production and affinity fingerprinting for the SI pocket of factor Vila. Anal. Biochem. 335, 50-57. 

---