Ligand structures function

Kramer B, M Rarey and T Lengauer 1999. Evaluation of the FLEXX Incremental Constructioi Algorithm for Protein-Ligand Docking. Proteins Structure, Function and Genetics 37 228-241. 

B and W J Howe 1991. Computer Design of Bioactive Molecules - A Method for Receptor-Based Novo Ligand Design. Proteins Structure, Function and Genetics 11 314-328. i H L 1965. The Generation of a Unique Machine Description for Chemical Structures - A hnique Developed at Chemical Abstracts Service. Journal of Chemical Documentation 5 107-113. J 1995. Computer-aided Estimation of Symthetic Accessibility. PhD thesis. University of Leeds, itan R, N Bauman, J S Dixon and R Venkataraghavan 1987. Topological Torsion A New )lecular Descriptor for SAR Applications. Comparison with Other Descriptors. Journal of emical Information and Computer Science 27 82-85. 

Moreover, molecular modeling is one key method of a wide range of computer-assisted methods to analyze and predict relationships between protein sequence, 3D-molecular structure, and biological function (sequence-structure-function relationships). In molecular pharmacology these methods focus predominantly on analysis of interactions between different proteins, and between ligands (hormones, drugs) and proteins as well gaining information at the amino acid and even to atomic level. 

The aim of the second dimension depth is to consider protein 3D-stmctures to uncover structure-function relationships. Starting from the protein sequences, the steps in the depth dimension are structure prediction, homology modeling of protein structures, and the simulation of protein-protein interactions and ligand-complexes. 

There are many ligands and group-specific reagents that have been demonstrated to alter the properties of H,K-ATPase, and which are not clinically useful. For example, there is a variety of chemicals that have been used in studies on structure-function relations of H,K-ATPase and that inhibit the enzyme in vitro by modification of its amino [49,67,158], sulfhydryl [95,165,166] or carboxyl groups [140]. 

New Free Energy Based Methods for Ligand Binding from Detailed Structure-Function to Multiple-Ligand Screening... 

S. Banba, Z. Guo, and C. L. Brooks III, New free energy based methods for ligand binding from detailed structure-function to multiple-ligand screening, in Free Energy... 

Glusker, J. P. (1991) Structural aspects of metal liganding to functional groups in proteins. Adv. Prot. Chem. 42,1-76. 

T. Yamamoto, T. Murauyama, Z.-H. Zhou, T. Ito, T. Fukuda, Y. Yoneda, F. Begum, T. Ikeda, S. Sasaki, H. Takezoe, A. Fukuda, and K. Kubota, -ir-Conjugated poly(pyridine-2,5-diyl), poly(2,2 -bipyridine-5,5 -diyl), and their alkyl derivatives. Preparation, linear structure, function as a ligand to form their transition metal complexes, catalytic reactions, //-type electrically conducting properties, optical properties, and alignment on substrates, J. Am. Chem. Soc., 116 4832-4845,... 

Olivier, B., Soudijn, W. and van Wijngaarden, I. (1999) The 5-HT1A receptor and it s ligands structure and function. Progress in Drug Research, 52, 103-165. 

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