Definition and display of steric, hydrophobic, and hydrogen bonding properties of ligand binding sites in proteins using Lee and Richards accessible surface: validation of a high-resolution graphical tool for drug design

1992 ◽  
Vol 35 (10) ◽  
pp. 1671-1684 ◽  
Author(s):  
Regine S. Bohacek ◽  
Colin McMartin
Keyword(s):  
Hydrogen Bonding ◽  
High Resolution ◽  
Drug Design ◽  
Ligand Binding ◽  
Binding Sites ◽  
Graphical Tool ◽  
Ligand Binding Sites ◽  
Bonding Properties ◽  
Accessible Surface

Automated site-directed drug design: a general algorithm for knowledge acquisition about hydrogen-bonding regions at protein surfaces

1989 ◽  
Vol 236 (1283) ◽  
pp. 101-113 ◽  
Keyword(s):  
Hydrogen Bonding ◽  
Drug Design ◽  
Knowledge Acquisition ◽  
Binding Sites ◽  
Grid Point ◽  
Data Bank ◽  
General Outline ◽  
Protein Surfaces ◽  
Starting Point ◽  
Accessible Surface

This is the first of four papers that begin to explore the possibility of automated site-directed drug design. A general outline is given of the logical steps involved in approaching the problem. The starting point is the process of knowledge acquisition about the site. An algorithm is described here for the construction of a map of hydrogen-bonding regions at protein surfaces directly from the Brookhaven Protein Data Bank coordinates. Hydrogen-bonding atoms are located, intramolecular bonds are searched for, hydrogen-bonding atoms at the surface are found and hydrogen-bonding regions are computed at the accessible surface. A grid is placed within each region discovered and the probability of hydrogen bonding at each grid point is computed. The output of the program is a map of hydrogen-bonding regions displayed within a user-defined window. This information can be used as part of a knowledge base for the automatic construction of novel ligands to fit specified binding sites.

scholarly journals Diaqua[(1R,2S,4R,8R,9S,11R)-2,9-dimethyl-1,4,8,11-tetraazacyclotetradecane]nickel(II) dichloride dihydrate

2012 ◽  
Vol 68 (8) ◽  
pp. m1111-m1112
Author(s):  
James Alan Townsend ◽  
John Desper
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Ligand Binding ◽  
Binding Sites ◽  
Title Complex ◽  
Ligand Binding Sites

The crystal structure of the title complex, [Ni(C12H28N4)(H2O)2]Cl2·2H2O, displays O—H...Cl and O—H...O hydrogen bonding. The tetraazacyclotetradecane ligand interacts with the NiIIatom in thecisV configuration and the final two ligand binding sites are occupied by water.

scholarly journals Diversity in the structures and ligand-binding sites of nematode fatty acid and retinol-binding proteins revealed by Na-FAR-1 from Necator americanus

2015 ◽  
Vol 471 (3) ◽  
pp. 403-414 ◽  
Author(s):  
M. Florencia Rey-Burusco ◽  
Marina Ibáñez-Shimabukuro ◽  
Mads Gabrielsen ◽  
Gisela R. Franchini ◽  
Andrew J. Roe ◽  
...  
Keyword(s):  
Fatty Acid ◽  
Ligand Binding ◽  
Tissue Distribution ◽  
Binding Sites ◽  
Binding Proteins ◽  
Retinol Binding Protein ◽  
Internal Cavity ◽  
Binding Characteristics ◽  
Necator Americanus ◽  
Ligand Binding Sites

Necator americanus fatty acid and retinol-binding protein-1 (Na-FAR-1) is an abundantly expressed FAR from a parasitic hookworm. The present work describes its tissue distribution, structure and ligand-binding characteristics and shows that Na-FAR-1 expands to transport multiple FA molecules in its internal cavity.

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