Detection of pockets on protein surfaces using small and large probe spheres to find putative ligand binding sites

2007 ◽  
Vol 68 (2) ◽  
pp. 516-529 ◽  
Author(s):  
Takeshi Kawabata ◽  
Nobuhiro Go
Keyword(s):  
Ligand Binding ◽  
Binding Sites ◽  
Protein Surfaces ◽  
Ligand Binding Sites ◽  
Putative Ligand Binding

scholarly journals Predicting Ligand Binding Sites on Protein Surfaces by 3-Dimensional Probability Density Distributions of Interacting Atoms

PLoS ONE ◽  
2016 ◽  
Vol 11 (8) ◽  
pp. e0160315 ◽  
Author(s):  
Jhih-Wei Jian ◽  
Pavadai Elumalai ◽  
Thejkiran Pitti ◽  
Chih Yuan Wu ◽  
Keng-Chang Tsai ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Probability Density ◽  
Binding Sites ◽  
Protein Surfaces ◽  
3 Dimensional ◽  
Density Distributions ◽  
Ligand Binding Sites ◽  
Probability Density Distributions ◽  
Interacting Atoms

scholarly journals PUTATIVE LIGAND-BINDING SITES OF THE TYPE C ATRIAL NATRIURETIC PEPTIDE RECEPTOR

1993 ◽  
Vol 14 (1) ◽  
pp. 1-4 ◽  
Author(s):  
AKIHIRO HIGUCHI ◽  
TAKASHI HAYASHI ◽  
KENZOU BAMBA ◽  
HIROMI HAGIWARA ◽  
SHIGEHISA HIROSE
Keyword(s):  
Atrial Natriuretic Peptide ◽  
Ligand Binding ◽  
Natriuretic Peptide ◽  
Binding Sites ◽  
Ligand Binding Sites ◽  
Type C ◽  
Putative Ligand Binding ◽  
Atrial Natriuretic

ON THE ASYMMETRY OF THE RESIDUE COMPOSITIONS OF THE BINDING SITES ON PROTEIN SURFACES

2009 ◽  
Vol 07 (06) ◽  
pp. 931-938 ◽  
Author(s):  
GÁBOR IVÁN ◽  
ZOLTÁN SZABADKA ◽  
VINCE GROLMUSZ
Keyword(s):  
Ligand Binding ◽  
Protein Data Bank ◽  
Binding Sites ◽  
Data Bank ◽  
Data Availability ◽  
Protein Chain ◽  
Protein Surfaces ◽  
Ligand Binding Sites ◽  
Folded Proteins ◽  
Well Data

By screening all the ligand binding sites in the Protein Data Bank, we have found that while it is geometrically possible that a loop, formed from a protein chain with residues ZYX, would "impersonate" another chain-loop with residues XYZ by a simple twisting of either the loop or the bound ligand, it almost never happens. This fact is rather surprising, and implies a notable asymmetry, since (i) loops in the folded proteins sometimes can be flexible enough to be twisted, but (ii) ligands are almost always extremely mobile before binding to the protein, therefore they can turn around and bind to residue-sequence ZYX as well. Data availability: The supplementary Table 3 lists the appearances of the residue-sequences and their inverses in the binding sites of the whole PDB, and is available at .

PDB-scale analysis of known and putative ligand-binding sites with structural sketches

2011 ◽  
Vol 80 (3) ◽  
pp. 747-763 ◽  
Author(s):  
Jun-Ichi Ito ◽  
Yasuo Tabei ◽  
Kana Shimizu ◽  
Kentaro Tomii ◽  
Koji Tsuda
Keyword(s):  
Ligand Binding ◽  
Binding Sites ◽  
Scale Analysis ◽  
Ligand Binding Sites ◽  
Putative Ligand Binding
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