scholarly journals Ligand Binding Site Comparison ‐ LiBiSCo – a web‐based tool for analyzing interactions between proteins and ligands to explore amino acid specificity within active sites

2021 ◽  
Author(s):  
Sameer Hassan ◽  
Mats Töpel ◽  
Henrik Aronsson
Keyword(s):  
Amino Acid ◽  
Ligand Binding ◽  
Binding Site ◽  
Active Sites ◽  
Ligand Binding Site ◽  
Web Based

scholarly journals Insertion Mutagenesis of the Ferric Pyoverdine Receptor FpvA ofPseudomonas aeruginosa: Identification of Permissive Sites and a Region Important for Ligand Binding

1998 ◽  
Vol 180 (24) ◽  
pp. 6753-6756 ◽  
Author(s):  
Laurie Kilburn ◽  
Keith Poole ◽  
Jean-Marie Meyer ◽  
Shadi Neshat
Keyword(s):  
Amino Acid ◽  
Ligand Binding ◽  
Binding Site ◽  
Insertion Mutagenesis ◽  
Ligand Binding Site ◽  
Receptor Function ◽  
Loop Regions

ABSTRACT Insertion of an 18-amino-acid-encoding sequence within thefpvA gene identified permissive sites at residues Y350, A402, R451, R521, and R558, consistent with these residues occurring in extramembranous loop regions of the protein. Insertions at R451, R521, and R558 did not adversely affect receptor function, although insertions at Y350 and A402 compromised ferric pyoverdine binding and uptake. The latter region likely contributes to or interacts with the ligand-binding site.

Recognition of ion ligand binding sites based on amino acid features with the fusion of energy, physicochemical and structural features

2020 ◽  
Vol 26 ◽  
Author(s):  
Shan Wang ◽  
Xiuzhen Hu ◽  
Zhenxing Feng ◽  
Liu Liu ◽  
Kai Sun ◽  
...  
Keyword(s):  
Amino Acid ◽  
Ligand Binding ◽  
Binding Site ◽  
Binding Sites ◽  
Metal Ion ◽  
Structural Features ◽  
Support Vector ◽  
Sequence Information ◽  
Ligand Binding Site ◽  
Ligand Binding Sites

Background: Rational drug molecular design based on virtual screening requires the ligand binding site to be known. Recently, the recognition of ion ligand binding site has become an important research direction in pharmacology. Methods: In this work, we selected the binding residues of 4 acid radical ion ligands(NO2 - , CO3 2- , SO4 2- and PO4 3- ) and 10 metal ion ligands (Zn2+,Cu2+, Fe2+, Fe3+, Ca2+, Mg2+, Mn2+, Na+ , K+ and Co2+) as research objects. Based on the protein sequence information, we extracted amino acid features, energy, physicochemical and structure features. Then we incorporating the above features and input them into the MultilayerPerceptron (MLP) and support vector machine (SVM) algorithms. Results: In the independent test, the best accuracy was higher than 92.5%, which was better than the previous result on Conclusion: Finally, we set up a free web server for the prediction of protein-ion ligand binding sites (http://39.104.77.103:8081/lsb/HomePage/HomePage.html). This study is helpful for molecular drug design.

Constraints of Opsin Structure on the Ligand-binding Site: Studies with Ring-fused Retinals¶

2002 ◽  
Vol 76 (6) ◽  
pp. 606 ◽  
Author(s):  
Takahiro Hirano ◽  
In Taek Lim ◽  
Don Moon Kim ◽  
Xiang-Guo Zheng ◽  
Kazuo Yoshihara ◽  
...  
Keyword(s):  
Ligand Binding ◽  
Binding Site ◽  
Ligand Binding Site

Capturing of the free cysteine residue in the ligand-binding site by affinity labeling of the ORL1 nociceptin receptor

2011 ◽  
Vol 19 (24) ◽  
pp. 7597-7602 ◽  
Author(s):  
Ayami Matsushima ◽  
Hirokazu Nishimura ◽  
Shogo Inamine ◽  
Shiho Uemura ◽  
Yasuyuki Shimohigashi
Keyword(s):  
Ligand Binding ◽  
Binding Site ◽  
Cysteine Residue ◽  
Affinity Labeling ◽  
Ligand Binding Site ◽  
Nociceptin Receptor

A Monoclonal Antibody against the Ligand Binding Site of the Receptor for Mouse Interferon-γ

1989 ◽  
Vol 9 (5) ◽  
pp. 551-562 ◽  
Author(s):  
MITALI BASU ◽  
JUDITH L. PACE ◽  
DAVID M. PINSON ◽  
STEPHEN W. RUSSELL
Keyword(s):  
Monoclonal Antibody ◽  
Ligand Binding ◽  
Binding Site ◽  
Interferon Γ ◽  
Ligand Binding Site
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