Using shape complementarity as an initial screen in designing ligands for a receptor binding site of known three-dimensional structure

1988 ◽  
Vol 31 (4) ◽  
pp. 722-729 ◽  
Author(s):  
Renee L. DesJarlais ◽  
Robert P. Sheridan ◽  
George L. Seibel ◽  
J. Scott Dixon ◽  
Irwin D. Kuntz ◽  
...  
Keyword(s):  
Binding Site ◽  
Receptor Binding ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Receptor Binding Site ◽  
Three Dimensional Structure ◽  
Shape Complementarity

THE THREE-DIMENSIONAL STRUCTURE OF THE ANTIGEN BINDING SITE OF McPC 603 PROTEIN

1974 ◽  
pp. 7-14 ◽  
Author(s):  
E.A. Padlan ◽  
D.M. Segal ◽  
G.H. Cohen ◽  
D.R. Davies ◽  
S. Rudikoff ◽  
...  
Keyword(s):  
Binding Site ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Antigen Binding ◽  
Antigen Binding Site ◽  
Three Dimensional Structure

Merging of Complementary Structural Techniques

1997 ◽  
Vol 3 (S2) ◽  
pp. 1119-1120
Author(s):  
P.L. Stewart ◽  
C.Y. Chiu ◽  
D.A. Haley
Keyword(s):  
Binding Site ◽  
Receptor Binding ◽  
Three Dimensional ◽  
Human Adenovirus ◽  
Maldi Mass Spectrometry ◽  
Fab Fragment ◽  
Receptor Binding Site ◽  
Viral Receptor ◽  
Peptide Epitope ◽  
Image Reconstruction Techniques

Cryo-electron microscopy (cryo-EM) and image reconstruction techniques provide a powerful way to study three-dimensional structures of biological complexes. As the resolution of the resulting three-dimensional reconstructions is typically in the range of 10-35 À, information from other structural techniques is often invaluable in analyzing the biological structure. We present the use of crystallographic coordinates to determine the amplitude of motion of a viral receptor binding site and molecular models to assess the degree of quaternary conformational flexibility within a multimeric protein assembly.In order to visualize the αv integrin receptor binding site on the surface of human adenovirus (150 MDa), we have reconstructed adenovirus in complex with a Fab fragment from a monoclonal antibody (DAV-1) targeted to this site. The peptide epitope of DAV-1 has been mapped by MALDI mass spectrometry to 9 residues within the penton base protein and includes the integrin binding Arg-Gly-Asp (RGD) residues.

scholarly journals A novel protein descriptor for the prediction of drug binding sites

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Mingjian Jiang ◽  
Zhen Li ◽  
Yujie Bian ◽  
Zhiqiang Wei
Keyword(s):  
Binding Site ◽  
Binding Sites ◽  
Three Dimensional ◽  
Drug Binding ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Site Prediction ◽  
Drug Binding Sites ◽  
Protein Descriptor ◽  
Novel Protein

Abstract Background Binding sites are the pockets of proteins that can bind drugs; the discovery of these pockets is a critical step in drug design. With the help of computers, protein pockets prediction can save manpower and financial resources. Results In this paper, a novel protein descriptor for the prediction of binding sites is proposed. Information on non-bonded interactions in the three-dimensional structure of a protein is captured by a combination of geometry-based and energy-based methods. Moreover, due to the rapid development of deep learning, all binding features are extracted to generate three-dimensional grids that are fed into a convolution neural network. Two datasets were introduced into the experiment. The sc-PDB dataset was used for descriptor extraction and binding site prediction, and the PDBbind dataset was used only for testing and verification of the generalization of the method. The comparison with previous methods shows that the proposed descriptor is effective in predicting the binding sites. Conclusions A new protein descriptor is proposed for the prediction of the drug binding sites of proteins. This method combines the three-dimensional structure of a protein and non-bonded interactions with small molecules to involve important factors influencing the formation of binding site. Analysis of the experiments indicates that the descriptor is robust for site prediction.

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