Predicting the three-dimensional structure of human P-glycoprotein in absence of ATP by computational techniques embodying crosslinking data: Insight into the mechanism of ligand migration and binding sites

2006 ◽  
Vol 63 (3) ◽  
pp. 466-478 ◽  
Author(s):  
Stéphane Vandevuer ◽  
Françoise Van Bambeke ◽  
Paul M. Tulkens ◽  
Martine Prévost
Keyword(s):  
Binding Sites ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Computational Techniques ◽  
Three Dimensional Structure ◽  
P Glycoprotein ◽  
Ligand Migration ◽  
Insight Into

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.

scholarly journals Metal Binding Sites in Plant Soluble Inorganic Pyrophosphatases. An Example of the Use of ROSETTA Design and Hidden Markov Models to Guide the Homology Modeling of Proteins

2017 ◽  
Vol 56 (1) ◽  
Author(s):  
Luis Rosales-León Rosales-León ◽  
Eric Edmundo Hernández-Domínguez ◽  
Samantha Gaytán-Mondragón ◽  
Rogelio Rodríguez-Sotres
Keyword(s):  
Homology Modeling ◽  
Metal Binding ◽  
Binding Sites ◽  
In Silico ◽  
Markov Models ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Magnesium Ions ◽  
Three Dimensional Structure ◽  
Metal Binding Sites

In contrast to their counterparts in bacteria and animals the soluble inorganic pyrophosphatases from plant cells are active as monomers. The isoforms 1 and 4 from <em>Arabidopsis thaliana</em> have been characterized with more detail, but their three-dimensional structure is unavailable. Here, a recently published protocol (ROSETTA design-HMMer), is used to guide well-known techniques for homology-modeling, in the production of reliable models for the three-dimensional structure of these two arabidopsis isoforms. Their interaction with magnesium ions and pyrophosphate is analyzed <em>in silico</em>in silico.

scholarly journals Monolayer-to-thin-film transition in supramolecular assemblies: the role of topological protection

Nanoscale ◽  
2017 ◽  
Vol 9 (33) ◽  
pp. 11959-11968 ◽  
Author(s):  
Zachary P. L. Laker ◽  
Alexander J. Marsden ◽  
Oreste De Luca ◽  
Ada Della Pia ◽  
Luís M. A. Perdigão ◽  
...  
Keyword(s):  
Thin Film ◽  
Three Dimensional ◽  
Supramolecular Assemblies ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Organic Layers ◽  
Insight Into

An innovative combination of TEM and STM sheds new insight into the growth of organic layers and reveals the importance of topology in controlling the transition from two- to three-dimensional structure.

The three-dimensional structure of the tenth type III module of fibronectin: An insight into RGD-mediated interactions

Cell ◽  
1992 ◽  
Vol 71 (4) ◽  
pp. 671-678 ◽  
Author(s):  
Alison L. Main ◽  
Timothy S. Harvey ◽  
Martin Baron ◽  
Jonathan Boyd ◽  
Iain D. Campbell
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Type Iii ◽  
Insight Into
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