scholarly journals Prediction of the Three-Dimensional Structure for the Rat Urotensin II Receptor, and Comparison of the Antagonist Binding Sites and Binding Selectivity between Human and Rat Receptors from Atomistic Simulations

ChemMedChem ◽  
2010 ◽  
Vol 5 (9) ◽  
pp. 1594-1608 ◽  
Author(s):  
Soo-Kyung Kim ◽  
Youyong Li ◽  
Changmoon Park ◽  
Ravinder Abrol ◽  
William A. Goddard
Keyword(s):  
Binding Sites ◽  
Three Dimensional ◽  
Atomistic Simulations ◽  
Dimensional Structure ◽  
Urotensin Ii ◽  
Binding Selectivity ◽  
Three Dimensional Structure ◽  
Antagonist Binding

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.

Locations of Anti-AIDS Drug Binding Sites and Resistance Mutations in the Three-dimensional Structure of HIV-1 Reverse Transcriptase

1994 ◽  
Vol 243 (3) ◽  
pp. 369-387 ◽  
Author(s):  
Chris Tantillo ◽  
Jianping Ding ◽  
Alfredo Jacobo-Molina ◽  
Raymond G. Nanni ◽  
Paul L. Boyer ◽  
...  
Keyword(s):  
Reverse Transcriptase ◽  
Binding Sites ◽  
Three Dimensional ◽  
Drug Binding ◽  
Dimensional Structure ◽  
Resistance Mutations ◽  
Three Dimensional Structure ◽  
Drug Binding Sites ◽  
Hiv 1

Conformation of Ribosomes from Escherichia Coli

1974 ◽  
Vol 32 ◽  
pp. 210-211
Author(s):  
M. Boublik ◽  
W. Hellmann ◽  
F. Jenkins
Keyword(s):  
Binding Sites ◽  
Ribosomal Proteins ◽  
Fluorescent Dyes ◽  
Protein Biosynthesis ◽  
Three Dimensional ◽  
Spatial Arrangement ◽  
Dimensional Structure ◽  
Complete Understanding ◽  
And Function

The present knowledge of the three-dimensional structure of ribosomes is far too limited to enable a complete understanding of the various roles which ribosomes play in protein biosynthesis. The spatial arrangement of proteins and ribonuclec acids in ribosomes can be analysed in many ways. Determination of binding sites for individual proteins on ribonuclec acid and locations of the mutual positions of proteins on the ribosome using labeling with fluorescent dyes, cross-linking reagents, neutron-diffraction or antibodies against ribosomal proteins seem to be most successful approaches. Structure and function of ribosomes can be correlated be depleting the complete ribosomes of some proteins to the functionally inactive core and by subsequent partial reconstitution in order to regain active ribosomal particles.

The Three-dimensional structure of frozen-hydrated nudaurelia capensis β virus

1987 ◽  
Vol 45 ◽  
pp. 650-651
Author(s):  
N. H. Olson ◽  
T. S. Baker ◽  
Wu Bo Mu ◽  
J. E. Johnson ◽  
D. A. Hendry
Keyword(s):  
South African ◽  
Rna Virus ◽  
Carbon Film ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Electron Dose ◽  
Total Electron ◽  
Three Dimensional Structure ◽  
Negative Stain ◽  
Dimensional Reconstruction

Nudaurelia capensis β virus (NβV) is an RNA virus of the South African Pine Emperor moth, Nudaurelia cytherea capensis (Lepidoptera: Saturniidae). The NβV capsid is a T = 4 icosahedron that contains 60T = 240 subunits of the coat protein (Mr = 61,000). A three-dimensional reconstruction of the NβV capsid was previously computed from visions embedded in negative stain suspended over holes in a carbon film. We have re-examined the three-dimensional structure of NβV, using cryo-microscopy to examine the native, unstained structure of the virion and to provide a initial phasing model for high-resolution x-ray crystallographic studiesNβV was purified and prepared for cryo-microscopy as described. Micrographs were recorded ∼1 - 2 μm underfocus at a magnification of 49,000X with a total electron dose of about 1800 e-/nm2.

Three Dimensional structure and organization of diploid chromosomes by optical section microscopy

1987 ◽  
Vol 45 ◽  
pp. 633-635
Author(s):  
David A. Agard ◽  
Yasushi Hiraoka ◽  
John W. Sedat
Keyword(s):  
Dimensional Space ◽  
Three Dimensional ◽  
Developmental State ◽  
Mitotic Cell ◽  
Biological Properties ◽  
Dimensional Structure ◽  
Specific Gene ◽  
Three Dimensional Structure ◽  
Complementary Techniques ◽  
Dynamic Structures

In an effort to understand the complex relationship between structure and biological function within the nucleus, we have embarked on a program to examine the three-dimensional structure and organization of Drosophila melanogaster embryonic chromosomes. Our overall goal is to determine how DNA and proteins are organized into complex and highly dynamic structures (chromosomes) and how these chromosomes are arranged in three dimensional space within the cell nucleus. Futher, we hope to be able to correlate structual data with such fundamental biological properties as stage in the mitotic cell cycle, developmental state and transcription at specific gene loci.Towards this end, we have been developing methodologies for the three-dimensional analysis of non-crystalline biological specimens using optical and electron microscopy. We feel that the combination of these two complementary techniques allows an unprecedented look at the structural organization of cellular components ranging in size from 100A to 100 microns.

Sign in / Sign up

Export Citation Format

Share Document