Using Curriculum Learning in Pattern Recognition of 3-dimensional Cryo-electron Microscopy Density Maps

2020 ◽  
Author(s):  
Yangmei Deng ◽  
Yongcheng Mu ◽  
Salim Sazzed ◽  
Jiangwen Sun ◽  
Jing He
Keyword(s):  
Electron Microscopy ◽  
Pattern Recognition ◽  
3 Dimensional ◽  
Cryo Electron Microscopy ◽  
Density Maps

scholarly journals Application of Cryo-Electron Microscopy on Drug Discovery

2021 ◽  
Vol 27 (S1) ◽  
pp. 3250-3250
Author(s):  
Viswanath Vittaladevaram ◽  
Kranthi Kuruti
Keyword(s):  
Electron Microscopy ◽  
Protein Complexes ◽  
Lead Discovery ◽  
Biologically Relevant ◽  
Biological Targets ◽  
3 Dimensional ◽  
Drug Molecules ◽  
Cryo Electron Microscopy ◽  
Therapeutic Molecules ◽  
Novel Drug

AbstractThe key aspect for development of novel drug molecules is to perform structural determination of target molecule associated with its ligand. One such tool that provides insights towards structure of molecule is Cryo-electron microscopy which covers biological targets that are intractable. Examination of proteins can be carried out in native state, as the samples are frozen at -175 degree Celsius i.e. cryogenic temperatures. In addition to this, there were no limits for molecular and functional structures of proteins that can be imagined in 3-dimensional form. This includes ligands which unravel mechanisms that are biologically relevant. This will enable to better understand the mechanisms that are used for development of new therapeutics. Application of Cryo-electron microscopy is not limited to protein complexes and is considered as non-specific. Intervention of Cryo-EM would allow to analyse the structures and also able to dissect the interaction with therapeutic molecules. The study determines the usage of cryo-EM for providing resolutions that are acceptable for lead discovery. It also provides support for lead optimization and also for discovery of vaccines and therapeutics.

scholarly journals Cylindrical Similarity Measurement for Helices in Medium-Resolution Cryo-Electron Microscopy Density Maps

2020 ◽  
Vol 60 (5) ◽  
pp. 2644-2650 ◽  
Author(s):  
Salim Sazzed ◽  
Peter Scheible ◽  
Maytha Alshammari ◽  
Willy Wriggers ◽  
Jing He
Keyword(s):  
Electron Microscopy ◽  
Similarity Measurement ◽  
Cryo Electron Microscopy ◽  
Density Maps ◽  
Medium Resolution

scholarly journals Opportunities and challenges for assigning cofactors in cryo-EM density maps of chlorophyll-containing proteins

2020 ◽  
Vol 3 (1) ◽  
Author(s):  
Christopher J. Gisriel ◽  
Jimin Wang ◽  
Gary W. Brudvig ◽  
Donald A. Bryant
Keyword(s):  
Electron Microscopy ◽  
Electrostatic Potential ◽  
Protein Function ◽  
Protein Complexes ◽  
Chemical Environment ◽  
Cryo Electron Microscopy ◽  
Functional Differences ◽  
Density Maps ◽  
Structural Differences

AbstractThe accurate assignment of cofactors in cryo-electron microscopy maps is crucial in determining protein function. This is particularly true for chlorophylls (Chls), for which small structural differences lead to important functional differences. Recent cryo-electron microscopy structures of Chl-containing protein complexes exemplify the difficulties in distinguishing Chl b and Chl f from Chl a. We use these structures as examples to discuss general issues arising from local resolution differences, properties of electrostatic potential maps, and the chemical environment which must be considered to make accurate assignments. We offer suggestions for how to improve the reliability of such assignments.

scholarly journals Advances in Structure Modeling Methods for Cryo-Electron Microscopy Maps

Molecules ◽  
2019 ◽  
Vol 25 (1) ◽  
pp. 82 ◽  
Author(s):  
Eman Alnabati ◽  
Daisuke Kihara
Keyword(s):  
Electron Microscopy ◽  
De Novo ◽  
Molecular Structures ◽  
Structure Modeling ◽  
Rapid Progress ◽  
Macromolecular Complexes ◽  
Modeling Methods ◽  
Cryo Electron Microscopy ◽  
Density Maps

Cryo-electron microscopy (cryo-EM) has now become a widely used technique for structure determination of macromolecular complexes. For modeling molecular structures from density maps of different resolutions, many algorithms have been developed. These algorithms can be categorized into rigid fitting, flexible fitting, and de novo modeling methods. It is also observed that machine learning (ML) techniques have been increasingly applied following the rapid progress of the ML field. Here, we review these different categories of macromolecule structure modeling methods and discuss their advances over time.

scholarly journals PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps. Corrigendum

2018 ◽  
Vol 74 (1) ◽  
pp. 65-66
Author(s):  
Guray Kuzu ◽  
Ozlem Keskin ◽  
Ruth Nussinov ◽  
Attila Gursoy
Keyword(s):  
Electron Microscopy ◽  
Protein Complexes ◽  
Acta Cryst ◽  
Cryo Electron Microscopy ◽  
Density Maps

A revised Table 6 and Supporting Information are provided for the article by Kuzuet al.[(2016),Acta Cryst.D72, 1137–1148].

Capsid structure of channel catfish virus, an evolutionarily distant herpesvirus, by cryo-Electron Microscopy

1994 ◽  
Vol 52 ◽  
pp. 114-115
Author(s):  
Benes L. Trus ◽  
Andrew J. Davison ◽  
Frank P. Booy ◽  
Alasdair C. Steven
Keyword(s):  
Electron Microscopy ◽  
Channel Catfish ◽  
3 Dimensional ◽  
Channel Catfish Virus ◽  
Cryo Electron Microscopy ◽  
Capsid Shell ◽  
Wide Range ◽  
Dimensional Reconstruction ◽  
Molecular Anatomy ◽  
Evident Relationship

Herpesviruses comprise an extensive family of enveloped DNA-containing animal viruses. Although they infect a wide range of vertebrate hosts and their linear double-stranded genomes vary substantially in size and other properties, the nucleocapsid appears to be a conservative element of viral design. The capsid shell is icosahedrally symmetric (T=16), and in the case of alphaherpesviruses is 125 nm in diameter and 15nm thick. Recently, we have studied the molecular anatomy of herpes simplex virus1 (HSV-1), whose capsid contains four major proteins, by combining cryo-electron microscopy and 3-dimensional reconstruction with biochemical depletion experiments and antibody-labelling. In order to probe structural perturbations attributable to evolutionary differences, we have extended these studies to channel catfish virus. CCV exhibits the gross morphology of a herpesvirus, although no evident relationship to other herpesviruses was found in an analysis of proteins predicted from its complete DNA sequence.

scholarly journals PRISM-EM: template interface-based modelling of multi-protein complexes guided by cryo-electron microscopy density maps

2016 ◽  
Vol 72 (10) ◽  
pp. 1137-1148 ◽  
Author(s):  
Guray Kuzu ◽  
Ozlem Keskin ◽  
Ruth Nussinov ◽  
Attila Gursoy
Keyword(s):  
Electron Microscopy ◽  
Protein Complexes ◽  
Three Dimensional ◽  
Protein Assemblies ◽  
New Approach ◽  
Cellular Processes ◽  
Cryo Electron Microscopy ◽  
Density Maps ◽  
Crystallographic Structures ◽  
Hiv 1

The structures of protein assemblies are important for elucidating cellular processes at the molecular level. Three-dimensional electron microscopy (3DEM) is a powerful method to identify the structures of assemblies, especially those that are challenging to study by crystallography. Here, a new approach, PRISM-EM, is reported to computationally generate plausible structural models using a procedure that combines crystallographic structures and density maps obtained from 3DEM. The predictions are validated against seven available structurally different crystallographic complexes. The models display mean deviations in the backbone of <5 Å. PRISM-EM was further tested on different benchmark sets; the accuracy was evaluated with respect to the structure of the complex, and the correlation with EM density maps and interface predictions were evaluated and compared with those obtained using other methods. PRISM-EM was then used to predict the structure of the ternary complex of the HIV-1 envelope glycoprotein trimer, the ligand CD4 and the neutralizing protein m36.

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