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Structure prediction of large complexes

Large macromolecular complexes and molecular machines present a particular challenge in structure determination. Generally too large to be crystallized, and too complex to solve by NMR, determining the structure of these objects usually requires the combination of high-resolution microscopy combined with computational refinement and analysis. The main techniques used are cryo-electron microscopy (Cryo-EM) and standard light microscopy.

Protein structure repositories

Most of the protein structures discovered to date can be found in a large protein repository called the RCSB Protein DataBank (PDB) . The Protein Data Bank (PDB) is a public domain repository that contains experimentally determined structures of three-dimensionalproteins. The majority of the proteins in the PDB have been determined by x-ray crystallography, but the number of proteins determined using NMRmethods has been increasing as efficient computational techniques to derive structures from NMR data have been developed. A few electron diffraction structures are also available. The PDB was originally established at Brookhaven National Laboratory in October, 1971, with 7structures. Currently, the database is maintained by Rutgers University, the State University of New Jersey, the San DiegoSupercomputer Center at the University of California, San Diego, and the National Institute of Standards and Technology. The current number of proteins (and/or nucleic acids) in the PDB database is displayed at the top-right corner of the main PDB page. The imaging method statistics of these structures (i.e., which methods were used for what fraction of the structures), as well as other classifications, can be found here . The European Bioinformatics Institute Macromolecular Structure Database group (UK) and the Institute forProtein Research at Osaka University (Japan) are international contributors to the contents of the PDB.

Visualizing protein structures

A few molecular visualization programs

  • Visual Molecular Dynamics (VMD) was originally developed for viewing molecular simulation trajectories. It is a very powerful, full-featured, and customizable molecular viewing package. Customization is available using Tcl/Tk scripting. Information on Tcl/Tk scripting can be found at this Tcl/Tk website.
  • PyMol is an open-source molecular viewer that can be used to generate professional-looking images. PyMol is highly customizable through the Python scripting language.
  • Protein Explorer is an easy-to-use, web browser-based visualization tool. Protein explorer is built using the MDL Chime browser plugin, which in turn is based on the RasMol viewer. Because Chime only works under Windows and Macintosh OS, the use of Protein Explorer is restricted to those platforms.
  • JMol is a Java-based molecular viewer. In applet form, it can be downloaded on-the-fly to view structures from the web. A stand-alone version also exists, which can be used independently of a web browser.
  • Chimera is a powerful visualizer and analysis tool that can be comfortably used with very large molecular complexes. It can also produce very high-quality images for use in presentations and publications.

Questions & Answers

I only see partial conversation and what's the question here!
Crow Reply
what about nanotechnology for water purification
RAW Reply
please someone correct me if I'm wrong but I think one can use nanoparticles, specially silver nanoparticles for water treatment.
Damian
what is the stm
Brian Reply
is there industrial application of fullrenes. What is the method to prepare fullrene on large scale.?
Rafiq
industrial application...? mmm I think on the medical side as drug carrier, but you should go deeper on your research, I may be wrong
Damian
How we are making nano material?
LITNING Reply
what is a peer
LITNING Reply
What is meant by 'nano scale'?
LITNING Reply
What is STMs full form?
LITNING
scanning tunneling microscope
Sahil
how nano science is used for hydrophobicity
Santosh
Do u think that Graphene and Fullrene fiber can be used to make Air Plane body structure the lightest and strongest. Rafiq
Rafiq
what is differents between GO and RGO?
Mahi
what is simplest way to understand the applications of nano robots used to detect the cancer affected cell of human body.? How this robot is carried to required site of body cell.? what will be the carrier material and how can be detected that correct delivery of drug is done Rafiq
Rafiq
what is Nano technology ?
Bob Reply
write examples of Nano molecule?
Bob
The nanotechnology is as new science, to scale nanometric
brayan
nanotechnology is the study, desing, synthesis, manipulation and application of materials and functional systems through control of matter at nanoscale
Damian
Is there any normative that regulates the use of silver nanoparticles?
Damian Reply
what king of growth are you checking .?
Renato
What fields keep nano created devices from performing or assimulating ? Magnetic fields ? Are do they assimilate ?
Stoney Reply
why we need to study biomolecules, molecular biology in nanotechnology?
Adin Reply
?
Kyle
yes I'm doing my masters in nanotechnology, we are being studying all these domains as well..
Adin
why?
Adin
what school?
Kyle
biomolecules are e building blocks of every organics and inorganic materials.
Joe
anyone know any internet site where one can find nanotechnology papers?
Damian Reply
research.net
kanaga
sciencedirect big data base
Ernesto
Introduction about quantum dots in nanotechnology
Praveena Reply
what does nano mean?
Anassong Reply
nano basically means 10^(-9). nanometer is a unit to measure length.
Bharti
do you think it's worthwhile in the long term to study the effects and possibilities of nanotechnology on viral treatment?
Damian Reply
absolutely yes
Daniel
how to know photocatalytic properties of tio2 nanoparticles...what to do now
Akash Reply
it is a goid question and i want to know the answer as well
Maciej
characteristics of micro business
Abigail
for teaching engĺish at school how nano technology help us
Anassong
How can I make nanorobot?
Lily
how did you get the value of 2000N.What calculations are needed to arrive at it
Smarajit Reply
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Source:  OpenStax, Geometric methods in structural computational biology. OpenStax CNX. Jun 11, 2007 Download for free at http://cnx.org/content/col10344/1.6
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