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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

what is the VA Ha D R X int Y int of f(x) =x²+4x+4/x+2 f(x) =x³-1/x-1
Shadow Reply
can I get help with this?
Wayne
Are they two separate problems or are the two functions a system?
Wilson
Also, is the first x squared in "x+4x+4"
Wilson
x^2+4x+4?
Wilson
thank you
Wilson
Please see ***imgur.com/a/lpTpDZk for solutions
Wilson
f(x)=x square-root 2 +2x+1 how to solve this value
Marjun Reply
factor or use quadratic formula
Wilson
what is algebra
Ige Reply
The product of two is 32. Find a function that represents the sum of their squares.
Paul
if theta =30degree so COS2 theta = 1- 10 square theta upon 1 + tan squared theta
Martin Reply
how to compute this 1. g(1-x) 2. f(x-2) 3. g (-x-/5) 4. f (x)- g (x)
Yanah Reply
hi
John
hi
Grace
what sup friend
John
not much For functions, there are two conditions for a function to be the inverse function:   1--- g(f(x)) = x for all x in the domain of f     2---f(g(x)) = x for all x in the domain of g Notice in both cases you will get back to the  element that you started with, namely, x.
Grace
sin theta=3/4.prove that sec square theta barabar 1 + tan square theta by cosec square theta minus cos square theta
Umesh Reply
acha se dhek ke bata sin theta ke value
Ajay
sin theta ke ja gha sin square theta hoga
Ajay
I want to know trigonometry but I can't understand it anyone who can help
Siyabonga Reply
Yh
Idowu
which part of trig?
Nyemba
functions
Siyabonga
trigonometry
Ganapathi
differentiation doubhts
Ganapathi
hi
Ganapathi
hello
Brittany
Prove that 4sin50-3tan 50=1
Sudip Reply
False statement so you cannot prove it
Wilson
f(x)= 1 x    f(x)=1x  is shifted down 4 units and to the right 3 units.
Sebit Reply
f (x) = −3x + 5 and g (x) = x − 5 /−3
Sebit
what are real numbers
Marty Reply
I want to know partial fraction Decomposition.
Adama Reply
classes of function in mathematics
Yazidu Reply
divide y2_8y2+5y2/y2
Sumanth Reply
wish i knew calculus to understand what's going on 🙂
Dashawn Reply
@dashawn ... in simple terms, a derivative is the tangent line of the function. which gives the rate of change at that instant. to calculate. given f(x)==ax^n. then f'(x)=n*ax^n-1 . hope that help.
Christopher
thanks bro
Dashawn
maybe when i start calculus in a few months i won't be that lost 😎
Dashawn
what's the derivative of 4x^6
Axmed Reply
24x^5
James
10x
Axmed
24X^5
Taieb
comment écrire les symboles de math par un clavier normal
SLIMANE
what's the easiest and fastest way to the synthesize AgNP?
Damian Reply
China
Cied
types of nano material
abeetha Reply
I start with an easy one. carbon nanotubes woven into a long filament like a string
Porter
many many of nanotubes
Porter
what is the k.e before it land
Yasmin
what is the function of carbon nanotubes?
Cesar
I'm interested in nanotube
Uday
what is nanomaterials​ and their applications of sensors.
Ramkumar Reply
what is nano technology
Sravani Reply
what is system testing?
AMJAD
preparation of nanomaterial
Victor Reply
Yes, Nanotechnology has a very fast field of applications and their is always something new to do with it...
Himanshu Reply
good afternoon madam
AMJAD
what is system testing
AMJAD
what is the application of nanotechnology?
Stotaw
In this morden time nanotechnology used in many field . 1-Electronics-manufacturad IC ,RAM,MRAM,solar panel etc 2-Helth and Medical-Nanomedicine,Drug Dilivery for cancer treatment etc 3- Atomobile -MEMS, Coating on car etc. and may other field for details you can check at Google
Azam
anybody can imagine what will be happen after 100 years from now in nano tech world
Prasenjit
after 100 year this will be not nanotechnology maybe this technology name will be change . maybe aftet 100 year . we work on electron lable practically about its properties and behaviour by the different instruments
Azam
name doesn't matter , whatever it will be change... I'm taking about effect on circumstances of the microscopic world
Prasenjit
how hard could it be to apply nanotechnology against viral infections such HIV or Ebola?
Damian
silver nanoparticles could handle the job?
Damian
not now but maybe in future only AgNP maybe any other nanomaterials
Azam
Hello
Uday
I'm interested in Nanotube
Uday
this technology will not going on for the long time , so I'm thinking about femtotechnology 10^-15
Prasenjit
can nanotechnology change the direction of the face of the world
Prasenjit Reply
At high concentrations (>0.01 M), the relation between absorptivity coefficient and absorbance is no longer linear. This is due to the electrostatic interactions between the quantum dots in close proximity. If the concentration of the solution is high, another effect that is seen is the scattering of light from the large number of quantum dots. This assumption only works at low concentrations of the analyte. Presence of stray light.
Ali Reply
the Beer law works very well for dilute solutions but fails for very high concentrations. why?
bamidele Reply
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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