0.3 Molecular shapes and surfaces  (Page 3/3)

 Page 3 / 3

From the Delaunay triangulation the α-shape is computed by removing all edges, triangles, and tetrahedra that have circumscribing spheres withradius greater than α. Formally, the α-complex is the part of the Delaunay triangulation that remains after removing edges longer than α. The α-shape is the boundary of the α-complex.

Pockets can be detected by comparing the α-shape to the whole Delauney triangulation. Missing tetrahedra represent indentations, concavity, and generally negative space in the overall volume occupied by the protein. Particularly large or deep pockets may indicate a substrate binding site.

Weighted alpha shapes

Regular α-shapes can be extended to deal with varying weights (i.e., spheres with different radii, such as different types of atoms) . The formal definitions become complicated, but the key idea is to use a pseudo distance measure that uses the weights.Suppose we have two atoms at positions p1 and p2 with weights w1 and w2. Then the pseudo distance is defined as the square of the Euclidean distance minus the weights. The pseudo distanceis zero if and only if two spheres centered at p1 and p2 with radii equal to `sqrt(w1)` and `sqrt(w2)` are just touching.

Calculating molecular volume using α-shapes

The volume of a molecule can be approximated using the space-filling model, in which each atom is modeled as a ball whose radius is α, where α is selected depending on the model being used: Van der Waals surface, molecular surface, solvent accessible surface, etc. Unfortunately, calculating the volume is not as simple as taking the sum of the ball volumes because they may overlap. Calculating the volume of a complex of overlapping balls is non-trivial because of the overlaps. If two spheres overlap, the volume is the sum of the volumes of the spheres minus the volume of the overlap, which was counted twice. If three overlap, the volume is the sum of the ball volumes, minus the volume of each pairwise overlap, plus the volume of the three-way overlap, which was subtracted one too many times in accounting for the pairwise overlaps. In the general case, all pairwise, three-way, four-way and so on to n-way intersections (assuming there are n atoms) must be considered. Proteins generally have thousands or tens of thousands of atoms, so the general n-way case may be computationally expensive and may introduce numerical error.

α-shapes provide a way around this undesirable combinatorial complexity , and this issue has been one of the motivating factors for introducing α-shapes. To calculate the volume of a protein, we take the sum of all ball volumes, then subtract only those pairwise intersections for which a corresponding edge exists in the α-complex. Only those three-way intersections for which the corresponding triangle is in the α-complex must then be added back. Finally, only four-way intersections corresponding to tetrahedra in the α-complex need to be subtracted. No higher-order intersections are necessary, and the number of volume calculations necessary corresponds directly to the complexity of the α-complex, which is O(n log n) in the number of atoms.

An example of how this approach works is given on page 4 of the Liang et al. article in the Recommended Reading section below. A proof of correctness and derivation is also provided in the article. Surface area calculations, such as solvent-accessible surface area, which is often used to estimate the strength of interactions between a protein and the solvent molecules surrounding it, are made by a similar use of the α-complex.

• H. Edelsbrunner, D. Kirkpatrick, and R. Seidel. [PDF] . "On the Shape of a Set of Points in the Plane." IEEE Transactions on Information Theory, 29(4):551-559, 1983. This is the original α-shapes paper (caution: the definition of α is different from that used in later papers--it is the negative reciprocal of α as presented above).
• H. Edelsbrunner and E.P. Mucke. [PDF] . "Three-dimensional Alpha Shapes." Workshop on Volume Visualization, Boston, MA. pp 75-82. 1992. This article shows how to extend α-shapes to three-dimensional point sets.
• J. Liang, H. Edelsbrunner, P. Fu, P.V. Sudhakar, and S. Subramaniam. [PDF] . Analytical shape computation of macromolecules: I. molecular area and volume through alpha shape. Proteins: Structure, Function, and Genetics, 33:1-17, 1998. This is a paper on using α-shapes to speed up volume and surface area calculations for molecular models.
• H. Edelsbrunner, M.Facello and Jie Liang. [PDF] . On the definition and the construction of pockets in macromolecules. Discrete and Applied Mathematics, 88:83-102, 1998.

Software

find the 15th term of the geometric sequince whose first is 18 and last term of 387
The given of f(x=x-2. then what is the value of this f(3) 5f(x+1)
hmm well what is the answer
Abhi
how do they get the third part x = (32)5/4
can someone help me with some logarithmic and exponential equations.
20/(×-6^2)
Salomon
okay, so you have 6 raised to the power of 2. what is that part of your answer
I don't understand what the A with approx sign and the boxed x mean
it think it's written 20/(X-6)^2 so it's 20 divided by X-6 squared
Salomon
I'm not sure why it wrote it the other way
Salomon
I got X =-6
Salomon
ok. so take the square root of both sides, now you have plus or minus the square root of 20= x-6
oops. ignore that.
so you not have an equal sign anywhere in the original equation?
hmm
Abhi
is it a question of log
Abhi
🤔.
Abhi
Commplementary angles
hello
Sherica
im all ears I need to learn
Sherica
right! what he said ⤴⤴⤴
Tamia
hii
Uday
what is a good calculator for all algebra; would a Casio fx 260 work with all algebra equations? please name the cheapest, thanks.
a perfect square v²+2v+_
kkk nice
algebra 2 Inequalities:If equation 2 = 0 it is an open set?
or infinite solutions?
Kim
The answer is neither. The function, 2 = 0 cannot exist. Hence, the function is undefined.
Al
y=10×
if |A| not equal to 0 and order of A is n prove that adj (adj A = |A|
rolling four fair dice and getting an even number an all four dice
Kristine 2*2*2=8
Differences Between Laspeyres and Paasche Indices
No. 7x -4y is simplified from 4x + (3y + 3x) -7y
how do you translate this in Algebraic Expressions
Need to simplify the expresin. 3/7 (x+y)-1/7 (x-1)=
. After 3 months on a diet, Lisa had lost 12% of her original weight. She lost 21 pounds. What was Lisa's original weight?
what's the easiest and fastest way to the synthesize AgNP?
China
Cied
types of nano material
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.
what is nano technology
what is system testing?
preparation of nanomaterial
Yes, Nanotechnology has a very fast field of applications and their is always something new to do with it...
what is system testing
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
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.
the Beer law works very well for dilute solutions but fails for very high concentrations. why?
how did you get the value of 2000N.What calculations are needed to arrive at it
Privacy Information Security Software Version 1.1a
Good
Got questions? Join the online conversation and get instant answers!