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    Topics in this module

  • Applications of Molecular Distance Measures
    • Protein Classification
    • Protein Alignment
  • Local Matching: Geometric Hashing, Pose Clustering, and Match Augmentation

In a previous module , the topic of comparing and quantifying the distance between different conformations of a given molecule was explored. Structure-based comparison is also of interest for distinct proteins, which lack the atom-by-atom correspondence necessary for RMSD calculations. In this case, an alignment is performed either based on amino acid sequence or on three-dimensional structure, and the subset of atoms successfully aligned are used as the basis for calculating conformational distance. Computing distances among entire proteins by doing a global alignment of their structures is useful for protein classification.

Protein classification

Protein classification is motivated by the notion of "descriptive biology". When faced with tremendous amounts of highly complex data, such as with the set of all proteins, one way to understand the data is by classification: the act of associating or grouping proteins into classes using certain criteria. One such criterion is protein sequence identity, where sequential similarity led to the development of phylogenetic trees and multiple sequence analyses. The same is done in protein structure classification, where the effort is to identify groups of similar proteins, with the hope that this will yield information about their biochemical function and biological purpose.

Proteins are classified by simultaneously applying a number of criteria, including sequence homology (evolutionary relatedness), function, folding motifs, structural features, and so on. The resulting hierarchies and clusters of protein structures provide a notion of the distance between two proteins and their structures. A couple of popular classification schemes are linked below. Note that a fair amount of manual annotation and classification was necessary to build these systems.

Protein alignment

The core computational problem of protein classification, using sequence or structure, is the problem of comparing two proteins. For structural classification, one method for comparison is structural alignment , which identifies an ideal superimposition between two protein structures, in order to compare them.

SSAP, Dali, Foldminer, Lock, and Geometric Hashing are algorithms which have been designed in part to align whole protein structures. Despite differences in algorithmic approach, all of these algorithms essentially evolved from the need to assign the best possible correlation between points in one structure and points in another. The problem of finding the optimal alignment is polynomial in the number of atoms in biological data, where we are assured that atoms cannot fall within a certain distance to each other (Van der Waals forces enforce this), but without this constraint the problem is exponential.

Protein alignment has been used for the classification and comparison of proteins in many existing algorithms. These include:

  • Dali is a structural comparison algorithm based on pairwise distance matrices. Dali uses patterns of residue contacts, similar to contact maps described above in the intramolecular distances section, in order to align structures. The alignments are found using a randomized (Monte Carlo) search.
  • FoldMiner and LOCK 2 . FoldMiner finds protein structures similar to an input structure by performing alignment the query structures secondary structure elements with proteins in its database using the LOCK 2 algorithm. LOCK 2 uses a combination of geometric hashing and dynamic programming to optimize the alignments of secondary structure elements of different proteins. Once a set of alignments to similar structures are found, motifs consisting of similar secondary structure arrangements are constructed and used to refine the similarity search.
  • Sequential Structure Alignment Program (SSAP) Given two protein structures, SSAP returns a structural alignment.

Questions & Answers

find the 15th term of the geometric sequince whose first is 18 and last term of 387
Jerwin Reply
The given of f(x=x-2. then what is the value of this f(3) 5f(x+1)
virgelyn Reply
hmm well what is the answer
Abhi
how do they get the third part x = (32)5/4
kinnecy Reply
can someone help me with some logarithmic and exponential equations.
Jeffrey Reply
sure. what is your question?
ninjadapaul
20/(×-6^2)
Salomon
okay, so you have 6 raised to the power of 2. what is that part of your answer
ninjadapaul
I don't understand what the A with approx sign and the boxed x mean
ninjadapaul
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
ninjadapaul
oops. ignore that.
ninjadapaul
so you not have an equal sign anywhere in the original equation?
ninjadapaul
hmm
Abhi
is it a question of log
Abhi
🤔.
Abhi
Commplementary angles
Idrissa Reply
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.
Kevin Reply
a perfect square v²+2v+_
Dearan Reply
kkk nice
Abdirahman Reply
algebra 2 Inequalities:If equation 2 = 0 it is an open set?
Kim Reply
or infinite solutions?
Kim
The answer is neither. The function, 2 = 0 cannot exist. Hence, the function is undefined.
Al
y=10×
Embra Reply
if |A| not equal to 0 and order of A is n prove that adj (adj A = |A|
Nancy Reply
rolling four fair dice and getting an even number an all four dice
ramon Reply
Kristine 2*2*2=8
Bridget Reply
Differences Between Laspeyres and Paasche Indices
Emedobi Reply
No. 7x -4y is simplified from 4x + (3y + 3x) -7y
Mary Reply
how do you translate this in Algebraic Expressions
linda Reply
Need to simplify the expresin. 3/7 (x+y)-1/7 (x-1)=
Crystal Reply
. After 3 months on a diet, Lisa had lost 12% of her original weight. She lost 21 pounds. What was Lisa's original weight?
Chris Reply
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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