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Given a set of structures of the same molecule, it is often necessary to decide which are more similar or less similar to each other. This module presents a few ways to approach that problem, including root mean squared distance (RMSD), least RMSD, and intramolecular distance measures.

    Topics in this module

  • Comparing Molecular Conformations
  • RMSD and lRMSD
  • Optimal Alignment for lRMSD Using Rotation Matrices
  • Optimal Alignment for lRMSD Using Quaternions
    • Introduction to Quaternions
    • Quaternions and Three-Dimensional Rotations
    • Optimal Alignment with Quaternions
  • Intramolecular Distance and Related Measures

Comparing molecular conformations

Molecules are not rigid. On the contrary, they are highly flexible objects, capable of changing shape dramatically through the rotation of dihedral angles. We need a measure to express how much a molecule changes going from one conformation to another, or alternatively, how different two conformations are from each other. Each distinct shape of a given molecule is called a conformation . Although one could conceivably compute the volume of the intersection of thealpha shapes for two conformations (see Molecular Shapes and Surfaces for an explanation of alpha shapes) to measure the shape change, this is prohibitively computationally expensive. Simpler measures of distance between conformations have been defined, based on variables such as the Cartesian coordinates for each atom, or the bond and torsion angles within the molecule. When working with Cartesian coordinates, one can represent a molecular conformation as a vector whose components are the Cartesian coordinates of the molecule's atoms. Therefore, a conformation for a molecule with N atoms can be represented as a 3N-dimensional vector of real numbers.

Rmsd and lrmsd

One of the most widely accepted difference measures for conformations of a molecule is least root mean square deviation (lRMSD) . To calculate the RMSD of a pair of structures (say x and y), each structure must be represented as a 3N-length (assuming N atoms) vector of coordinates. The RMSD is the square root of the average of the squared distances between corresponding atoms of x and y. It is a measure of the average atomic displacement between the two conformations:

However, when molecular conformations are sampled from molecular dynamics or other forms of sampling, it is often the case that the molecule drifts away from the origin and rotates in an arbitrary way. The lRMSD distance aims at compensating for these facts by representing the minimum RMSD over all possible relative positions and orientations of the two conformations under consideration. Calculating the lRMSD consists of first finding an optimal alignment of the two structures, and then calculating their RMSD. Note that aligning two conformations may require both a translation and rotation. In other words, before computing the RMSD distance, it is necessary to remove the translation of the centroid of both conformations and to perform an "optimal alignment" or "optimal rotation" of them, since these two factors artificially increase the RMSD distance between them.

Questions & Answers

Do somebody tell me a best nano engineering book for beginners?
s. Reply
what is fullerene does it is used to make bukky balls
Devang Reply
are you nano engineer ?
s.
what is the Synthesis, properties,and applications of carbon nano chemistry
Abhijith Reply
so some one know about replacing silicon atom with phosphorous in semiconductors device?
s. Reply
Yeah, it is a pain to say the least. You basically have to heat the substarte up to around 1000 degrees celcius then pass phosphene gas over top of it, which is explosive and toxic by the way, under very low pressure.
Harper
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SUYASH Reply
for screen printed electrodes ?
SUYASH
What is lattice structure?
s. Reply
of graphene you mean?
Ebrahim
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Ebrahim
in general
s.
Graphene has a hexagonal structure
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what's the easiest and fastest way to the synthesize AgNP?
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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
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what is the function of carbon nanotubes?
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I'm interested in nanotube
Uday
what is nanomaterials​ and their applications of sensors.
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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
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name doesn't matter , whatever it will be change... I'm taking about effect on circumstances of the microscopic world
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how hard could it be to apply nanotechnology against viral infections such HIV or Ebola?
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silver nanoparticles could handle the job?
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not now but maybe in future only AgNP maybe any other nanomaterials
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this technology will not going on for the long time , so I'm thinking about femtotechnology 10^-15
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Prasenjit 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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