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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

Is there any normative that regulates the use of silver nanoparticles?
Damian Reply
what king of growth are you checking .?
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
yes I'm doing my masters in nanotechnology, we are being studying all these domains as well..
what school?
biomolecules are e building blocks of every organics and inorganic materials.
anyone know any internet site where one can find nanotechnology papers?
Damian Reply
sciencedirect big data base
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.
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
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
characteristics of micro business
for teaching engĺish at school how nano technology help us
Do somebody tell me a best nano engineering book for beginners?
s. Reply
there is no specific books for beginners but there is book called principle of nanotechnology
what is fullerene does it is used to make bukky balls
Devang Reply
are you nano engineer ?
fullerene is a bucky ball aka Carbon 60 molecule. It was name by the architect Fuller. He design the geodesic dome. it resembles a soccer ball.
what is the actual application of fullerenes nowadays?
That is a great question Damian. best way to answer that question is to Google it. there are hundreds of applications for buck minister fullerenes, from medical to aerospace. you can also find plenty of research papers that will give you great detail on the potential applications of fullerenes.
what is the Synthesis, properties,and applications of carbon nano chemistry
Abhijith Reply
Mostly, they use nano carbon for electronics and for materials to be strengthened.
is Bucky paper clear?
carbon nanotubes has various application in fuel cells membrane, current research on cancer drug,and in electronics MEMS and NEMS etc
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.
Do you know which machine is used to that process?
how to fabricate graphene ink ?
for screen printed electrodes ?
What is lattice structure?
s. Reply
of graphene you mean?
or in general
in general
Graphene has a hexagonal structure
On having this app for quite a bit time, Haven't realised there's a chat room in it.
what is biological synthesis of nanoparticles
Sanket 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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