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Testing similarity measures with continuous and discrete protein models

Wallin, Stefan LU ; Farwer, J and Bastolla, U (2003) In Proteins 50(1). p.144-157
Abstract
There are many ways to define the distance between two protein structures, thus assessing their similarity. Here, we investigate and compare the properties of five different distance measures, including the standard root-mean-square deviation (cRMSD). The performance of these measures is studied from different perspectives with two different protein models, one continuous and the other discrete. Using the continuous model, we examine the correlation between energy and native distance, and the ability of the different measures to discriminate between the two possible topologies of a three-helix bundle. Using the discrete model, we perform fits to real protein structures by minimizing different distance measures. The properties of the fitted... (More)
There are many ways to define the distance between two protein structures, thus assessing their similarity. Here, we investigate and compare the properties of five different distance measures, including the standard root-mean-square deviation (cRMSD). The performance of these measures is studied from different perspectives with two different protein models, one continuous and the other discrete. Using the continuous model, we examine the correlation between energy and native distance, and the ability of the different measures to discriminate between the two possible topologies of a three-helix bundle. Using the discrete model, we perform fits to real protein structures by minimizing different distance measures. The properties of the fitted structures are found to depend strongly on the distance measure used and the scale considered. We find that the cRMSD measure very effectively describes long-range features but is less effective with short-range features, and it correlates weakly with energy. A stronger correlation with energy and a better description of short-range properties is obtained, when we use measures based on intramolecular distances. (Less)
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author
organization
publishing date
type
Contribution to journal
publication status
published
subject
keywords
protein structure comparison, protein folding, distance measure, root-mean-square deviation
in
Proteins
volume
50
issue
1
pages
144 - 157
publisher
John Wiley & Sons
external identifiers
  • pmid:12471607
  • wos:000180131100014
  • scopus:0037233516
ISSN
0887-3585
DOI
10.1002/prot.10271
language
English
LU publication?
yes
id
a159d4d0-8f7d-402a-b034-10fb18507d51 (old id 320102)
date added to LUP
2007-09-23 14:36:04
date last changed
2017-08-20 04:17:24
@article{a159d4d0-8f7d-402a-b034-10fb18507d51,
  abstract     = {There are many ways to define the distance between two protein structures, thus assessing their similarity. Here, we investigate and compare the properties of five different distance measures, including the standard root-mean-square deviation (cRMSD). The performance of these measures is studied from different perspectives with two different protein models, one continuous and the other discrete. Using the continuous model, we examine the correlation between energy and native distance, and the ability of the different measures to discriminate between the two possible topologies of a three-helix bundle. Using the discrete model, we perform fits to real protein structures by minimizing different distance measures. The properties of the fitted structures are found to depend strongly on the distance measure used and the scale considered. We find that the cRMSD measure very effectively describes long-range features but is less effective with short-range features, and it correlates weakly with energy. A stronger correlation with energy and a better description of short-range properties is obtained, when we use measures based on intramolecular distances.},
  author       = {Wallin, Stefan and Farwer, J and Bastolla, U},
  issn         = {0887-3585},
  keyword      = {protein structure comparison,protein folding,distance measure,root-mean-square deviation},
  language     = {eng},
  number       = {1},
  pages        = {144--157},
  publisher    = {John Wiley & Sons},
  series       = {Proteins},
  title        = {Testing similarity measures with continuous and discrete protein models},
  url          = {http://dx.doi.org/10.1002/prot.10271},
  volume       = {50},
  year         = {2003},
}