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ACCURACY OF PROTEIN FLEXIBILITY PREDICTIONS

Vihinen, Mauno LU ; TORKKILA, E and RIIKONEN, P (1994) In Proteins 19(2). p.141-149
Abstract
Protein structural flexibility is important for catalysis, binding, and allostery. Flexibility has been predicted from amino acid sequence with a sliding window averaging technique and applied primarily to epitope search. New prediction parameters were derived from 92 refined protein structures in an unbiased selection of the Protein Data Bank by developing further the method of Karplus and Schulz (Naturwissenschaften 72:212-213, 1985). The accuracy of four flexibility prediction techniques was studied by comparing atomic temperature factors of known three-dimensional protein structures to predictions by using correlation coefficients. The size of the prediction window was optimized for each method. Predictions made with our new... (More)
Protein structural flexibility is important for catalysis, binding, and allostery. Flexibility has been predicted from amino acid sequence with a sliding window averaging technique and applied primarily to epitope search. New prediction parameters were derived from 92 refined protein structures in an unbiased selection of the Protein Data Bank by developing further the method of Karplus and Schulz (Naturwissenschaften 72:212-213, 1985). The accuracy of four flexibility prediction techniques was studied by comparing atomic temperature factors of known three-dimensional protein structures to predictions by using correlation coefficients. The size of the prediction window was optimized for each method. Predictions made with our new parameters, using an optimized window size of 9 residues in the prediction window, were giving the best results. The difference from another previously used technique was small, whereas two other methods were much poorer. Applicability of the predictions was also tested by searching for known epitopes from amino acid sequences. The best techniques predicted correctly 20 of 31 continuous epitopes in seven proteins. Flexibility parameters have previously been used for calculating protein average flexibility indices which are inversely correlated to protein stability. Indices with the new parameters showed better correlation to protein stability than those used previously; furthermore they had relationship even when the old parameters failed. (C) 1994 Wiley-Liss, Inc. (Less)
Please use this url to cite or link to this publication:
author
publishing date
type
Contribution to journal
publication status
published
subject
keywords
DYNAMICS, FLEXIBILITY INDEX, PROTEIN STABILITY, ANTIGENIC REGIONS, EPITOPES
in
Proteins
volume
19
issue
2
pages
141 - 149
publisher
John Wiley & Sons
external identifiers
  • wos:A1994NR17900006
  • scopus:0028361031
ISSN
0887-3585
DOI
10.1002/prot.340190207
language
English
LU publication?
no
id
45de63c2-79ed-4d55-b85a-83bac0885481 (old id 3853399)
date added to LUP
2013-06-28 14:49:55
date last changed
2017-08-13 04:22:40
@article{45de63c2-79ed-4d55-b85a-83bac0885481,
  abstract     = {Protein structural flexibility is important for catalysis, binding, and allostery. Flexibility has been predicted from amino acid sequence with a sliding window averaging technique and applied primarily to epitope search. New prediction parameters were derived from 92 refined protein structures in an unbiased selection of the Protein Data Bank by developing further the method of Karplus and Schulz (Naturwissenschaften 72:212-213, 1985). The accuracy of four flexibility prediction techniques was studied by comparing atomic temperature factors of known three-dimensional protein structures to predictions by using correlation coefficients. The size of the prediction window was optimized for each method. Predictions made with our new parameters, using an optimized window size of 9 residues in the prediction window, were giving the best results. The difference from another previously used technique was small, whereas two other methods were much poorer. Applicability of the predictions was also tested by searching for known epitopes from amino acid sequences. The best techniques predicted correctly 20 of 31 continuous epitopes in seven proteins. Flexibility parameters have previously been used for calculating protein average flexibility indices which are inversely correlated to protein stability. Indices with the new parameters showed better correlation to protein stability than those used previously; furthermore they had relationship even when the old parameters failed. (C) 1994 Wiley-Liss, Inc.},
  author       = {Vihinen, Mauno and TORKKILA, E and RIIKONEN, P},
  issn         = {0887-3585},
  keyword      = {DYNAMICS,FLEXIBILITY INDEX,PROTEIN STABILITY,ANTIGENIC REGIONS,EPITOPES},
  language     = {eng},
  number       = {2},
  pages        = {141--149},
  publisher    = {John Wiley & Sons},
  series       = {Proteins},
  title        = {ACCURACY OF PROTEIN FLEXIBILITY PREDICTIONS},
  url          = {http://dx.doi.org/10.1002/prot.340190207},
  volume       = {19},
  year         = {1994},
}