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Evaluation of accuracy and applicability of protein models: retrospective analysis of biological and biomedical predictions.

Khan, Sofia and Vihinen, Mauno LU (2009) In In Silico Biology 9(5). p.307-331
Abstract
In order to study protein function and activity structural data is required. Since experimental structures are available for just a small fraction of all known protein sequences, computational methods such as protein modelling can provide useful information. Over the last few decades we have predicted, with homology modelling methods, the structures for numerous proteins. In this study we assess the structural quality and validity of the biological and medical interpretations and predictions made based on the models. All the models had correct scaffolding and were ranked at least as correct or good by numerical evaluators even though the sequence identity with the template was as low as 8%. The biological explanations made based on models... (More)
In order to study protein function and activity structural data is required. Since experimental structures are available for just a small fraction of all known protein sequences, computational methods such as protein modelling can provide useful information. Over the last few decades we have predicted, with homology modelling methods, the structures for numerous proteins. In this study we assess the structural quality and validity of the biological and medical interpretations and predictions made based on the models. All the models had correct scaffolding and were ranked at least as correct or good by numerical evaluators even though the sequence identity with the template was as low as 8%. The biological explanations made based on models were well in line with experimental structures and other experimental studies. Retrospective analysis of homology models indicates the power of protein modelling when made carefully from sequence alignment to model building and refinement. Modelling can be applied to studying and predicting different kinds of biological phenomena and according to our results it can be done so with success. (Less)
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author
publishing date
type
Contribution to journal
publication status
published
subject
in
In Silico Biology
volume
9
issue
5
pages
307 - 331
publisher
IOS Press
external identifiers
  • pmid:22430434
  • scopus:84885917614
ISSN
1386-6338
DOI
10.3233/ISB-2009-0408
language
English
LU publication?
no
id
80e2e706-41c0-44c0-8926-d5c20941e683 (old id 3634993)
alternative location
http://www.ncbi.nlm.nih.gov/pubmed/22430434?dopt=Abstract
date added to LUP
2013-06-12 16:31:34
date last changed
2017-01-01 07:34:05
@article{80e2e706-41c0-44c0-8926-d5c20941e683,
  abstract     = {In order to study protein function and activity structural data is required. Since experimental structures are available for just a small fraction of all known protein sequences, computational methods such as protein modelling can provide useful information. Over the last few decades we have predicted, with homology modelling methods, the structures for numerous proteins. In this study we assess the structural quality and validity of the biological and medical interpretations and predictions made based on the models. All the models had correct scaffolding and were ranked at least as correct or good by numerical evaluators even though the sequence identity with the template was as low as 8%. The biological explanations made based on models were well in line with experimental structures and other experimental studies. Retrospective analysis of homology models indicates the power of protein modelling when made carefully from sequence alignment to model building and refinement. Modelling can be applied to studying and predicting different kinds of biological phenomena and according to our results it can be done so with success.},
  author       = {Khan, Sofia and Vihinen, Mauno},
  issn         = {1386-6338},
  language     = {eng},
  number       = {5},
  pages        = {307--331},
  publisher    = {IOS Press},
  series       = {In Silico Biology},
  title        = {Evaluation of accuracy and applicability of protein models: retrospective analysis of biological and biomedical predictions.},
  url          = {http://dx.doi.org/10.3233/ISB-2009-0408},
  volume       = {9},
  year         = {2009},
}