Recursive protein modeling

A divide and conquer strategy for protein structure prediction and its case study in CASP9

Jianlin Cheng, Zheng Wang, Jesse Eickholt, Xin Deng

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Citations (Scopus)

Abstract

After decades of research, protein structure prediction remains a very challenging problem. In order to address the different levels of complexity of modeling structure, two types of modeling techniques - template-based modeling and template-free modeling - have been developed. Template-based modeling can often generate a moderate to high resolution model when a similar, homologous template structure is found for a query protein but fails if no template or only incorrect templates are found. Template-free modeling such as fragment-based assembly may generate models of moderate resolution for small proteins of low topological complexity. Seldom have the two techniques been integrated together to improve protein modeling. Here we develop a recursive protein modeling approach to selectively and collaboratively apply template-based and template-free modeling methods to model template-covered (i.e., certain) and template-free (i.e., uncertain) regions of a protein. A preliminary implementation of the approach was tested on a number of hard modeling cases during the 9th Critical Assessment of Techniques for Protein Structure Prediction (CASP9) and successfully improved the quality of modeling in most of these cases. Recursive modeling can significantly reduce the complexity of protein structure modeling and integrate template-based and template-free modeling to improve the quality and efficiency of protein structure prediction.

Original languageEnglish (US)
Title of host publication2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011
Pages352-357
Number of pages6
DOIs
StatePublished - Dec 1 2011
Externally publishedYes
Event2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011 - Atlanta, GA, United States
Duration: Nov 12 2011Nov 15 2011

Other

Other2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011
CountryUnited States
CityAtlanta, GA
Period11/12/1111/15/11

Fingerprint

Proteins
Research

Keywords

  • CASP9
  • protein structure prediction
  • recursive protein modeling
  • template-based modeling
  • template-free modeling

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics
  • Health Information Management

Cite this

Cheng, J., Wang, Z., Eickholt, J., & Deng, X. (2011). Recursive protein modeling: A divide and conquer strategy for protein structure prediction and its case study in CASP9. In 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011 (pp. 352-357). [6112398] https://doi.org/10.1109/BIBMW.2011.6112398

Recursive protein modeling : A divide and conquer strategy for protein structure prediction and its case study in CASP9. / Cheng, Jianlin; Wang, Zheng; Eickholt, Jesse; Deng, Xin.

2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011. 2011. p. 352-357 6112398.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Cheng, J, Wang, Z, Eickholt, J & Deng, X 2011, Recursive protein modeling: A divide and conquer strategy for protein structure prediction and its case study in CASP9. in 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011., 6112398, pp. 352-357, 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011, Atlanta, GA, United States, 11/12/11. https://doi.org/10.1109/BIBMW.2011.6112398
Cheng J, Wang Z, Eickholt J, Deng X. Recursive protein modeling: A divide and conquer strategy for protein structure prediction and its case study in CASP9. In 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011. 2011. p. 352-357. 6112398 https://doi.org/10.1109/BIBMW.2011.6112398
Cheng, Jianlin ; Wang, Zheng ; Eickholt, Jesse ; Deng, Xin. / Recursive protein modeling : A divide and conquer strategy for protein structure prediction and its case study in CASP9. 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011. 2011. pp. 352-357
@inproceedings{61c5daca144e4a5c92a4a2b995083d23,
title = "Recursive protein modeling: A divide and conquer strategy for protein structure prediction and its case study in CASP9",
abstract = "After decades of research, protein structure prediction remains a very challenging problem. In order to address the different levels of complexity of modeling structure, two types of modeling techniques - template-based modeling and template-free modeling - have been developed. Template-based modeling can often generate a moderate to high resolution model when a similar, homologous template structure is found for a query protein but fails if no template or only incorrect templates are found. Template-free modeling such as fragment-based assembly may generate models of moderate resolution for small proteins of low topological complexity. Seldom have the two techniques been integrated together to improve protein modeling. Here we develop a recursive protein modeling approach to selectively and collaboratively apply template-based and template-free modeling methods to model template-covered (i.e., certain) and template-free (i.e., uncertain) regions of a protein. A preliminary implementation of the approach was tested on a number of hard modeling cases during the 9th Critical Assessment of Techniques for Protein Structure Prediction (CASP9) and successfully improved the quality of modeling in most of these cases. Recursive modeling can significantly reduce the complexity of protein structure modeling and integrate template-based and template-free modeling to improve the quality and efficiency of protein structure prediction.",
keywords = "CASP9, protein structure prediction, recursive protein modeling, template-based modeling, template-free modeling",
author = "Jianlin Cheng and Zheng Wang and Jesse Eickholt and Xin Deng",
year = "2011",
month = "12",
day = "1",
doi = "10.1109/BIBMW.2011.6112398",
language = "English (US)",
isbn = "9781457716133",
pages = "352--357",
booktitle = "2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011",

}

TY - GEN

T1 - Recursive protein modeling

T2 - A divide and conquer strategy for protein structure prediction and its case study in CASP9

AU - Cheng, Jianlin

AU - Wang, Zheng

AU - Eickholt, Jesse

AU - Deng, Xin

PY - 2011/12/1

Y1 - 2011/12/1

N2 - After decades of research, protein structure prediction remains a very challenging problem. In order to address the different levels of complexity of modeling structure, two types of modeling techniques - template-based modeling and template-free modeling - have been developed. Template-based modeling can often generate a moderate to high resolution model when a similar, homologous template structure is found for a query protein but fails if no template or only incorrect templates are found. Template-free modeling such as fragment-based assembly may generate models of moderate resolution for small proteins of low topological complexity. Seldom have the two techniques been integrated together to improve protein modeling. Here we develop a recursive protein modeling approach to selectively and collaboratively apply template-based and template-free modeling methods to model template-covered (i.e., certain) and template-free (i.e., uncertain) regions of a protein. A preliminary implementation of the approach was tested on a number of hard modeling cases during the 9th Critical Assessment of Techniques for Protein Structure Prediction (CASP9) and successfully improved the quality of modeling in most of these cases. Recursive modeling can significantly reduce the complexity of protein structure modeling and integrate template-based and template-free modeling to improve the quality and efficiency of protein structure prediction.

AB - After decades of research, protein structure prediction remains a very challenging problem. In order to address the different levels of complexity of modeling structure, two types of modeling techniques - template-based modeling and template-free modeling - have been developed. Template-based modeling can often generate a moderate to high resolution model when a similar, homologous template structure is found for a query protein but fails if no template or only incorrect templates are found. Template-free modeling such as fragment-based assembly may generate models of moderate resolution for small proteins of low topological complexity. Seldom have the two techniques been integrated together to improve protein modeling. Here we develop a recursive protein modeling approach to selectively and collaboratively apply template-based and template-free modeling methods to model template-covered (i.e., certain) and template-free (i.e., uncertain) regions of a protein. A preliminary implementation of the approach was tested on a number of hard modeling cases during the 9th Critical Assessment of Techniques for Protein Structure Prediction (CASP9) and successfully improved the quality of modeling in most of these cases. Recursive modeling can significantly reduce the complexity of protein structure modeling and integrate template-based and template-free modeling to improve the quality and efficiency of protein structure prediction.

KW - CASP9

KW - protein structure prediction

KW - recursive protein modeling

KW - template-based modeling

KW - template-free modeling

UR - http://www.scopus.com/inward/record.url?scp=84862972847&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84862972847&partnerID=8YFLogxK

U2 - 10.1109/BIBMW.2011.6112398

DO - 10.1109/BIBMW.2011.6112398

M3 - Conference contribution

SN - 9781457716133

SP - 352

EP - 357

BT - 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011

ER -