Retrieving backbone string neighbors provides insights into structural modeling of membrane proteins
Sun, Jiangming LU
; Li, Tong Hua
; Cong, Pei Sheng
; Tang, Sheng Nan
and Xiong, Wen Wei
(2012)
In Molecular and Cellular Proteomics
11(7).
- Abstract
Identification of protein structural neighbors to a query is fundamental in structure and function prediction. Here we present BS-align, a systematic method to retrieve backbone string neighbors from primary sequences as templates for protein modeling. The backbone conformation of a protein is represented by the backbone string, as defined in Ramachandran space. The backbone string of a query can be accurately predicted by two innovative technologies: a knowledge-driven sequence alignment and encoding of a backbone string element profile. Then, the predicted backbone string is employed to align against a backbone string database and retrieve a set of backbone string neighbors. The backbone string neighbors were shown to be close to... (More)
Identification of protein structural neighbors to a query is fundamental in structure and function prediction. Here we present BS-align, a systematic method to retrieve backbone string neighbors from primary sequences as templates for protein modeling. The backbone conformation of a protein is represented by the backbone string, as defined in Ramachandran space. The backbone string of a query can be accurately predicted by two innovative technologies: a knowledge-driven sequence alignment and encoding of a backbone string element profile. Then, the predicted backbone string is employed to align against a backbone string database and retrieve a set of backbone string neighbors. The backbone string neighbors were shown to be close to native structures of query proteins. BS-align was successfully employed to predict models of 10 membrane proteins with lengths ranging between 229 and 595 residues, and whose high-resolution structural determinations were difficult to elucidate both by experiment and prediction. The obtained TM-scores and root mean square deviations of the models confirmed that the models based on the backbone string neighbors retrieved by the BS-align were very close to the native membrane structures although the query and the neighbor shared a very low sequence identity. The backbone string system represents a new road for the prediction of protein structure from sequence, and suggests that the similarity of the backbone string would be more informative than describing a protein as belonging to a fold.
(Less)
- author
- Sun, Jiangming
LU
; Li, Tong Hua
; Cong, Pei Sheng
; Tang, Sheng Nan
and Xiong, Wen Wei
- publishing date
- 2012-07
- type
- Contribution to journal
- publication status
- published
- subject
- in
- Molecular and Cellular Proteomics
- volume
- 11
- issue
- 7
- publisher
- American Society for Biochemistry and Molecular Biology
- external identifiers
-
- pmid:22415040
- scopus:84863806527
- ISSN
- 1535-9476
- DOI
- 10.1074/mcp.M111.016808
- language
- English
- LU publication?
- no
- id
- ff53a54c-4082-4ffd-b651-bb3aa049983a
- date added to LUP
- 2023-04-24 15:32:03
- date last changed
- 2024-01-05 00:47:46
@article{ff53a54c-4082-4ffd-b651-bb3aa049983a,
abstract = {{<p>Identification of protein structural neighbors to a query is fundamental in structure and function prediction. Here we present BS-align, a systematic method to retrieve backbone string neighbors from primary sequences as templates for protein modeling. The backbone conformation of a protein is represented by the backbone string, as defined in Ramachandran space. The backbone string of a query can be accurately predicted by two innovative technologies: a knowledge-driven sequence alignment and encoding of a backbone string element profile. Then, the predicted backbone string is employed to align against a backbone string database and retrieve a set of backbone string neighbors. The backbone string neighbors were shown to be close to native structures of query proteins. BS-align was successfully employed to predict models of 10 membrane proteins with lengths ranging between 229 and 595 residues, and whose high-resolution structural determinations were difficult to elucidate both by experiment and prediction. The obtained TM-scores and root mean square deviations of the models confirmed that the models based on the backbone string neighbors retrieved by the BS-align were very close to the native membrane structures although the query and the neighbor shared a very low sequence identity. The backbone string system represents a new road for the prediction of protein structure from sequence, and suggests that the similarity of the backbone string would be more informative than describing a protein as belonging to a fold.</p>}},
author = {{Sun, Jiangming and Li, Tong Hua and Cong, Pei Sheng and Tang, Sheng Nan and Xiong, Wen Wei}},
issn = {{1535-9476}},
language = {{eng}},
number = {{7}},
publisher = {{American Society for Biochemistry and Molecular Biology}},
series = {{Molecular and Cellular Proteomics}},
title = {{Retrieving backbone string neighbors provides insights into structural modeling of membrane proteins}},
url = {{http://dx.doi.org/10.1074/mcp.M111.016808}},
doi = {{10.1074/mcp.M111.016808}},
volume = {{11}},
year = {{2012}},
}