Show/Hide Menu
Hide/Show Apps
Logout
Türkçe
Türkçe
Search
Search
Login
Login
OpenMETU
OpenMETU
About
About
Open Science Policy
Open Science Policy
Open Access Guideline
Open Access Guideline
Postgraduate Thesis Guideline
Postgraduate Thesis Guideline
Communities & Collections
Communities & Collections
Help
Help
Frequently Asked Questions
Frequently Asked Questions
Guides
Guides
Thesis submission
Thesis submission
MS without thesis term project submission
MS without thesis term project submission
Publication submission with DOI
Publication submission with DOI
Publication submission
Publication submission
Supporting Information
Supporting Information
General Information
General Information
Copyright, Embargo and License
Copyright, Embargo and License
Contact us
Contact us
Distance-based Indexing of Residue Contacts for Protein Structure Retrieval and Alignment
Date
2008-10-10
Author
Sacan, Ahmet
Toroslu, İsmail Hakkı
Ferhatosmanoglu, Hakan
Metadata
Show full item record
This work is licensed under a
Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License
.
Item Usage Stats
210
views
0
downloads
Cite This
New protein structures are continuously being determined with the hope of deriving insights into the function and mechanisms of proteins, and consequently, protein structure repositories are growing by leaps and bounds. However, we are still far from having the right methods for sensitive and effective use of the available structural data. The fact that current structural analysis tools are impractical for large-scale applications have given rise to several approaches that try to quickly identify candidate proteins worthy of further analysis. Nonetheless, these approaches do not provide the desired sensitivity of identifying important structural similarities. In this study, we propose a new protein structure retrieval method (RCIndex: Residue-Contacts Index) that is based on accurate and efficient identification of similar residue contacts from a database of available protein structures. By defining a metric distance function for biologically meaningful comparison of residue contacts, distance-based indexing is made applicable for quick retrieval of similar residue contact seeds. These seeds are extended into high scoring segment pairs, which induce structural superpositions. The results show that RCIndex is effective in not only identifying related proteins, but also producing remarkably high quality structural alignments that are comparable to or better than those produced by popular pairwise alignment tools. To the best of our knowledge, this is the first time the protein structure retrieval and alignment tasks are successfully handled together.
Subject Keywords
Protein structure
,
Distance-based indexing
,
Alignment
,
Similarity search
URI
https://hdl.handle.net/11511/41432
DOI
https://doi.org/10.1109/bibe.2008.4696701
Collections
Department of Computer Engineering, Conference / Seminar
Suggestions
OpenMETU
Core
Amino acid substitution matrices based on 4-body Delaunay contact profiles
Sacan, Ahmet; Toroslu, İsmail Hakkı (2007-10-17)
Sequence similarity search of proteins is one of the basic and most common steps followed in bioninformatics research and is used in making evolutionary, structural, and functional inferences. The quality of the search and the alignment of the protein sequences depend crucially on the underlying amino-acid substitution matrix. We present a method for deriving amino acid substitution matrices from 4-body contact propensities of amino-acids in 3D protein structures. Unlike current popular methods, our method ...
Prediction of protein subcellular localization based on primary sequence data
Özarar, Mert; Atalay, Mehmet Volkan; Department of Computer Engineering (2003)
Subcellular localization is crucial for determining the functions of proteins. A system called prediction of protein subcellular localization (P2SL) that predicts the subcellular localization of proteins in eukaryotic organisms based on the amino acid content of primary sequences using amino acid order is designed. The approach for prediction is to nd the most frequent motifs for each protein in a given class based on clustering via self organizing maps and then to use these most frequent motifs as features...
Multi-view subcellular localization prediction of human proteins
Özsarı, Gökhan; Atalay, M. Volkan.; Department of Computer Engineering (2019)
Determining the subcellular localization of proteins is crucial for Understanding the functions of proteins, drug targeting, systems biology, and proteomics research. Experimental validation of subcellular localization is an expensive and challenging process. There exist several computational methods for automated prediction of protein subcellular localization; however, there is still room for better performance. Here, we propose a multi-view SVM-based approach that provides predictions for human proteins. ...
Immobilization of proteins on zeolite and zeo-type materials for biosensor applications based on conductometric biosensors and ion sensitive field effect transistors
Soy, Esin; Akata Kurç, Burcu; Özen, Can; Department of Micro and Nanotechnology (2011)
Over the last decade, immobilization of proteins onto inorganic materials is becoming more crucial to extend a deep understanding of interaction between proteins and nanoparticles. With understanding of the real interaction lying under the protein-nanoparticle relations, it is possible to organize the conformation and orientation of surface and framework species of nanoparticles to generate ideal surfaces for potential biotechnological applications. Due to their unique properties such as large clean surface...
Architectures and functional coverage of protein-protein interfaces
Tunçbağ, Nurcan; Guney, Emre; NUSSINOV, Ruth; Keskin, Ozlem (2008-09-05)
The diverse range of cellular functions is performed by a limited number of protein folds existing in nature. One may similarly expect that cellular functional diversity would be covered by a limited number of protein-protein interface architectures. Here, we present 8205 interface clusters, each representing a unique interface architecture. This data set of protein-protein interfaces is analyzed and compared with older data sets. We observe that the number of both biological and crystal interfaces increase...
Citation Formats
IEEE
ACM
APA
CHICAGO
MLA
BibTeX
A. Sacan, İ. H. Toroslu, and H. Ferhatosmanoglu, “Distance-based Indexing of Residue Contacts for Protein Structure Retrieval and Alignment,” 2008, Accessed: 00, 2020. [Online]. Available: https://hdl.handle.net/11511/41432.