poster

Incorporating several features in the protein ray descriptor for more accurate protein 3D structure retrieval

Authors:

Georgina Mirceva,

Danco DavcevAuthors Info & Claims

3DOR '10: Proceedings of the ACM workshop on 3D object retrieval

Pages 51 - 56

https://doi.org/10.1145/1877808.1877820

Published: 25 October 2010 Publication History

Abstract

The retrieval of protein structures is one of the most popular topics in bioinformatics community nowadays, since it can be further used for determining protein function. With the technology innovation, the number of protein tertiary structures increases every day, so the necessity of accurate, robust and efficient algorithms for protein 3D structure retrieval arises. In this paper we improve the ray based descriptor, in sense of achieving higher precision. First, the protein backbone is uniformly interpolated, as in the process of extraction of the existing protein ray based descriptor. Then, for each of the approximation points, beside the Euclidean distance from the point to the centre of mass, the ASA, RASA and hydrophobicity of the nearest amino acid are extracted and added to the descriptor. The analysis showed that by incorporating these features, we achieve higher precision (2.26% improvement) than by using only the Euclidean distance as a single feature.

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Digital Library

Cited By

Li ZLiang FZhuang HLi JLi C(2019)Research on protein folding of cannabinoid receptor type II based on HP modelJournal of Physics: Conference Series10.1088/1742-6596/1237/5/0520031237(052003)Online publication date: 12-Jul-2019
https://doi.org/10.1088/1742-6596/1237/5/052003
Pavlovikj NIvanoska IKalajdziski S(2012)Comparison of Protein Descriptors Used in Hierarchical Multi-label Classification Based on Gene OntologyICT Innovations 201110.1007/978-3-642-28664-3_6(61-71)Online publication date: 2012
https://doi.org/10.1007/978-3-642-28664-3_6
Mirceva GDavcev D(2011)Incorporating the depth and protrusion index in the protein ray based descriptor2011 Eighth International Conference on Fuzzy Systems and Knowledge Discovery (FSKD)10.1109/FSKD.2011.6019859(1592-1596)Online publication date: Jul-2011
https://doi.org/10.1109/FSKD.2011.6019859

Index Terms

Incorporating several features in the protein ray descriptor for more accurate protein 3D structure retrieval
1. Computing methodologies
  1. Computer graphics
    1. Shape modeling
      1. Parametric curve and surface models
      2. Volumetric models
  2. Machine learning
    1. Machine learning algorithms
      1. Feature selection
2. Information systems
  1. Information retrieval
    1. Retrieval models and ranking
    2. Retrieval tasks and goals
      1. Document filtering
      2. Information extraction

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Published In

cover image ACM Conferences

3DOR '10: Proceedings of the ACM workshop on 3D object retrieval

October 2010

96 pages

ISBN:9781450301602

DOI:10.1145/1877808

Program Chairs:
Mohamed Doudi
TELECOM Lille1/LIFL, France
,
Michela Spagnuolo
CNR-IMATI, Italy
,
Remco Veltkamp
Utrecht University, The Netherlands

Copyright © 2010 ACM.

Permission to make digital or hard copies of all or part of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for components of this work owned by others than ACM must be honored. Abstracting with credit is permitted. To copy otherwise, or republish, to post on servers or to redistribute to lists, requires prior specific permission and/or a fee. Request permissions from [email protected]

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Published: 25 October 2010

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Cited By

Li ZLiang FZhuang HLi JLi C(2019)Research on protein folding of cannabinoid receptor type II based on HP modelJournal of Physics: Conference Series10.1088/1742-6596/1237/5/0520031237(052003)Online publication date: 12-Jul-2019
https://doi.org/10.1088/1742-6596/1237/5/052003
Pavlovikj NIvanoska IKalajdziski S(2012)Comparison of Protein Descriptors Used in Hierarchical Multi-label Classification Based on Gene OntologyICT Innovations 201110.1007/978-3-642-28664-3_6(61-71)Online publication date: 2012
https://doi.org/10.1007/978-3-642-28664-3_6
Mirceva GDavcev D(2011)Incorporating the depth and protrusion index in the protein ray based descriptor2011 Eighth International Conference on Fuzzy Systems and Knowledge Discovery (FSKD)10.1109/FSKD.2011.6019859(1592-1596)Online publication date: Jul-2011
https://doi.org/10.1109/FSKD.2011.6019859

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