BibTex RIS Cite

-

Year 2013, Volume: 3 Issue: 6, 91 - 98, 06.03.2014

Abstract

This paper presents a new approach for motif retrieval by comparing protein secondary structures. This approach is tested as two different methods based on Generalized Hough Transform (GHT). In the first one secondary structure couples are used, and midpoint distance, axis distance and axis angle, related to the couple, are considered comparison parameters. In the second one secondary structure triplets are used, the triangles are defined by joining the midpoints of secondary structures and the edge lengths of triangles are considered as comparison parameters. In both methods the barycenter of the motif is assigned as reference point (RP). Then motif couples and motif triplets are compared with protein couples and triplets respectively using the first and second methods, and

References

  • Can, T. ve Wang, Y.F., “CTSS:A Robust and Efficient Method for Protein Structure Alignment Based on Local Geometrical and Biological Features”, IEEE Computer Society Conference on Bioinformatics, pp. 169-179, 2003.
  • Camoğlu, O., Kahveci, T. ve Singh, A. “PSI: Indexing protein structures for fast similarity search”, Bioinformatics, vol.19, suppl.1, pp.81-83, 2003.
  • Chionh, C.H., Huang, Z., Tan, K.L. ve Yao, Z., “Augmenting SSEs with Structural Properties for Rapid Protein Structure Comparison”, IEEE Symposium on Bioinformatics and Bioengineering, pp.341-348, 2003.
  • Shuoyong, S., Zhong, Y., Majumdar, I., Krishna S.S. ve Grishin, N.V., ”Searching for three-dimensional secondary structural patterns in proteins with ProSMoS”, Bioinformatics, vol.23, no.11, pp. 1331-1338, 2007.
  • Chi, P.H., Scott, G. ve Shyu, C.R., ”A Fast Protein Structure Retrieval System Using Image Based Distance Matrices and Multidimensional Index”, International Journal of Software Engineering and Knowledge Engineering, Special Issue on Software and Knowledge Engineering Support in Bioinformatics, pp.522-532, 2004.
  • Albrecht, B., Grant, G.H., Sisu, C. ve Richards, W.G., “Classification of proteins based on similarity of two-dimensional protein maps”, Biophysical Chemistry, pp.11-22, 2008.
  • Zotenko, E., Dogan, R.I., Wilbur, W.J., O'Leary, D.P. ve Przytycka, T.M., “Structural Footprinting in Protein Structure Comparison: The Impact of Structural Fragments”, BMC Structural Biology, vol.7, 7:53, 2007.
  • Cantoni, V., Ferone, A. ve Petrosino, A., “Protein Motif Retrieval through Secondary Structure Spatial Co-occurrences”, New Tools and Methods for Pattern Recognition in Complex Biological Systems, in press.
  • Cantoni, V., Ferone, A., Ozbudak, O., Petrosino, A., “Protein structural blocks representation and search through unsupervised NN”, ICANN 2012, September 11-14, Lausanne, Switzerland, vol. 7553, p. 515-522.
  • Hough, P.V.C., “Methods and means for recognizing complex patterns”, US Patent 3069654, 1962.
  • Duda, R.O. ve Hart, P.E., “Use of the Hough transformation to detect lines and curves in pictures”, Comm. ACM, vol.15, no.1, pp. 11-15, 1972.
  • Wechsler, H. ve Sklansky, J., “Automatic detection of ribs in chest radiographs”, Pattern Recognition, vol.9, pp.21-30, 1977.
  • Ballard, D.H., “Generalizing the Hough transform to detect arbitrary shapes”, Pattern Recognition, vol.13, no.2, pp. 111-122, 1981.
  • http://www.rcsb.org/pdb/.
  • Kabsach, W. and Sander, C., “Dictionary of Protein Secondary Structure: pattern recognition of hydrogen bonded and geometrical features”, Biopolymers, 22(12), pp.2577-2637, 1983.

Hough Dönüşümü Kullanılarak Protein Yapısal Bloklarının Karşılaştırılması - Protein Structural Block Comparison by using Hough Transform

Year 2013, Volume: 3 Issue: 6, 91 - 98, 06.03.2014

Abstract

Bu çalışma motif çıkarılması için üç boyutlu protein sekonder yapılarının karşılaştırılmasında yeni bir yaklaşım sunmaktadır. Bu yaklaşım Genelleştirilmiş Hough Dönüşümüne (GHT) dayalı olarak iki ayrı şekilde test edilmektedir. Bunlardan birincisinde sekonder yapı ikilileri kullanılmaktadır ve bu ikililere ilişkin olarak, sekonder yapıların orta noktaları arasındaki mesafe, eksenleri arasındaki mesafe ve eksenler arasındaki açı karşılaştırma parametreleri olarak seçilmektedir. İkincisinde ise sekonder yapı üçlüleri kullanılmakta,  sekonder yapıların orta noktaları birleştirilerek üçgenler oluşturulmakta ve bu üçgenlerin kenar uzunlukları karşılaştırma parametreleri olarak seçilmektedir. Her iki yöntemde de aranan motifin ağırlık merkezi referans noktası (RN) olarak belirlenmektedir. Sonrasında birinci yöntem ve ikinci yöntem için sırasıyla motif ikilileri ve motif üçlüleri proteinlerdeki tüm ikili ve üçlülerle karşılaştırılır ve her bir eşleşme için özel bir haritalama kuralı ile belirlenen noktaya bir oy verilir. Oylama sonucunda en fazla oya sahip olan nokta aday RN olarak belirlenir. Bu çalışmada dört ve beş sekonder yapıdan oluşan motifler test edilmiştir. Test sonuçları motif RN'nin hatasız bir şekilde belirlendiğini ve motif çıkarılmasında bu iki yöntemin kolay uygulanabilir, hesaplama açısından etkin ve hızlı olduğunu göstermiştir.

This paper presents a new approach for motif retrieval by comparing protein secondary structures. This approach is tested as two different methods based on Generalized Hough Transform (GHT). In the first one secondary structure couples are used, and midpoint distance, axis distance and axis angle, related to the couple, are considered comparison parameters. In the second one secondary structure triplets are used, the triangles are defined by joining the midpoints of secondary structures and the edge lengths of triangles are considered as comparison parameters. In both methods the barycenter of the motif is assigned as reference point (RP). Then motif couples and motif triplets are compared with protein couples and triplets respectively using the first and second methods, and for every correspondence a vote is given to the point which is defined with a special mapping rule. After the voting process, the point having the highest number of votes is defined as candidate RP. In this paper the motifs, formed by four and five secondary structures, are tested. Experimental results showed that the RP is determined precisely and both methods to retrieve the motif are simple to implement, computationally efficient and fast.

References

  • Can, T. ve Wang, Y.F., “CTSS:A Robust and Efficient Method for Protein Structure Alignment Based on Local Geometrical and Biological Features”, IEEE Computer Society Conference on Bioinformatics, pp. 169-179, 2003.
  • Camoğlu, O., Kahveci, T. ve Singh, A. “PSI: Indexing protein structures for fast similarity search”, Bioinformatics, vol.19, suppl.1, pp.81-83, 2003.
  • Chionh, C.H., Huang, Z., Tan, K.L. ve Yao, Z., “Augmenting SSEs with Structural Properties for Rapid Protein Structure Comparison”, IEEE Symposium on Bioinformatics and Bioengineering, pp.341-348, 2003.
  • Shuoyong, S., Zhong, Y., Majumdar, I., Krishna S.S. ve Grishin, N.V., ”Searching for three-dimensional secondary structural patterns in proteins with ProSMoS”, Bioinformatics, vol.23, no.11, pp. 1331-1338, 2007.
  • Chi, P.H., Scott, G. ve Shyu, C.R., ”A Fast Protein Structure Retrieval System Using Image Based Distance Matrices and Multidimensional Index”, International Journal of Software Engineering and Knowledge Engineering, Special Issue on Software and Knowledge Engineering Support in Bioinformatics, pp.522-532, 2004.
  • Albrecht, B., Grant, G.H., Sisu, C. ve Richards, W.G., “Classification of proteins based on similarity of two-dimensional protein maps”, Biophysical Chemistry, pp.11-22, 2008.
  • Zotenko, E., Dogan, R.I., Wilbur, W.J., O'Leary, D.P. ve Przytycka, T.M., “Structural Footprinting in Protein Structure Comparison: The Impact of Structural Fragments”, BMC Structural Biology, vol.7, 7:53, 2007.
  • Cantoni, V., Ferone, A. ve Petrosino, A., “Protein Motif Retrieval through Secondary Structure Spatial Co-occurrences”, New Tools and Methods for Pattern Recognition in Complex Biological Systems, in press.
  • Cantoni, V., Ferone, A., Ozbudak, O., Petrosino, A., “Protein structural blocks representation and search through unsupervised NN”, ICANN 2012, September 11-14, Lausanne, Switzerland, vol. 7553, p. 515-522.
  • Hough, P.V.C., “Methods and means for recognizing complex patterns”, US Patent 3069654, 1962.
  • Duda, R.O. ve Hart, P.E., “Use of the Hough transformation to detect lines and curves in pictures”, Comm. ACM, vol.15, no.1, pp. 11-15, 1972.
  • Wechsler, H. ve Sklansky, J., “Automatic detection of ribs in chest radiographs”, Pattern Recognition, vol.9, pp.21-30, 1977.
  • Ballard, D.H., “Generalizing the Hough transform to detect arbitrary shapes”, Pattern Recognition, vol.13, no.2, pp. 111-122, 1981.
  • http://www.rcsb.org/pdb/.
  • Kabsach, W. and Sander, C., “Dictionary of Protein Secondary Structure: pattern recognition of hydrogen bonded and geometrical features”, Biopolymers, 22(12), pp.2577-2637, 1983.
There are 15 citations in total.

Details

Primary Language Turkish
Journal Section Özel Sayı Makaleleri (ELECO)
Authors

Özlem Özbudak

Zümray Dokur

Virginio Cantoni This is me

Publication Date March 6, 2014
Submission Date May 30, 2013
Published in Issue Year 2013 Volume: 3 Issue: 6

Cite

APA Özbudak, Ö., Dokur, Z., & Cantoni, V. (2014). Hough Dönüşümü Kullanılarak Protein Yapısal Bloklarının Karşılaştırılması - Protein Structural Block Comparison by using Hough Transform. EMO Bilimsel Dergi, 3(6), 91-98.
AMA Özbudak Ö, Dokur Z, Cantoni V. Hough Dönüşümü Kullanılarak Protein Yapısal Bloklarının Karşılaştırılması - Protein Structural Block Comparison by using Hough Transform. EMO Bilimsel Dergi. March 2014;3(6):91-98.
Chicago Özbudak, Özlem, Zümray Dokur, and Virginio Cantoni. “Hough Dönüşümü Kullanılarak Protein Yapısal Bloklarının Karşılaştırılması - Protein Structural Block Comparison by Using Hough Transform”. EMO Bilimsel Dergi 3, no. 6 (March 2014): 91-98.
EndNote Özbudak Ö, Dokur Z, Cantoni V (March 1, 2014) Hough Dönüşümü Kullanılarak Protein Yapısal Bloklarının Karşılaştırılması - Protein Structural Block Comparison by using Hough Transform. EMO Bilimsel Dergi 3 6 91–98.
IEEE Ö. Özbudak, Z. Dokur, and V. Cantoni, “Hough Dönüşümü Kullanılarak Protein Yapısal Bloklarının Karşılaştırılması - Protein Structural Block Comparison by using Hough Transform”, EMO Bilimsel Dergi, vol. 3, no. 6, pp. 91–98, 2014.
ISNAD Özbudak, Özlem et al. “Hough Dönüşümü Kullanılarak Protein Yapısal Bloklarının Karşılaştırılması - Protein Structural Block Comparison by Using Hough Transform”. EMO Bilimsel Dergi 3/6 (March 2014), 91-98.
JAMA Özbudak Ö, Dokur Z, Cantoni V. Hough Dönüşümü Kullanılarak Protein Yapısal Bloklarının Karşılaştırılması - Protein Structural Block Comparison by using Hough Transform. EMO Bilimsel Dergi. 2014;3:91–98.
MLA Özbudak, Özlem et al. “Hough Dönüşümü Kullanılarak Protein Yapısal Bloklarının Karşılaştırılması - Protein Structural Block Comparison by Using Hough Transform”. EMO Bilimsel Dergi, vol. 3, no. 6, 2014, pp. 91-98.
Vancouver Özbudak Ö, Dokur Z, Cantoni V. Hough Dönüşümü Kullanılarak Protein Yapısal Bloklarının Karşılaştırılması - Protein Structural Block Comparison by using Hough Transform. EMO Bilimsel Dergi. 2014;3(6):91-8.

EMO BİLİMSEL DERGİ
Elektrik, Elektronik, Bilgisayar, Biyomedikal, Kontrol Mühendisliği Bilimsel Hakemli Dergisi
TMMOB ELEKTRİK MÜHENDİSLERİ ODASI 
IHLAMUR SOKAK NO:10 KIZILAY/ANKARA
TEL: +90 (312) 425 32 72 (PBX) - FAKS: +90 (312) 417 38 18
bilimseldergi@emo.org.tr