A short survey on protein blocks

被引：99
作者：
Joseph A.P. [1 ,2 ,3 ]
Agarwal G. [4 ]
Mahajan S. [4 ,5 ]
Gelly J.-C. [1 ,2 ,3 ]
Swapna L.S. [4 ]
Offmann B. [6 ,7 ]
Cadet F. [6 ,7 ]
Bornot A. [1 ,2 ,3 ]
Tyagi M. [8 ]
Valadié H. [9 ]
Schneider B. [10 ]
Etchebest C. [1 ,2 ,3 ]
Srinivasan N. [4 ]
de Brevern A.G. [1 ,2 ,3 ]
机构：
[1] Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Université Paris Diderot Paris 7, Paris Cedex 15, 75739, 6, rue Alexandre Cabanel
[2] Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), INSERM, UMR-S 665, Paris Cedex 15, 75739, 6, rue Alexandre Cabanel
[3] Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), Institut National de la Transfusion Sanguine (INTS), Paris Cedex 15, 75739, 6, rue Alexandre Cabanel
[4] Molecular Biophysics Unit, Indian Institute of Science, Bangalore
[5] National Centre for Biological Sciences, Tata Institute of Fundamental Research, Bangalore, 560 065, UAS-GKVK Campus, Bellary Road
[6] INSERM, UMR-S 665, Dynamique des Structures et Interactions des Macromolécules Biologiques (DSIMB), 97715 Saint Denis Messag Cedex 09, La Réunion, 15 Avenue René Cassin
[7] Faculté des Sciences et Technologies, Université de La Réunion, 97715 Saint Denis Messag Cedex 09, La Réunion, 15 Avenue René Cassin
[8] Computational Biology Branch, National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), Bethesda, MD, 20894
[9] UMR 5168 CNRS-CEA-INRA-Université Joseph Fourier, Institut de Recherches en Technologies et Sciences pour le Vivant, Grenoble Cedex 9, 17 avenue des Martyrs
[10] Institute of Biotechnology AS CR, 142 20 Prague
来源：
Biophysical Reviews | 2010年 / 2卷 / 3期
基金：
美国国家卫生研究院;
关键词：
Binding site; Mutation; Protein structures; Secondary structures; Structural alphabet; Structural superimposition; Structure prediction;
D O I：
10.1007/s12551-010-0036-1
中图分类号：
学科分类号：
摘要：
Protein structures are classically described in terms of secondary structures. However, even if the regular secondary structures have relevant physical meaning, their recognition based on atomic coordinates has a number of important limitations, such as uncertainties in the assignment of the boundaries of the helical and β-strand regions. In addition, an average of about 50% of all residues are assigned to an irregular state, i. e., the coil. These limitations have led different research teams to focus on abstracting the conformation of the protein backbone in the localized short stretches. To this end, different geometric measures are being used to cluster local stretches in protein structures in a chosen number of states. A prototype representative of the local structures in each cluster is then generally defined. These libraries of local structure prototypes are named "structural alphabets". We have developed a structural alphabet, denoted protein blocks, not only to approximate the protein structure but also to predict them from the sequence. Since its development, we and others have explored numerous new research fields using this structural alphabet. Here, we review some of the most interesting applications of this structural alphabet. © 2010 International Union for Pure and Applied Biophysics (IUPAB) and Springer.
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页码：137 / 145
页数：8
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