Browsing the SLoop database of structurally classified loops connecting elements of protein secondary structure

被引:36
作者
Burke, DF [1 ]
Deane, CM [1 ]
Blundell, TL [1 ]
机构
[1] Univ Cambridge, Dept Biochem, Cambridge CB1 2GA1, England
关键词
D O I
10.1093/bioinformatics/16.6.513
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
We describe a web sewer which provides easy access to the SLoop database of loop conformations connecting elements of protein secondary structure. The loops are classified according to their length, the type of bounding secondary structures and the conformation of the mainchain. The current release of the database consists of over 8000 loops of up to 20 residues in length. A loop prediction method, which selects conformers on the basis of the sequence and the positions of the elements of secondary structure, is also implemented.
引用
收藏
页码:513 / 519
页数:7
相关论文
共 36 条
[1]   18TH KREBS,HANS LECTURE - KNOWLEDGE-BASED PROTEIN MODELING AND DESIGN [J].
BLUNDELL, T ;
CARNEY, D ;
GARDNER, S ;
HAYES, F ;
HOWLIN, B ;
HUBBARD, T ;
OVERINGTON, J ;
SINGH, DA ;
SIBANDA, BL ;
SUTCLIFFE, M .
EUROPEAN JOURNAL OF BIOCHEMISTRY, 1988, 172 (03) :513-520
[2]   PREDICTION OF THE FOLDING OF SHORT POLYPEPTIDE SEGMENTS BY UNIFORM CONFORMATIONAL SAMPLING [J].
BRUCCOLERI, RE ;
KARPLUS, M .
BIOPOLYMERS, 1987, 26 (01) :137-168
[3]   CONFORMATIONAL SAMPLING USING HIGH-TEMPERATURE MOLECULAR-DYNAMICS [J].
BRUCCOLERI, RE ;
KARPLUS, M .
BIOPOLYMERS, 1990, 29 (14) :1847-1862
[4]   STRUCTURE OF ANTIBODY HYPERVARIABLE LOOPS REPRODUCED BY A CONFORMATIONAL SEARCH ALGORITHM [J].
BRUCCOLERI, RE ;
HABER, E ;
NOVOTNY, J .
NATURE, 1988, 335 (6190) :564-568
[5]   MODELING THE POLYPEPTIDE BACKBONE WITH SPARE PARTS FROM KNOWN PROTEIN STRUCTURES [J].
CLAESSENS, M ;
VANCUTSEM, E ;
LASTERS, I ;
WODAK, S .
PROTEIN ENGINEERING, 1989, 2 (05) :335-345
[6]   Conformational analysis and clustering of short and medium size loops connecting regular secondary structures: A database for modeling and prediction [J].
Donate, LE ;
Rufino, SD ;
Canard, LHJ ;
Blundell, TL .
PROTEIN SCIENCE, 1996, 5 (12) :2600-2616
[7]  
EFIMOV AV, 1991, PROTEIN ENG, V1, P173
[8]  
FELSENSTEIN J, 1985, EVOLUTION, V39, P783, DOI 10.1111/j.1558-5646.1985.tb00420.x
[9]   USING KNOWN SUBSTRUCTURES IN PROTEIN MODEL-BUILDING AND CRYSTALLOGRAPHY [J].
JONES, TA ;
THIRUP, S .
EMBO JOURNAL, 1986, 5 (04) :819-822
[10]   DICTIONARY OF PROTEIN SECONDARY STRUCTURE - PATTERN-RECOGNITION OF HYDROGEN-BONDED AND GEOMETRICAL FEATURES [J].
KABSCH, W ;
SANDER, C .
BIOPOLYMERS, 1983, 22 (12) :2577-2637