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

We describe a web server, 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. These web pages are freely accessible over the internet at http://www-cryst.bioc.cam.ac.uk/ approximately sloop.

[1]  E. Milner-White,et al.  Four classes of beta-hairpins in proteins. , 1986, The Biochemical journal.

[2]  T. Blundell,et al.  Conformational analysis and clustering of short and medium size loops connecting regular secondary structures: A database for modeling and prediction , 1996, Protein science : a publication of the Protein Society.

[3]  M. Karplus,et al.  Prediction of the folding of short polypeptide segments by uniform conformational sampling , 1987, Biopolymers.

[4]  J M Thornton,et al.  Long loops in proteins. , 1995, Protein engineering.

[5]  M. Karplus,et al.  PDB-based protein loop prediction: parameters for selection and methods for optimization. , 1997, Journal of molecular biology.

[6]  Jiří Novotný,et al.  Structure of antibody hypervariable loops reproduced by a conformational search algorithm , 1988, Nature.

[7]  A. Efimov,et al.  Structure of alpha-alpha-hairpins with short connections. , 1991, Protein engineering.

[8]  T L Blundell,et al.  CAMPASS: a database of structurally aligned protein superfamilies. , 1998, Structure.

[9]  B. L. Sibanda,et al.  Beta-hairpin families in globular proteins. , 1985, Nature.

[10]  Baldomero Oliva,et al.  An automated classification of the structure of protein loops. , 1997, Journal of molecular biology.

[11]  R A Sayle,et al.  RASMOL: biomolecular graphics for all. , 1995, Trends in biochemical sciences.

[12]  T. Blundell,et al.  Predicting the conformational class of short and medium size loops connecting regular secondary structures: application to comparative modelling. , 1997, Journal of molecular biology.

[13]  H. Meirovitch,et al.  Backbone entropy of loops as a measure of their flexibility: Application to a Ras protein simulated by molecular dynamics , 1997, Proteins.

[14]  John P. Overington,et al.  HOMSTRAD: A database of protein structure alignments for homologous families , 1998, Protein science : a publication of the Protein Society.

[15]  S. Sudarsanam,et al.  Modeling protein loops using a ϕi+1, Ψi dimer database , 1995, Protein science : a publication of the Protein Society.

[16]  S. Wodak,et al.  Modelling the polypeptide backbone with 'spare parts' from known protein structures. , 1989, Protein engineering.

[17]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[18]  John P. Overington,et al.  18th Sir Hans Krebs lecture. Knowledge-based protein modelling and design. , 1988, European journal of biochemistry.

[19]  Andrew J. Martin,et al.  Structural families in loops of homologous proteins: automatic classification, modelling and application to antibodies. , 1996, Journal of molecular biology.

[20]  S. Wodak,et al.  Automatic classification and analysis of alpha alpha-turn motifs in proteins. , 1996, Journal of molecular biology.

[21]  B. L. Sibanda,et al.  β-Hairpin families in globular proteins , 1985, Nature.

[22]  J. Felsenstein.  CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP , 1985, Evolution; international journal of organic evolution.

[23]  G. Rose,et al.  Loops in globular proteins: a novel category of secondary structure. , 1986, Science.

[24]  A. V. Efimov,et al.  Structure of α-α-hairpins with short connections , 1991 .

[25]  Charlotte M. Deane,et al.  JOY: protein sequence-structure representation and analysis , 1998, Bioinform..

[26]  M. Karplus,et al.  Conformational sampling using high‐temperature molecular dynamics , 1990, Biopolymers.

[27]  J. Wójcik,et al.  New efficient statistical sequence-dependent structure prediction of short to medium-sized protein loops based on an exhaustive loop classification. , 1999, Journal of molecular biology.

[28]  T. A. Jones,et al.  Using known substructures in protein model building and crystallography. , 1986, The EMBO journal.

[29]  A C Martin,et al.  Modeling antibody hypervariable loops: a combined algorithm. , 1989, Proceedings of the National Academy of Sciences of the United States of America.

[30]  L. Lai,et al.  Protein loops on structurally similar scaffolds: database and conformational analysis. , 1999, Biopolymers.

[31]  J. Kwasigroch,et al.  A global taxonomy of loops in globular proteins. , 1996, Journal of molecular biology.

[32]  B. L. Sibanda,et al.  Conformation of beta-hairpins in protein structures. A systematic classification with applications to modelling by homology, electron density fitting and protein engineering. , 1989, Journal of molecular biology.

[33]  F. Cohen,et al.  Taxonomy and conformational analysis of loops in proteins. , 1992, Journal of molecular biology.

[34]  T. Blundell,et al.  Knowledge based modelling of homologous proteins, Part I: Three-dimensional frameworks derived from the simultaneous superposition of multiple structures. , 1987, Protein engineering.

[35]  John P. Overington,et al.  Knowledge‐based protein modelling and design , 1988 .

[36]  John P. Overington,et al.  Fragment ranking in modelling of protein structure. Conformationally constrained environmental amino acid substitution tables. , 1993, Journal of molecular biology.