Literature DB >> 12520049

CADB: Conformation Angles DataBase of proteins.

S S Sheik1, P Ananthalakshmi, G Ramya Bhargavi, K Sekar.   

Abstract

Conformation Angles DataBase (CADB) provides an online resource to access data on conformation angles (both main-chain and side-chain) of protein structures in two data sets corresponding to 25% and 90% sequence identity between any two proteins, available in the Protein Data Bank. In addition, the database contains the necessary crystallographic parameters. The package has several flexible options and display facilities to visualize the main-chain and side-chain conformation angles for a particular amino acid residue. The package can also be used to study the interrelationship between the main-chain and side-chain conformation angles. A web based JAVA graphics interface has been deployed to display the user interested information on the client machine. The database is being updated at regular intervals and can be accessed over the World Wide Web interface at the following URL: http://144.16.71.148/cadb/.

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Year:  2003        PMID： 12520049      PMCID： PMC165531          DOI： 10.1093/nar/gkg084

Source DB:  PubMed          Journal:  Nucleic Acids Res        ISSN： 0305-1048            Impact factor:   16.971


  13 in total

1.  The penultimate rotamer library.

Authors:  S C Lovell; J M Word; J S Richardson; D C Richardson
Journal:  Proteins       Date:  2000-08-15

2.  The Protein Data Bank: unifying the archive.

Authors:  John Westbrook; Zukang Feng; Shri Jain; T N Bhat; Narmada Thanki; Veerasamy Ravichandran; Gary L Gilliland; Wolfgang Bluhm; Helge Weissig; Douglas S Greer; Philip E Bourne; Helen M Berman
Journal:  Nucleic Acids Res       Date:  2002-01-01       Impact factor: 16.971

3.  Prediction of protein side chain conformations: a study on the influence of backbone accuracy on conformation stability in the rotamer space.

Authors:  P Tufféry; C Etchebest; S Hazout
Journal:  Protein Eng       Date:  1997-04

4.  Bayesian statistical analysis of protein side-chain rotamer preferences.

Authors:  R L Dunbrack; F E Cohen
Journal:  Protein Sci       Date:  1997-08       Impact factor: 6.725

5.  Prediction of protein side-chain rotamers from a backbone-dependent rotamer library: a new homology modeling tool.

Authors:  M J Bower; F E Cohen; R L Dunbrack
Journal:  J Mol Biol       Date:  1997-04-18       Impact factor: 5.469

6.  Tertiary templates for proteins. Use of packing criteria in the enumeration of allowed sequences for different structural classes.

Authors:  J W Ponder; F M Richards
Journal:  J Mol Biol       Date:  1987-02-20       Impact factor: 5.469

7.  Construction of a three-dimensional model of the polypeptide backbone of the variable region of kappa immunoglobulin light chains.

Authors:  E A Kabat; T T Wu
Journal:  Proc Natl Acad Sci U S A       Date:  1972-04       Impact factor: 11.205

8.  The influence of nearest-neighboring amino acid residues on aspects of secondary structure of proteins. Attempts to locate -helices and -sheets.

Authors:  E A Kabat; T T Wu
Journal:  Biopolymers       Date:  1973-04       Impact factor: 2.505

9.  IUPAC-IUB Commission on Biochemical Nomenclature. Abbreviations and symbols for the description of the conformation of polypeptide chains.

Authors: 
Journal:  J Mol Biol       Date:  1970-08-28       Impact factor: 5.469

10.  An attempt to locate the non-helical and permissively helical sequences of proteins: application to the variable regions of immunoglobulin light and heavy chains.

Authors:  T T Wu; E A Kabat
Journal:  Proc Natl Acad Sci U S A       Date:  1971-07       Impact factor: 11.205
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  3 in total

1.  Dihedral-angle information entropy as a gauge of secondary structure propensity.

Authors:  Shi Zhong; Jeremy M Moix; Stephen Quirk; Rigoberto Hernandez
Journal:  Biophys J       Date:  2006-09-15       Impact factor: 4.033

2.  Protein Geometry Database: a flexible engine to explore backbone conformations and their relationships to covalent geometry.

Authors:  Donald S Berkholz; Peter B Krenesky; John R Davidson; P Andrew Karplus
Journal:  Nucleic Acids Res       Date:  2009-11-11       Impact factor: 16.971

3.  Analysis and validation of carbohydrate three-dimensional structures.

Authors:  Thomas Lütteke
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-01-20
  3 in total

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