Warning: Undefined array key "mm" in /www/wwwroot/www.ai-bt.com/si.php on line 10 Deprecated: trim(): Passing null to parameter #1 ($string) of type string is deprecated in /www/wwwroot/www.ai-bt.com/si.php on line 10 DipoCoup: A versatile program for 3D-structure homology comparison based on residual dipolar couplings and pseudocontact shifts.

Literature DB >> 11014592

DipoCoup: A versatile program for 3D-structure homology comparison based on residual dipolar couplings and pseudocontact shifts.

Abstract

A program, DipoCoup, is presented that allows to search the protein data bank for proteins which have a three dimensional fold that is at least partially homologous to a protein under investigation. The three dimensional homology search uses secondary structure alignment based on chemical shifts and dipolar couplings or pseudocontact shifts for the three dimensional orientation of secondary structure elements. Moreover, the program offers additional tools for handling and analyzing dipolar couplings.

Mesh：

Substances：

Year: 2000 PMID： 11014592 DOI： 10.1023/a:1008362931964

Source DB: PubMed Journal: J Biomol NMR ISSN： 0925-2738 Impact factor: 2.835

25 in total

1. Domain orientation and dynamics in multidomain proteins from residual dipolar couplings.

Authors: M W Fischer; J A Losonczi; J L Weaver; J H Prestegard
Journal: Biochemistry Date: 1999-07-13 Impact factor: 3.162

2. A new approach for applying residual dipolar couplings as restraints in structure elucidation.

Authors: J Meiler; N Blomberg; M Nilges; C Griesinger
Journal: J Biomol NMR Date: 2000-03 Impact factor: 2.835

3. Induced alignment and measurement of dipolar couplings of an SH2 domain through direct binding with filamentous phage.

Authors: D Dahlke Ojennus; R M Mitton-Fry; D S Wuttke
Journal: J Biomol NMR Date: 1999-06 Impact factor: 2.835

Review 4. The helix-turn-helix DNA binding motif.

Authors: R G Brennan; B W Matthews
Journal: J Biol Chem Date: 1989-02-05 Impact factor: 5.157

Review 5. 100,000 protein structures for the biologist.

Authors: A Sali
Journal: Nat Struct Biol Date: 1998-12

6. A robust method for determining the magnitude of the fully asymmetric alignment tensor of oriented macromolecules in the absence of structural information.

Authors: G M Clore; A M Gronenborn; A Bax
Journal: J Magn Reson Date: 1998-07 Impact factor: 2.229

7. High-resolution heteronuclear NMR of human ubiquitin in an aqueous liquid crystalline medium.

Authors: A Bax; N Tjandra
Journal: J Biomol NMR Date: 1997-10 Impact factor: 2.835

8. The NMR solution conformation of unligated human cyclophilin A.

Authors: M Ottiger; O Zerbe; P Güntert; K Wüthrich
Journal: J Mol Biol Date: 1997-09-12 Impact factor: 5.469

9. A Kazal-type inhibitor with thrombin specificity from Rhodnius prolixus.

Authors: T Friedrich; B Kröger; S Bialojan; H G Lemaire; H W Höffken; P Reuschenbach; M Otte; J Dodt
Journal: J Biol Chem Date: 1993-08-05 Impact factor: 5.157

10. Order matrix analysis of residual dipolar couplings using singular value decomposition.

Authors: J A Losonczi; M Andrec; M W Fischer; J H Prestegard
Journal: J Magn Reson Date: 1999-06 Impact factor: 2.229

26 in total

1. Protein backbone structure determination using only residual dipolar couplings from one ordering medium.

Authors: M Andrec; P Du; R M Levy
Journal: J Biomol NMR Date: 2001-12 Impact factor: 2.835

2. Secondary chemical shifts in immobilized peptides and proteins: a qualitative basis for structure refinement under magic angle spinning.

Authors: S Luca; D V Filippov; J H van Boom; H Oschkinat; H J de Groot; M Baldus
Journal: J Biomol NMR Date: 2001-08 Impact factor: 2.835

DipoCoup: A versatile program for 3D-structure homology comparison based on residual dipolar couplings and pseudocontact shifts.

1. Domain orientation and dynamics in multidomain proteins from residual dipolar couplings.

2. A new approach for applying residual dipolar couplings as restraints in structure elucidation.

3. Induced alignment and measurement of dipolar couplings of an SH2 domain through direct binding with filamentous phage.

Review 4. The helix-turn-helix DNA binding motif.

Review 5. 100,000 protein structures for the biologist.

6. A robust method for determining the magnitude of the fully asymmetric alignment tensor of oriented macromolecules in the absence of structural information.

7. High-resolution heteronuclear NMR of human ubiquitin in an aqueous liquid crystalline medium.

8. The NMR solution conformation of unligated human cyclophilin A.

9. A Kazal-type inhibitor with thrombin specificity from Rhodnius prolixus.

10. Order matrix analysis of residual dipolar couplings using singular value decomposition.

1. Protein backbone structure determination using only residual dipolar couplings from one ordering medium.

2. Secondary chemical shifts in immobilized peptides and proteins: a qualitative basis for structure refinement under magic angle spinning.

3. A novel interactive tool for rigid-body modeling of multi-domain macromolecules using residual dipolar couplings.

4. Rapid protein fold determination using unassigned NMR data.

5. Protein structure prediction using sparse dipolar coupling data.

Review 6. Applications of NMR to structure-based drug design in structural genomics.

7. Complete protein structure determination using backbone residual dipolar couplings and sidechain rotamer prediction.

Review 8. Weak alignment offers new NMR opportunities to study protein structure and dynamics.

9. Determination of residual dipolar couplings in homonuclear MOCCA-SIAM experiments.

10. A thorough dynamic interpretation of residual dipolar couplings in ubiquitin.