Literature DB >> 9008363

AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR.

R A Laskowski1, J A Rullmannn, M W MacArthur, R Kaptein, J M Thornton.   

Abstract

The AQUA and PROCHECK-NMR programs provide a means of validating the geometry and restraint violations of an ensemble of protein structures solved by solution NMR. The outputs include a detailed breakdown of the restraint violations, a number of plots in PostScript format and summary statistics. These various analyses indicate both the degree of agreement of the model structures with the experimental dat, and the quality of their geometrical properties. They are intended to be of use both to support ongoing NMR structure determination and in the validation of the final results.

Mesh:

Substances:

Year:  1996        PMID: 9008363     DOI: 10.1007/bf00228148

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


  13 in total

1.  Stereochemical quality of protein structure coordinates.

Authors:  A L Morris; M W MacArthur; E G Hutchinson; J M Thornton
Journal:  Proteins       Date:  1992-04

Review 2.  An evaluation of computational strategies for use in the determination of protein structure from distance constraints obtained by nuclear magnetic resonance.

Authors:  T F Havel
Journal:  Prog Biophys Mol Biol       Date:  1991       Impact factor: 3.667

3.  Efficient computation of three-dimensional protein structures in solution from nuclear magnetic resonance data using the program DIANA and the supporting programs CALIBA, HABAS and GLOMSA.

Authors:  P Güntert; W Braun; K Wüthrich
Journal:  J Mol Biol       Date:  1991-02-05       Impact factor: 5.469

4.  Protein solution structure determination using distances from two-dimensional nuclear Overhauser effect experiments: effect of approximations on the accuracy of derived structures.

Authors:  P D Thomas; V J Basus; T L James
Journal:  Proc Natl Acad Sci U S A       Date:  1991-02-15       Impact factor: 11.205

5.  MOLMOL: a program for display and analysis of macromolecular structures.

Authors:  R Koradi; M Billeter; K Wüthrich
Journal:  J Mol Graph       Date:  1996-02

6.  The Protein Data Bank: a computer-based archival file for macromolecular structures.

Authors:  F C Bernstein; T F Koetzle; G J Williams; E F Meyer; M D Brice; J R Rodgers; O Kennard; T Shimanouchi; M Tasumi
Journal:  J Mol Biol       Date:  1977-05-25       Impact factor: 5.469

7.  Exploring the limits of precision and accuracy of protein structures determined by nuclear magnetic resonance spectroscopy.

Authors:  G M Clore; M A Robien; A M Gronenborn
Journal:  J Mol Biol       Date:  1993-05-05       Impact factor: 5.469

8.  Conformational analysis of protein structures derived from NMR data.

Authors:  M W MacArthur; J M Thornton
Journal:  Proteins       Date:  1993-11

9.  Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.

Authors:  W Kabsch; C Sander
Journal:  Biopolymers       Date:  1983-12       Impact factor: 2.505

10.  An assessment of the precision and accuracy of protein structures determined by NMR. Dependence on distance errors.

Authors:  D Zhao; O Jardetzky
Journal:  J Mol Biol       Date:  1994-06-24       Impact factor: 5.469

View more
  1827 in total

1.  A novel mechanism of PKA anchoring revealed by solution structures of anchoring complexes.

Authors:  M G Newlon; M Roy; D Morikis; D W Carr; R Westphal; J D Scott; P A Jennings
Journal:  EMBO J       Date:  2001-04-02       Impact factor: 11.598

2.  Designed protein G core variants fold to native-like structures: sequence selection by ORBIT tolerates variation in backbone specification.

Authors:  S A Ross; C A Sarisky; A Su; S L Mayo
Journal:  Protein Sci       Date:  2001-02       Impact factor: 6.725

3.  Unraveling the symmetry ambiguity in a hexamer: calculation of the R6 human insulin structure.

Authors:  S I O'Donoghue; X Chang; R Abseher; M Nilges; J J Led
Journal:  J Biomol NMR       Date:  2000-02       Impact factor: 2.835

4.  Refinement of the protein backbone angle psi in NMR structure calculations.

Authors:  R Sprangers; M J Bottomley; J P Linge; J Schultz; M Nilges; M Sattler
Journal:  J Biomol NMR       Date:  2000-01       Impact factor: 2.835

5.  Solution structure of the human BTK SH3 domain complexed with a proline-rich peptide from p120cbl.

Authors:  S R Tzeng; Y C Lou; M T Pai; M L Jain; J W Cheng
Journal:  J Biomol NMR       Date:  2000-04       Impact factor: 2.835

6.  The structure and dynamics in solution of Cu(I) pseudoazurin from Paracoccus pantotrophus.

Authors:  G S Thompson; Y C Leung; S J Ferguson; S E Radford; C Redfield
Journal:  Protein Sci       Date:  2000-05       Impact factor: 6.725

7.  Rotamer strain as a determinant of protein structural specificity.

Authors:  G A Lazar; E C Johnson; J R Desjarlais; T M Handel
Journal:  Protein Sci       Date:  1999-12       Impact factor: 6.725

8.  Validation of a new restraint docking method for solution structure determinations of protein-ligand complexes.

Authors:  V I Polshakov; W D Morgan; B Birdsall; J Feeney
Journal:  J Biomol NMR       Date:  1999-06       Impact factor: 2.835

9.  Completeness of NOEs in protein structure: a statistical analysis of NMR.

Authors:  J F Doreleijers; M L Raves; T Rullmann; R Kaptein
Journal:  J Biomol NMR       Date:  1999-06       Impact factor: 2.835

10.  Variability in automated assignment of NOESY spectra and three-dimensional structure determination: a test case on three small disulfide-bonded proteins.

Authors:  P Savarin; S Zinn-Justin; B Gilquin
Journal:  J Biomol NMR       Date:  2001-01       Impact factor: 2.835

View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.