Literature DB >> 1418827

Conjugate-direction minimization: an improved method for the refinement of macromolecules.

D E Tronrud1.   

Abstract

A novel method of function minimization that combines the power of the diagonal approximation to the normal matrix with conjugate directions is described. This method approaches closer to the local minimum than the methods that are commonly used in macromolecular refinement. The weakness of the current methods are analyzed to explain the advantage of the conjugate-direction method.

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Year:  1992        PMID： 1418827     DOI： 10.1107/s0108767392005415

Source DB:  PubMed          Journal:  Acta Crystallogr A        ISSN： 0108-7673            Impact factor:   2.290


  22 in total

1.  Structure and stability effects of mutations designed to increase the primary sequence symmetry within the core region of a beta-trefoil.

Authors:  S R Brych; S I Blaber; T M Logan; M Blaber
Journal:  Protein Sci       Date:  2001-12       Impact factor: 6.725

2.  Accommodation of a highly symmetric core within a symmetric protein superfold.

Authors:  Stephen R Brych; Jaewon Kim; Timothy M Logan; Michael Blaber
Journal:  Protein Sci       Date:  2003-12       Impact factor: 6.725

3.  Using a conformation-dependent stereochemical library improves crystallographic refinement of proteins.

Authors:  Dale E Tronrud; Donald S Berkholz; P Andrew Karplus
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-06-19

4.  Crystal structure of an engineered Cro monomer bound nonspecifically to DNA: possible implications for nonspecific binding by the wild-type protein.

Authors:  R A Albright; M C Mossing; B W Matthews
Journal:  Protein Sci       Date:  1998-07       Impact factor: 6.725

5.  Structure of cubic insulin crystals in glucose solutions.

Authors:  B Yu; D L Caspar
Journal:  Biophys J       Date:  1998-01       Impact factor: 4.033

6.  Alternative type I and I' turn conformations in the beta8/beta9 beta-hairpin of human acidic fibroblast growth factor.

Authors:  Jaewon Kim; Sachiko I Blaber; Michael Blaber
Journal:  Protein Sci       Date:  2002-03       Impact factor: 6.725

7.  Structure and function of the N-linked glycans of HBP/CAP37/azurocidin: crystal structure determination and biological characterization of nonglycosylated HBP.

Authors:  L F Iversen; J S Kastrup; S E Bjørn; F C Wiberg; I K Larsen; H J Flodgaard; P B Rasmussen
Journal:  Protein Sci       Date:  1999-10       Impact factor: 6.725

8.  Deleterious effects of beta-branched residues in the S1 specificity pocket of Streptomyces griseus proteinase B (SGPB): crystal structures of the turkey ovomucoid third domain variants Ile18I, Val18I, Thr18I, and Ser18I in complex with SGPB.

Authors:  K S Bateman; S Anderson; W Lu; M A Qasim; M Laskowski; M N James
Journal:  Protein Sci       Date:  2000-01       Impact factor: 6.725

9.  Refinement of the structure of human basic fibroblast growth factor at 1.6 A resolution and analysis of presumed heparin binding sites by selenate substitution.

Authors:  A E Eriksson; L S Cousens; B W Matthews
Journal:  Protein Sci       Date:  1993-08       Impact factor: 6.725

10.  Evaluation at atomic resolution of the role of strain in destabilizing the temperature-sensitive T4 lysozyme mutant Arg 96 --> His.

Authors:  Blaine H M Mooers; Dale E Tronrud; Brian W Matthews
Journal:  Protein Sci       Date:  2009-05       Impact factor: 6.725
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