Literature DB >> 10666596

A stochastic approach to molecular replacement.

N M Glykos1, M Kokkinidis.   

Abstract

The classical approach to the problem of placing n copies of a search model in the asymmetric unit of a target crystal structure is to divide this 6n-dimensional optimization problem into a succession of three-dimensional searches (rotation-function followed by translation-function searches for each of the models). Here, it is shown that a structure-determination method based on a reverse Monte Carlo minimization of a suitably chosen statistic in the 6n-dimensional space defined by the rotational and translational parameters of the n molecules is both feasible and practical, at least for small n. Because all parameters of all molecules are determined simultaneously, this algorithm is expected to improve the signal-to-noise ratio in difficult cases involving high crystallographic/non-crystallographic symmetry in tightly packed crystal forms. Preliminary results from the application of this method (obtained with a space-group general computer program which has been developed for this purpose) are presented.

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Year:  2000        PMID: 10666596     DOI: 10.1107/s0907444999015322

Source DB:  PubMed          Journal:  Acta Crystallogr D Biol Crystallogr        ISSN: 0907-4449


  8 in total

1.  On the combination of molecular replacement and single-wavelength anomalous diffraction phasing for automated structure determination.

Authors:  Santosh Panjikar; Venkataraman Parthasarathy; Victor S Lamzin; Manfred S Weiss; Paul A Tucker
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-09-16

2.  MR-REX: molecular replacement by cooperative conformational search and occupancy optimization on low-accuracy protein models.

Authors:  Jouko J Virtanen; Yang Zhang
Journal:  Acta Crystallogr D Struct Biol       Date:  2018-06-08       Impact factor: 7.652

3.  Improved technologies now routinely provide protein NMR structures useful for molecular replacement.

Authors:  Binchen Mao; Rongjin Guan; Gaetano T Montelione
Journal:  Structure       Date:  2011-06-08       Impact factor: 5.006

4.  The JCSG MR pipeline: optimized alignments, multiple models and parallel searches.

Authors:  Robert Schwarzenbacher; Adam Godzik; Lukasz Jaroszewski
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2007-12-05

5.  Type II dehydroquinase: molecular replacement with many copies.

Authors:  Kirsty Anne Stewart; David Alexander Robinson; Adrian Jonathan Lapthorn
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2007-12-05

Review 6.  Molecular replacement then and now.

Authors:  Giovanna Scapin
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2013-10-18

7.  How far are we from automatic crystal structure solution via molecular-replacement techniques?

Authors:  Maria Cristina Burla; Benedetta Carrozzini; Giovanni Luca Cascarano; Carmelo Giacovazzo; Giampiero Polidori
Journal:  Acta Crystallogr D Struct Biol       Date:  2020-01-01       Impact factor: 7.652

8.  Phaser crystallographic software.

Authors:  Airlie J McCoy; Ralf W Grosse-Kunstleve; Paul D Adams; Martyn D Winn; Laurent C Storoni; Randy J Read
Journal:  J Appl Crystallogr       Date:  2007-07-13       Impact factor: 3.304

  8 in total

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