Literature DB >> 24587790

The geometry of Niggli reduction: SAUC - search of alternative unit cells.

Keith J McGill1, Mojgan Asadi1, Maria T Karakasheva1, Lawrence C Andrews2, Herbert J Bernstein1.   

Abstract

A database of lattices using the G6 representation of the Niggli-reduced cell as the search key provides a more robust and complete search than older techniques. Searching is implemented by finding the distance from the probe cell to other cells using a topological embedding of the Niggli reduction in G6, so that all cells representing similar lattices will be found. The embedding provides the first fully linear measure of distances between unit cells. Comparison of results with those from older cell-based search algorithms suggests significant value in the new approach.

Keywords:  Bravais lattice determination; Niggli reduction; computer programs

Year:  2014        PMID: 24587790      PMCID: PMC3937814          DOI: 10.1107/S1600576713031014

Source DB:  PubMed          Journal:  J Appl Crystallogr        ISSN: 0021-8898            Impact factor:   3.304


  9 in total

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Authors:  Isolde Le Trong; Ronald E Stenkamp
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2007-03-16

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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

3.  Crystal structure of a carbohydrate induced homodimer of phospholipase A2 from Bungarus caeruleus at 2.1A resolution.

Authors:  Garima Singh; S Gourinath; K Sarvanan; Sujata Sharma; S Bhanumathi; Ch Betzel; Savita Yadav; A Srinivasan; T P Singh
Journal:  J Struct Biol       Date:  2005-03       Impact factor: 2.867

4.  The geometry of Niggli reduction: BGAOL -embedding Niggli reduction and analysis of boundaries.

Authors:  Lawrence C Andrews; Herbert J Bernstein
Journal:  J Appl Crystallogr       Date:  2014-01-30       Impact factor: 3.304

5.  Sequence-induced trimerization of phospholipase A2: structure of a trimeric isoform of PLA2 from common krait (Bungarus caeruleus) at 2.5 A resolution.

Authors:  Garima Singh; S Gourinath; K Saravanan; Sujata Sharma; S Bhanumathi; Ch Betzel; A Srinivasan; T P Singh
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2004-10-16

6.  Passive acquisition of ligand by the MopII molbindin from Clostridium pasteurianum: structures of apo and oxyanion-bound forms.

Authors:  Alexander W Schüttelkopf; Jennifer A Harrison; David H Boxer; William N Hunter
Journal:  J Biol Chem       Date:  2002-02-08       Impact factor: 5.157

7.  Sequence and crystal structure determination of a basic phospholipase A2 from common krait (Bungarus caeruleus) at 2.4 A resolution: identification and characterization of its pharmacological sites.

Authors:  G Singh; S Gourinath; S Sharma; M Paramasivam; A Srinivasan; T P Singh
Journal:  J Mol Biol       Date:  2001-04-06       Impact factor: 5.469

8.  WebCSD: the online portal to the Cambridge Structural Database.

Authors:  Ian R Thomas; Ian J Bruno; Jason C Cole; Clare F Macrae; Elna Pidcock; Peter A Wood
Journal:  J Appl Crystallogr       Date:  2010-02-12       Impact factor: 3.304

9.  Nearest-cell: a fast and easy tool for locating crystal matches in the PDB.

Authors:  V Ramraj; G Evans; J M Diprose; R M Esnouf
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2012-11-09
  9 in total
  7 in total

1.  The geometry of Niggli reduction: BGAOL -embedding Niggli reduction and analysis of boundaries.

Authors:  Lawrence C Andrews; Herbert J Bernstein
Journal:  J Appl Crystallogr       Date:  2014-01-30       Impact factor: 3.304

2.  NearTree, a data structure and a software toolkit for the nearest-neighbor problem.

Authors:  Lawrence C Andrews; Herbert J Bernstein
Journal:  J Appl Crystallogr       Date:  2016-04-12       Impact factor: 3.304

3.  Data Exploration Toolkit for serial diffraction experiments.

Authors:  Oliver B Zeldin; Aaron S Brewster; Johan Hattne; Monarin Uervirojnangkoorn; Artem Y Lyubimov; Qiangjun Zhou; Minglei Zhao; William I Weis; Nicholas K Sauter; Axel T Brunger
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2015-01-23

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Authors:  Jason C Cole; Colin R Groom; Murray G Read; Ilenia Giangreco; Patrick McCabe; Anthony M Reilly; Gregory P Shields
Journal:  Acta Crystallogr B Struct Sci Cryst Eng Mater       Date:  2016-07-16

5.  Challenge data set for macromolecular multi-microcrystallography.

Authors:  James M Holton
Journal:  Acta Crystallogr D Struct Biol       Date:  2019-02-06       Impact factor: 7.652

6.  ID23-2: an automated and high-performance microfocus beamline for macromolecular crystallography at the ESRF.

Authors:  Max Nanao; Shibom Basu; Ulrich Zander; Thierry Giraud; John Surr; Matias Guijarro; Mario Lentini; Franck Felisaz; Jeremy Sinoir; Christian Morawe; Amparo Vivo; Antonia Beteva; Marcus Oscarsson; Hugo Caserotto; Fabien Dobias; David Flot; Didier Nurizzo; Jonathan Gigmes; Nicolas Foos; Ralf Siebrecht; Thomas Roth; Pascal Theveneau; Olof Svensson; Gergely Papp; Bernard Lavault; Florent Cipriani; Ray Barrett; Carole Clavel; Gordon Leonard
Journal:  J Synchrotron Radiat       Date:  2022-02-22       Impact factor: 2.616

7.  SIMBAD: a sequence-independent molecular-replacement pipeline.

Authors:  Adam J Simpkin; Felix Simkovic; Jens M H Thomas; Martin Savko; Andrey Lebedev; Ville Uski; Charles Ballard; Marcin Wojdyr; Rui Wu; Ruslan Sanishvili; Yibin Xu; María Natalia Lisa; Alejandro Buschiazzo; William Shepard; Daniel J Rigden; Ronan M Keegan
Journal:  Acta Crystallogr D Struct Biol       Date:  2018-06-08       Impact factor: 7.652

  7 in total

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