Literature DB >> 19700309

Recent developments in phasing and structure refinement for macromolecular crystallography.

Paul D Adams1, Pavel V Afonine, Ralf W Grosse-Kunstleve, Randy J Read, Jane S Richardson, David C Richardson, Thomas C Terwilliger.   

Abstract

Central to crystallographic structure solution is obtaining accurate phases in order to build a molecular model, ultimately followed by refinement of that model to optimize its fit to the experimental diffraction data and prior chemical knowledge. Recent advances in phasing and model refinement and validation algorithms make it possible to arrive at better electron density maps and more accurate models.

Entities:  

Mesh：

Substances：

Year:  2009        PMID： 19700309      PMCID： PMC2763973          DOI： 10.1016/j.sbi.2009.07.014

Source DB:  PubMed          Journal:  Curr Opin Struct Biol        ISSN： 0959-440X            Impact factor:   6.809


  59 in total

1.  SFCHECK: a unified set of procedures for evaluating the quality of macromolecular structure-factor data and their agreement with the atomic model.

Authors:  A A Vaguine; J Richelle; S J Wodak
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1999-01-01

2.  Substructure solution with SHELXD.

Authors:  Thomas R Schneider; George M Sheldrick
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2002-09-28

3.  The Uppsala Electron-Density Server.

Authors:  Gerard J Kleywegt; Mark R Harris; Jin Yu Zou; Thomas C Taylor; Anders Wählby; T Alwyn Jones
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2004-11-26

4.  Normal-mode refinement of anisotropic thermal parameters for potassium channel KcsA at 3.2 A crystallographic resolution.

Authors:  Xiaorui Chen; Billy K Poon; Athanasios Dousis; Qinghua Wang; Jianpeng Ma
Journal:  Structure       Date:  2007-08       Impact factor: 5.006

5.  Macromolecular structure solution by charge flipping.

Authors:  Christian Dumas; Arie van der Lee
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2008-07-17

6.  Automated MAD and MIR structure solution.

Authors:  T C Terwilliger; J Berendzen
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  1999-04

7.  Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard.

Authors:  Thomas C Terwilliger; Ralf W Grosse-Kunstleve; Pavel V Afonine; Nigel W Moriarty; Peter H Zwart; Li Wei Hung; Randy J Read; Paul D Adams
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2007-12-05

8.  BALBES: a molecular-replacement pipeline.

Authors:  Fei Long; Alexei A Vagin; Paul Young; Garib N Murshudov
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2007-12-05

9.  Exploiting the anisotropy of anomalous scattering boosts the phasing power of SAD and MAD experiments.

Authors:  Marc Schiltz; Gérard Bricogne
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2008-06-18

10.  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
View more
  13 in total

1.  Biocrystallography: past, present, future.

Authors:  Richard Giegé; Claude Sauter
Journal:  HFSP J       Date:  2010-04-22

2.  Ab initio structure solution of a proteolytic fragment using ARCIMBOLDO.

Authors:  Jan Abendroth; Banumathi Sankaran; Peter J Myler; Donald D Lorimer; Thomas E Edwards
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2018-08-29       Impact factor: 1.056

Review 3.  Advances, interactions, and future developments in the CNS, Phenix, and Rosetta structural biology software systems.

Authors:  Paul D Adams; David Baker; Axel T Brunger; Rhiju Das; Frank DiMaio; Randy J Read; David C Richardson; Jane S Richardson; Thomas C Terwilliger
Journal:  Annu Rev Biophys       Date:  2013-02-28       Impact factor: 12.981

4.  Intramolecular hydrogen-bonding in aqueous carbohydrates as a cause or consequence of conformational preferences: a molecular dynamics study of cellobiose stereoisomers.

Authors:  Dongqi Wang; Maria Lovísa Ámundadóttir; Wilfred F van Gunsteren; Philippe H Hünenberger
Journal:  Eur Biophys J       Date:  2013-05-10       Impact factor: 1.733

5.  Structural conservation of the myoviridae phage tail sheath protein fold.

Authors:  Anastasia A Aksyuk; Lidia P Kurochkina; Andrei Fokine; Farhad Forouhar; Vadim V Mesyanzhinov; Liang Tong; Michael G Rossmann
Journal:  Structure       Date:  2011-12-07       Impact factor: 5.006

6.  Crystal structure of arrestin-3 reveals the basis of the difference in receptor binding between two non-visual subtypes.

Authors:  Xuanzhi Zhan; Luis E Gimenez; Vsevolod V Gurevich; Benjamin W Spiller
Journal:  J Mol Biol       Date:  2011-01-06       Impact factor: 5.469

7.  With phases: how two wrongs can sometimes make a right.

Authors:  Pietro Roversi; Steven Johnson; Susan M Lea
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-03-24

8.  PHENIX: a comprehensive Python-based system for macromolecular structure solution.

Authors:  Paul D Adams; Pavel V Afonine; Gábor Bunkóczi; Vincent B Chen; Ian W Davis; Nathaniel Echols; Jeffrey J Headd; Li-Wei Hung; Gary J Kapral; Ralf W Grosse-Kunstleve; Airlie J McCoy; Nigel W Moriarty; Robert Oeffner; Randy J Read; David C Richardson; Jane S Richardson; Thomas C Terwilliger; Peter H Zwart
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-01-22

Review 9.  Computational Methodologies for Real-Space Structural Refinement of Large Macromolecular Complexes.

Authors:  Boon Chong Goh; Jodi A Hadden; Rafael C Bernardi; Abhishek Singharoy; Ryan McGreevy; Till Rudack; C Keith Cassidy; Klaus Schulten
Journal:  Annu Rev Biophys       Date:  2016-05-02       Impact factor: 12.981

10.  MolProbity: all-atom structure validation for macromolecular crystallography.

Authors:  Vincent B Chen; W Bryan Arendall; Jeffrey J Headd; Daniel A Keedy; Robert M Immormino; Gary J Kapral; Laura W Murray; Jane S Richardson; David C Richardson
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-12-21
View more

北京卡尤迪生物科技股份有限公司 © 2022-2023.