Literature DB >> 15572775

Towards complete validated models in the next generation of ARP/wARP.

Serge X Cohen1, Richard J Morris, Francisco J Fernandez, Marouane Ben Jelloul, Mattheos Kakaris, Venkataraman Parthasarathy, Victor S Lamzin, Gerard J Kleywegt, Anastassis Perrakis.   

Abstract

The design of a new versatile control system that will underlie future releases of the automated model-building package ARP/wARP is presented. A sophisticated expert system is under development that will transform ARP/wARP from a very useful model-building aid to a truly automated package capable of delivering complete, well refined and validated models comparable in quality to the result of intensive manual checking, rebuilding, hypothesis testing, refinement and validation cycles of an experienced crystallographer. In addition to the presentation of this control system, recent advances, ideas and future plans for improving the current model-building algorithms, especially for completing partially built models, are presented. Furthermore, a concept for integrating validation routines into the iterative model-building process is also presented.

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Year:  2004        PMID: 15572775     DOI: 10.1107/S0907444904027556

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


  96 in total

1.  Constructing and validating initial Cα models from subnanometer resolution density maps with pathwalking.

Authors:  Mariah R Baker; Ian Rees; Steven J Ludtke; Wah Chiu; Matthew L Baker
Journal:  Structure       Date:  2012-03-07       Impact factor: 5.006

2.  Bifidobacterium longum subsp. infantis ATCC 15697 α-fucosidases are active on fucosylated human milk oligosaccharides.

Authors:  David A Sela; Daniel Garrido; Larry Lerno; Shuai Wu; Kemin Tan; Hyun-Ju Eom; Andrzej Joachimiak; Carlito B Lebrilla; David A Mills
Journal:  Appl Environ Microbiol       Date:  2011-12-02       Impact factor: 4.792

3.  Lysozyme contamination facilitates crystallization of a heterotrimeric cortactin-Arg-lysozyme complex.

Authors:  Weizhi Liu; Stacey M MacGrath; Anthony J Koleske; Titus J Boggon
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2012-01-25

4.  The 1.4 A resolution structure of Paracoccus pantotrophus pseudoazurin.

Authors:  Shabir Najmudin; Sofia R Pauleta; Isabel Moura; Maria J Romão
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2010-05-25

5.  N. meningitidis 1681 is a member of the FinO family of RNA chaperones.

Authors:  Steven Chaulk; Jun Lu; Kemin Tan; David C Arthur; Ross A Edwards; Laura S Frost; Andrzej Joachimiak; J N Mark Glover
Journal:  RNA Biol       Date:  2010-11-01       Impact factor: 4.652

6.  Novel α-glucosidase from human gut microbiome: substrate specificities and their switch.

Authors:  Kemin Tan; Christine Tesar; Rosemarie Wilton; Laura Keigher; Gyorgy Babnigg; Andrzej Joachimiak
Journal:  FASEB J       Date:  2010-06-25       Impact factor: 5.191

7.  Insights into substrate specificity of geranylgeranyl reductases revealed by the structure of digeranylgeranylglycerophospholipid reductase, an essential enzyme in the biosynthesis of archaeal membrane lipids.

Authors:  Qingping Xu; Tadashi Eguchi; Irimpan I Mathews; Christopher L Rife; Hsiu-Ju Chiu; Carol L Farr; Julie Feuerhelm; Lukasz Jaroszewski; Heath E Klock; Mark W Knuth; Mitchell D Miller; Dana Weekes; Marc-André Elsliger; Ashley M Deacon; Adam Godzik; Scott A Lesley; Ian A Wilson
Journal:  J Mol Biol       Date:  2010-10-01       Impact factor: 5.469

8.  Structural studies of the spinosyn rhamnosyltransferase, SpnG.

Authors:  Eta A Isiorho; Hung-wen Liu; Adrian T Keatinge-Clay
Journal:  Biochemistry       Date:  2012-02-03       Impact factor: 3.162

9.  The closed MTIP-myosin A-tail complex from the malaria parasite invasion machinery.

Authors:  Jürgen Bosch; Stewart Turley; Claudia M Roach; Thomas M Daly; Lawrence W Bergman; Wim G J Hol
Journal:  J Mol Biol       Date:  2007-06-09       Impact factor: 5.469

10.  A beta-l-Arabinopyranosidase from Streptomyces avermitilis is a novel member of glycoside hydrolase family 27.

Authors:  Hitomi Ichinose; Zui Fujimoto; Mariko Honda; Koichi Harazono; Yukifumi Nishimoto; Atsuko Uzura; Satoshi Kaneko
Journal:  J Biol Chem       Date:  2009-07-16       Impact factor: 5.157

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