Literature DB >> 16002620

Inferential structure determination.

Wolfgang Rieping1, Michael Habeck, Michael Nilges.   

Abstract

Macromolecular structures calculated from nuclear magnetic resonance data are not fully determined by experimental data but depend on subjective choices in data treatment and parameter settings. This makes it difficult to objectively judge the precision of the structures. We used Bayesian inference to derive a probability distribution that represents the unknown structure and its precision. This probability distribution also determines additional unknowns, such as theory parameters, that previously had to be chosen empirically. We implemented this approach by using Markov chain Monte Carlo techniques. Our method provides an objective figure of merit and improves structural quality.

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Year:  2005        PMID: 16002620     DOI: 10.1126/science.1110428

Source DB:  PubMed          Journal:  Science        ISSN: 0036-8075            Impact factor:   47.728


  124 in total

1.  A Bayesian approach for determining protein side-chain rotamer conformations using unassigned NOE data.

Authors:  Jianyang Zeng; Kyle E Roberts; Pei Zhou; Bruce Randall Donald
Journal:  J Comput Biol       Date:  2011-10-04       Impact factor: 1.479

2.  Accurate protein structure modeling using sparse NMR data and homologous structure information.

Authors:  James M Thompson; Nikolaos G Sgourakis; Gaohua Liu; Paolo Rossi; Yuefeng Tang; Jeffrey L Mills; Thomas Szyperski; Gaetano T Montelione; David Baker
Journal:  Proc Natl Acad Sci U S A       Date:  2012-06-04       Impact factor: 11.205

Review 3.  A community resource of experimental data for NMR / X-ray crystal structure pairs.

Authors:  John K Everett; Roberto Tejero; Sarath B K Murthy; Thomas B Acton; James M Aramini; Michael C Baran; Jordi Benach; John R Cort; Alexander Eletsky; Farhad Forouhar; Rongjin Guan; Alexandre P Kuzin; Hsiau-Wei Lee; Gaohua Liu; Rajeswari Mani; Binchen Mao; Jeffrey L Mills; Alexander F Montelione; Kari Pederson; Robert Powers; Theresa Ramelot; Paolo Rossi; Jayaraman Seetharaman; David Snyder; G V T Swapna; Sergey M Vorobiev; Yibing Wu; Rong Xiao; Yunhuang Yang; Cheryl H Arrowsmith; John F Hunt; Michael A Kennedy; James H Prestegard; Thomas Szyperski; Liang Tong; Gaetano T Montelione
Journal:  Protein Sci       Date:  2015-09-22       Impact factor: 6.725

4.  Bayesian Weighing of Electron Cryo-Microscopy Data for Integrative Structural Modeling.

Authors:  Massimiliano Bonomi; Samuel Hanot; Charles H Greenberg; Andrej Sali; Michael Nilges; Michele Vendruscolo; Riccardo Pellarin
Journal:  Structure       Date:  2018-11-01       Impact factor: 5.006

5.  Inferential backbone assignment for sparse data.

Authors:  Olga Vitek; Chris Bailey-Kellogg; Bruce Craig; Jan Vitek
Journal:  J Biomol NMR       Date:  2006-07       Impact factor: 2.835

6.  Weighting of experimental evidence in macromolecular structure determination.

Authors:  Michael Habeck; Wolfgang Rieping; Michael Nilges
Journal:  Proc Natl Acad Sci U S A       Date:  2006-01-30       Impact factor: 11.205

7.  An automated assignment-free Bayesian approach for accurately identifying proton contacts from NOESY data.

Authors:  Ling-Hong Hung; Ram Samudrala
Journal:  J Biomol NMR       Date:  2006-10-03       Impact factor: 2.835

8.  The expanded FindCore method for identification of a core atom set for assessment of protein structure prediction.

Authors:  David A Snyder; Jennifer Grullon; Yuanpeng J Huang; Roberto Tejero; Gaetano T Montelione
Journal:  Proteins       Date:  2014-02

9.  White matter pathology isolates the hippocampal formation in Alzheimer's disease.

Authors:  D H Salat; D S Tuch; A J W van der Kouwe; D N Greve; V Pappu; S Y Lee; N D Hevelone; A K Zaleta; J H Growdon; S Corkin; B Fischl; H D Rosas
Journal:  Neurobiol Aging       Date:  2010-02       Impact factor: 4.673

10.  Flexible backbone sampling methods to model and design protein alternative conformations.

Authors:  Noah Ollikainen; Colin A Smith; James S Fraser; Tanja Kortemme
Journal:  Methods Enzymol       Date:  2013       Impact factor: 1.600

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