Literature DB >> 19339173

Hybrid approaches: applying computational methods in cryo-electron microscopy.

Steffen Lindert1, Phoebe L Stewart, Jens Meiler.   

Abstract

Recent advances in cryo-electron microscopy have led to an increasing number of high (3-5A) to medium (5-10A) resolution cryoEM density maps. These density maps contain valuable information about the protein structure but frequently require computational algorithms to aid their structural interpretation. It is these hybrid approaches between cryoEM and computational protein structure prediction algorithms that will shape protein structure elucidation from density maps.

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Year:  2009        PMID: 19339173      PMCID: PMC2726835          DOI: 10.1016/j.sbi.2009.02.010

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


  50 in total

1.  Protein secondary structure prediction based on position-specific scoring matrices.

Authors:  D T Jones
Journal:  J Mol Biol       Date:  1999-09-17       Impact factor: 5.469

2.  Situs: A package for docking crystal structures into low-resolution maps from electron microscopy.

Authors:  W Wriggers; R A Milligan; J A McCammon
Journal:  J Struct Biol       Date:  1999 Apr-May       Impact factor: 2.867

3.  De novo prediction of three-dimensional structures for major protein families.

Authors:  Richard Bonneau; Charlie E M Strauss; Carol A Rohl; Dylan Chivian; Phillip Bradley; Lars Malmström; Tim Robertson; David Baker
Journal:  J Mol Biol       Date:  2002-09-06       Impact factor: 5.469

4.  Transmembrane proteins in the Protein Data Bank: identification and classification.

Authors:  Gábor E Tusnády; Zsuzsanna Dosztányi; István Simon
Journal:  Bioinformatics       Date:  2004-06-04       Impact factor: 6.937

5.  A Structural-informatics approach for tracing beta-sheets: building pseudo-C(alpha) traces for beta-strands in intermediate-resolution density maps.

Authors:  Yifei Kong; Xing Zhang; Timothy S Baker; Jianpeng Ma
Journal:  J Mol Biol       Date:  2004-05-21       Impact factor: 5.469

6.  Toward high-resolution de novo structure prediction for small proteins.

Authors:  Philip Bradley; Kira M S Misura; David Baker
Journal:  Science       Date:  2005-09-16       Impact factor: 47.728

7.  Near-atomic resolution using electron cryomicroscopy and single-particle reconstruction.

Authors:  Xing Zhang; Ethan Settembre; Chen Xu; Philip R Dormitzer; Richard Bellamy; Stephen C Harrison; Nikolaus Grigorieff
Journal:  Proc Natl Acad Sci U S A       Date:  2008-01-31       Impact factor: 11.205

8.  Predicting protein structure using hidden Markov models.

Authors:  K Karplus; K Sjölander; C Barrett; M Cline; D Haussler; R Hughey; L Holm; C Sander
Journal:  Proteins       Date:  1997

9.  The atomic structure of rice dwarf virus reveals the self-assembly mechanism of component proteins.

Authors:  Atsushi Nakagawa; Naoyuki Miyazaki; Junichiro Taka; Hisashi Naitow; Akira Ogawa; Zui Fujimoto; Hiroshi Mizuno; Takahiko Higashi; Yasuo Watanabe; Toshihiro Omura; R Holland Cheng; Tomitake Tsukihara
Journal:  Structure       Date:  2003-10       Impact factor: 5.006

10.  Refinement of protein structures by iterative comparative modeling and CryoEM density fitting.

Authors:  Maya Topf; Matthew L Baker; Marc A Marti-Renom; Wah Chiu; Andrej Sali
Journal:  J Mol Biol       Date:  2006-02-02       Impact factor: 5.469

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  24 in total

1.  Ab initio protein modeling into CryoEM density maps using EM-Fold.

Authors:  Steffen Lindert; Tommy Hofmann; Nils Wötzel; Mert Karakaş; Phoebe L Stewart; Jens Meiler
Journal:  Biopolymers       Date:  2012-02-03       Impact factor: 2.505

2.  Fitting multimeric protein complexes into electron microscopy maps using 3D Zernike descriptors.

Authors:  Juan Esquivel-Rodríguez; Daisuke Kihara
Journal:  J Phys Chem B       Date:  2012-03-30       Impact factor: 2.991

3.  Integrative structure modeling of macromolecular assemblies from proteomics data.

Authors:  Keren Lasker; Jeremy L Phillips; Daniel Russel; Javier Velázquez-Muriel; Dina Schneidman-Duhovny; Elina Tjioe; Ben Webb; Avner Schlessinger; Andrej Sali
Journal:  Mol Cell Proteomics       Date:  2010-05-27       Impact factor: 5.911

4.  Consensus among flexible fitting approaches improves the interpretation of cryo-EM data.

Authors:  Aqeel Ahmed; Paul C Whitford; Karissa Y Sanbonmatsu; Florence Tama
Journal:  J Struct Biol       Date:  2011-10-13       Impact factor: 2.867

5.  Using NMR Chemical Shifts and Cryo-EM Density Restraints in Iterative Rosetta-MD Protein Structure Refinement.

Authors:  Sumudu P Leelananda; Steffen Lindert
Journal:  J Chem Inf Model       Date:  2019-12-24       Impact factor: 4.956

6.  Modeling protein assemblies in the proteome.

Authors:  Guray Kuzu; Ozlem Keskin; Ruth Nussinov; Attila Gursoy
Journal:  Mol Cell Proteomics       Date:  2014-01-20       Impact factor: 5.911

7.  Structural and mechanistic insights into human splicing factor SF3b complex derived using an integrated approach guided by the cryo-EM density maps.

Authors:  Ramachandran Rakesh; Agnel Praveen Joseph; Ramachandra M Bhaskara; Narayanaswamy Srinivasan
Journal:  RNA Biol       Date:  2016-08-11       Impact factor: 4.652

8.  EM-fold: De novo folding of alpha-helical proteins guided by intermediate-resolution electron microscopy density maps.

Authors:  Steffen Lindert; René Staritzbichler; Nils Wötzel; Mert Karakaş; Phoebe L Stewart; Jens Meiler
Journal:  Structure       Date:  2009-07-15       Impact factor: 5.006

Review 9.  Practically useful: what the Rosetta protein modeling suite can do for you.

Authors:  Kristian W Kaufmann; Gordon H Lemmon; Samuel L Deluca; Jonathan H Sheehan; Jens Meiler
Journal:  Biochemistry       Date:  2010-04-13       Impact factor: 3.162

10.  A fast mathematical programming procedure for simultaneous fitting of assembly components into cryoEM density maps.

Authors:  Shihua Zhang; Daven Vasishtan; Min Xu; Maya Topf; Frank Alber
Journal:  Bioinformatics       Date:  2010-06-15       Impact factor: 6.937

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