Literature DB >> 32422044

Practical Considerations for Atomistic Structure Modeling with Cryo-EM Maps.

Doo Nam Kim1, Dominik Gront2, Karissa Y Sanbonmatsu3,4.   

Abstract

We describe common approaches to atomistic structure modeling with single particle analysis derived cryo-EM maps. Several strategies for atomistic model building and atomistic model fitting methods are discussed, including selection criteria and implementation procedures. In covering basic concepts and caveats, this short perspective aims to help facilitate active discussion between scientists at different levels with diverse backgrounds.

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Year:  2020        PMID： 32422044      PMCID： PMC7891309          DOI： 10.1021/acs.jcim.0c00090

Source DB:  PubMed          Journal:  J Chem Inf Model        ISSN： 1549-9596            Impact factor:   4.956


  62 in total

1.  Quantitative analysis of cryo-EM density map segmentation by watershed and scale-space filtering, and fitting of structures by alignment to regions.

Authors:  Grigore D Pintilie; Junjie Zhang; Thomas D Goddard; Wah Chiu; David C Gossard
Journal:  J Struct Biol       Date:  2010-03-23       Impact factor: 2.867

2.  Protein homology detection by HMM-HMM comparison.

Authors:  Johannes Söding
Journal:  Bioinformatics       Date:  2004-11-05       Impact factor: 6.937

3.  Small-molecule ligand docking into comparative models with Rosetta.

Authors:  Steven A Combs; Samuel L Deluca; Stephanie H Deluca; Gordon H Lemmon; David P Nannemann; Elizabeth D Nguyen; Jordan R Willis; Jonathan H Sheehan; Jens Meiler
Journal:  Nat Protoc       Date:  2013-06-06       Impact factor: 13.491

4.  Structures of the bacterial ribosome in classical and hybrid states of tRNA binding.

Authors:  Jack A Dunkle; Leyi Wang; Michael B Feldman; Arto Pulk; Vincent B Chen; Gary J Kapral; Jonas Noeske; Jane S Richardson; Scott C Blanchard; Jamie H Doudna Cate
Journal:  Science       Date:  2011-05-20       Impact factor: 47.728

5.  Generalized fragment picking in Rosetta: design, protocols and applications.

Authors:  Dominik Gront; Daniel W Kulp; Robert M Vernon; Charlie E M Strauss; David Baker
Journal:  PLoS One       Date:  2011-08-24       Impact factor: 3.240

6.  UniRef clusters: a comprehensive and scalable alternative for improving sequence similarity searches.

Authors:  Baris E Suzek; Yuqi Wang; Hongzhan Huang; Peter B McGarvey; Cathy H Wu
Journal:  Bioinformatics       Date:  2014-11-13       Impact factor: 6.937

7.  Protein structure prediction using multiple deep neural networks in the 13th Critical Assessment of Protein Structure Prediction (CASP13).

Authors:  Andrew W Senior; Richard Evans; John Jumper; James Kirkpatrick; Laurent Sifre; Tim Green; Chongli Qin; Augustin Žídek; Alexander W R Nelson; Alex Bridgland; Hugo Penedones; Stig Petersen; Karen Simonyan; Steve Crossan; Pushmeet Kohli; David T Jones; David Silver; Koray Kavukcuoglu; Demis Hassabis
Journal:  Proteins       Date:  2019-12

8.  Improved de novo structure prediction in CASP11 by incorporating coevolution information into Rosetta.

Authors:  Sergey Ovchinnikov; David E Kim; Ray Yu-Ruei Wang; Yuan Liu; Frank DiMaio; David Baker
Journal:  Proteins       Date:  2016-02-24

Review 9.  Applications of contact predictions to structural biology.

Authors:  Felix Simkovic; Sergey Ovchinnikov; David Baker; Daniel J Rigden
Journal:  IUCrJ       Date:  2017-04-18       Impact factor: 4.769

10.  Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.

Authors:  Dorothee Liebschner; Pavel V Afonine; Matthew L Baker; Gábor Bunkóczi; Vincent B Chen; Tristan I Croll; Bradley Hintze; Li Wei Hung; Swati Jain; Airlie J McCoy; Nigel W Moriarty; Robert D Oeffner; Billy K Poon; Michael G Prisant; Randy J Read; Jane S Richardson; David C Richardson; Massimo D Sammito; Oleg V Sobolev; Duncan H Stockwell; Thomas C Terwilliger; Alexandre G Urzhumtsev; Lizbeth L Videau; Christopher J Williams; Paul D Adams
Journal:  Acta Crystallogr D Struct Biol       Date:  2019-10-02       Impact factor: 7.652
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  3 in total

1.  Faces of Contemporary CryoEM Information and Modeling.

Authors:  Giulia Palermo; Yuji Sugita; Willy Wriggers; Rommie E Amaro
Journal:  J Chem Inf Model       Date:  2020-05-26       Impact factor: 4.956

2.  State-dependent sequential allostery exhibited by chaperonin TRiC/CCT revealed by network analysis of Cryo-EM maps.

Authors:  Yan Zhang; James Krieger; Karolina Mikulska-Ruminska; Burak Kaynak; Carlos Oscar S Sorzano; José-María Carazo; Jianhua Xing; Ivet Bahar
Journal:  Prog Biophys Mol Biol       Date:  2020-08-28       Impact factor: 3.667

3.  Molecular Dynamics to Predict Cryo-EM: Capturing Transitions and Short-Lived Conformational States of Biomolecules.

Authors:  Łukasz Nierzwicki; Giulia Palermo
Journal:  Front Mol Biosci       Date:  2021-04-05
  3 in total

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