Cryo‐EM map interpretation and protein model‐building using iterative map segmentation

doi:10.1002/pro.3740

Title: Cryo‐EM map interpretation and protein model‐building using iterative map segmentation

Authors:

^[1]; Adams, Paul D. ^[2]; Afonine, Pavel V. ^[3]; Sobolev, Oleg V. ^[3]

Los Alamos National Laboratory Los Alamos New Mexico, New Mexico Consortium Los Alamos New Mexico
Molecular Biophysics &, Integrated Bioimaging DivisionLawrence Berkeley National Laboratory Berkeley California, Department of BioengineeringUniversity of California Berkeley Berkeley California
Molecular Biophysics &, Integrated Bioimaging DivisionLawrence Berkeley National Laboratory Berkeley California

Publication Date:: 2019-10-24

Sponsoring Org.:: USDOE

OSTI Identifier:: 1571696

Alternate Identifier(s):: OSTI ID: 1571697

Grant/Contract Number:: DE‐AC02‐05CH11231

Resource Type:: Published Article

Journal Name:: Protein Science

Additional Journal Information:: Journal Name: Protein Science; Journal ID: ISSN 0961-8368

Publisher:: Wiley Blackwell (John Wiley & Sons)

Country of Publication:: United Kingdom

Language:: English

Citation Formats


                    Terwilliger, Thomas C., Adams, Paul D., Afonine, Pavel V., and Sobolev, Oleg V. Cryo‐EM map interpretation and protein model‐building using iterative map segmentation.  United Kingdom: N. p., 2019. 
        Web.  doi:10.1002/pro.3740.

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                    Terwilliger, Thomas C., Adams, Paul D., Afonine, Pavel V., & Sobolev, Oleg V. Cryo‐EM map interpretation and protein model‐building using iterative map segmentation.  United Kingdom.  doi:10.1002/pro.3740.

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                    Terwilliger, Thomas C., Adams, Paul D., Afonine, Pavel V., and Sobolev, Oleg V. Thu .  
        "Cryo‐EM map interpretation and protein model‐building using iterative map segmentation".  United Kingdom.  doi:10.1002/pro.3740.

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@article{osti_1571696,

  title        = {Cryo‐EM map interpretation and protein model‐building using iterative map segmentation},

  author       = {Terwilliger, Thomas C. and Adams, Paul D. and Afonine, Pavel V. and Sobolev, Oleg V.},

  abstractNote = {},

  doi          = {10.1002/pro.3740},

  journal      = {Protein Science},

  number       = ,

  volume       = ,

  place        = {United Kingdom},

  year         = {2019},

  month        = {10}

}

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DOI: 10.1002/pro.3740

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Works referenced in this record:

The Buccaneer software for automated model building. 1. Tracing protein chains
journal, August 2006

Cowtan, Kevin
Acta Crystallographica Section D Biological Crystallography, Vol. 62, Issue 9
DOI: 10.1107/S0907444906022116

A note on two problems in connexion with graphs
journal, December 1959

Dijkstra, E. W.
Numerische Mathematik, Vol. 1, Issue 1
DOI: 10.1007/BF01386390

EMDataBank unified data resource for 3DEM
journal, November 2015

Lawson, Catherine L.; Patwardhan, Ardan; Baker, Matthew L.
Nucleic Acids Research, Vol. 44, Issue D1
DOI: 10.1093/nar/gkv1126

Measuring the optimal exposure for single particle cryo-EM using a 2.6 Å reconstruction of rotavirus VP6
journal, May 2015

Grant, Timothy; Grigorieff, Nikolaus
eLife, Vol. 4
DOI: 10.7554/eLife.06980

RosettaES: a sampling strategy enabling automated interpretation of difficult cryo-EM maps
journal, June 2017

Frenz, Brandon; Walls, Alexandra C.; Egelman, Edward H.
Nature Methods, Vol. 14, Issue 8
DOI: 10.1038/nmeth.4340

Bridging the information gap: computational tools for intermediate resolution structure interpretation
journal, May 2001

Jiang, Wen; Baker, Matthew L.; Ludtke, Steven J.
Journal of Molecular Biology, Vol. 308, Issue 5
DOI: 10.1006/jmbi.2001.4633

The Resolution Revolution
journal, March 2014

Kuhlbrandt, W.
Science, Vol. 343, Issue 6178
DOI: 10.1126/science.1251652

Features and development of Coot
journal, March 2010

Emsley, P.; Lohkamp, B.; Scott, W. G.
Acta Crystallographica Section D Biological Crystallography, Vol. 66, Issue 4
DOI: 10.1107/S0907444910007493

De novo protein structure determination from near-atomic-resolution cryo-EM maps
journal, February 2015

Wang, Ray Yu-Ruei; Kudryashev, Mikhail; Li, Xueming
Nature Methods, Vol. 12, Issue 4
DOI: 10.1038/nmeth.3287

Structure of -galactosidase at 3.2-A resolution obtained by cryo-electron microscopy
journal, July 2014

Bartesaghi, A.; Matthies, D.; Banerjee, S.
Proceedings of the National Academy of Sciences, Vol. 111, Issue 32
DOI: 10.1073/pnas.1402809111

EM-Fold: De Novo Atomic-Detail Protein Structure Determination from Medium-Resolution Density Maps
journal, March 2012

Lindert, Steffen; Alexander, Nathan; Wötzel, Nils
Structure, Vol. 20, Issue 3
DOI: 10.1016/j.str.2012.01.023

The crystal structure of the bacterial chaperonln GroEL at 2.8 Å
journal, October 1994

Braig, Kerstin; Otwinowski, Zbyszek; Hegde, Rashmi
Nature, Vol. 371, Issue 6498
DOI: 10.1038/371578a0

Accurate model annotation of a near-atomic resolution cryo-EM map
journal, March 2017

Hryc, Corey F.; Chen, Dong-Hua; Afonine, Pavel V.
Proceedings of the National Academy of Sciences, Vol. 114, Issue 12
DOI: 10.1073/pnas.1621152114

Fast procedure for reconstruction of full-atom protein models from reduced representations
journal, January 2008

Rotkiewicz, Piotr; Skolnick, Jeffrey
Journal of Computational Chemistry, Vol. 29, Issue 9
DOI: 10.1002/jcc.20906

Tertiary templates for proteins
journal, February 1987

Ponder, Jay W.; Richards, Frederic M.
Journal of Molecular Biology, Vol. 193, Issue 4
DOI: 10.1016/0022-2836(87)90358-5

A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps
journal, October 2018

Terwilliger, Thomas C.; Adams, Paul D.; Afonine, Pavel V.
Nature Methods, Vol. 15, Issue 11
DOI: 10.1038/s41592-018-0173-1

Overview and future of single particle electron cryomicroscopy
journal, September 2015

Henderson, Richard
Archives of Biochemistry and Biophysics, Vol. 581
DOI: 10.1016/j.abb.2015.02.036

A Structural-informatics Approach for Mining β-Sheets: Locating Sheets in Intermediate-resolution Density Maps
journal, September 2003

Kong, Yifei; Ma, Jianpeng
Journal of Molecular Biology, Vol. 332, Issue 2
DOI: 10.1016/S0022-2836(03)00859-3

Subunit conformational variation within individual GroEL oligomers resolved by Cryo-EM
journal, July 2017

Roh, Soung-Hun; Hryc, Corey F.; Jeong, Hyun-Hwan
Proceedings of the National Academy of Sciences, Vol. 114, Issue 31
DOI: 10.1073/pnas.1704725114

Automated main-chain model building by template matching and iterative fragment extension
journal, December 2002

Terwilliger, Thomas C.
Acta Crystallographica Section D Biological Crystallography, Vol. 59, Issue 1
DOI: 10.1107/S0907444902018036

Cryo-EM structures of the human endolysosomal TRPML3 channel in three distinct states
journal, November 2017

Zhou, Xiaoyuan; Li, Minghui; Su, Deyuan
Nature Structural & Molecular Biology, Vol. 24, Issue 12
DOI: 10.1038/nsmb.3502

Modeling protein structure at near atomic resolutions with Gorgon
journal, May 2011

Baker, Matthew L.; Abeysinghe, Sasakthi S.; Schuh, Stephen
Journal of Structural Biology, Vol. 174, Issue 2
DOI: 10.1016/j.jsb.2011.01.015

The Protein Data Bank
journal, January 2000

Berman, H. M.
Nucleic Acids Research, Vol. 28, Issue 1
DOI: 10.1093/nar/28.1.235

A Multi-model Approach to Assessing Local and Global Cryo-EM Map Quality
journal, February 2019

Herzik, Mark A.; Fraser, James S.; Lander, Gabriel C.
Structure, Vol. 27, Issue 2
DOI: 10.1016/j.str.2018.10.003

De Novo modeling in cryo-EM density maps with Pathwalking
journal, December 2016

Chen, Muyuan; Baldwin, Philip R.; Ludtke, Steven J.
Journal of Structural Biology, Vol. 196, Issue 3
DOI: 10.1016/j.jsb.2016.06.004

Structure of the E. coli ribosome–EF-Tu complex at <3 Å resolution by Cs-corrected cryo-EM
journal, February 2015

Fischer, Niels; Neumann, Piotr; Konevega, Andrey L.
Nature, Vol. 520, Issue 7548
DOI: 10.1038/nature14275

De novo main-chain modeling for EM maps using MAINMAST
journal, April 2018

Terashi, Genki; Kihara, Daisuke
Nature Communications, Vol. 9, Issue 1
DOI: 10.1038/s41467-018-04053-7

Advances in the molecular dynamics flexible fitting method for cryo-EM modeling
journal, May 2016

McGreevy, Ryan; Teo, Ivan; Singharoy, Abhishek
Methods, Vol. 100
DOI: 10.1016/j.ymeth.2016.01.009

EMBuilder: A Template Matching-based Automatic Model-building Program for High-resolution Cryo-Electron Microscopy Maps
journal, June 2017

Zhou, Niyun; Wang, Hongwei; Wang, Jiawei
Scientific Reports, Vol. 7, Issue 1
DOI: 10.1038/s41598-017-02725-w

How Good Can Single-Particle Cryo-EM Become? What Remains Before It Approaches Its Physical Limits?
journal, May 2019

Glaeser, Robert M.
Annual Review of Biophysics, Vol. 48, Issue 1
DOI: 10.1146/annurev-biophys-070317-032828

The development of cryo-EM into a mainstream structural biology technique
journal, December 2015

Nogales, Eva
Nature Methods, Vol. 13, Issue 1
DOI: 10.1038/nmeth.3694

UCSF Chimera?A visualization system for exploratory research and analysis
journal, January 2004

Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C.
Journal of Computational Chemistry, Vol. 25, Issue 13
DOI: 10.1002/jcc.20084

How cryo-electron microscopy and X-ray crystallography complement each other: Cryo-EM and X-Ray Crystallography Complement Each Other
journal, September 2016

Wang, Hong-Wei; Wang, Jia-Wei
Protein Science, Vol. 26, Issue 1
DOI: 10.1002/pro.3022

Identification of Secondary Structure Elements in Intermediate-Resolution Density Maps
journal, January 2007

Baker, Matthew L.; Ju, Tao; Chiu, Wah
Structure, Vol. 15, Issue 1
DOI: 10.1016/j.str.2006.11.008

A Structural-informatics Approach for Tracing β-Sheets: Building Pseudo-Cα Traces for β-Strands in Intermediate-resolution Density Maps
journal, May 2004

Kong, Yifei; Zhang, Xing; Baker, Timothy S.
Journal of Molecular Biology, Vol. 339, Issue 1
DOI: 10.1016/j.jmb.2004.03.038

Three-dimensional pattern recognition: An approach to automated interpretation of electron density maps of proteins
journal, January 1974

Greer, Jonathan
Journal of Molecular Biology, Vol. 82, Issue 3
DOI: 10.1016/0022-2836(74)90591-9

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Similar Records

Title: Cryo‐EM map interpretation and protein model‐building using iterative map segmentation

Citation Formats

The Buccaneer software for automated model building. 1. Tracing protein chains journal, August 2006

A note on two problems in connexion with graphs journal, December 1959

EMDataBank unified data resource for 3DEM journal, November 2015

Measuring the optimal exposure for single particle cryo-EM using a 2.6 Å reconstruction of rotavirus VP6 journal, May 2015

RosettaES: a sampling strategy enabling automated interpretation of difficult cryo-EM maps journal, June 2017

Bridging the information gap: computational tools for intermediate resolution structure interpretation journal, May 2001

The Resolution Revolution journal, March 2014

Features and development of Coot journal, March 2010

De novo protein structure determination from near-atomic-resolution cryo-EM maps journal, February 2015

Structure of -galactosidase at 3.2-A resolution obtained by cryo-electron microscopy journal, July 2014

EM-Fold: De Novo Atomic-Detail Protein Structure Determination from Medium-Resolution Density Maps journal, March 2012

The crystal structure of the bacterial chaperonln GroEL at 2.8 Å journal, October 1994

Accurate model annotation of a near-atomic resolution cryo-EM map journal, March 2017

Fast procedure for reconstruction of full-atom protein models from reduced representations journal, January 2008

Tertiary templates for proteins journal, February 1987

A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps journal, October 2018

Overview and future of single particle electron cryomicroscopy journal, September 2015

A Structural-informatics Approach for Mining β-Sheets: Locating Sheets in Intermediate-resolution Density Maps journal, September 2003

Subunit conformational variation within individual GroEL oligomers resolved by Cryo-EM journal, July 2017

Automated main-chain model building by template matching and iterative fragment extension journal, December 2002

Cryo-EM structures of the human endolysosomal TRPML3 channel in three distinct states journal, November 2017

Modeling protein structure at near atomic resolutions with Gorgon journal, May 2011

The Protein Data Bank journal, January 2000

A Multi-model Approach to Assessing Local and Global Cryo-EM Map Quality journal, February 2019

De Novo modeling in cryo-EM density maps with Pathwalking journal, December 2016

Structure of the E. coli ribosome–EF-Tu complex at <3 Å resolution by Cs-corrected cryo-EM journal, February 2015

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EMBuilder: A Template Matching-based Automatic Model-building Program for High-resolution Cryo-Electron Microscopy Maps journal, June 2017

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UCSF Chimera?A visualization system for exploratory research and analysis journal, January 2004

How cryo-electron microscopy and X-ray crystallography complement each other: Cryo-EM and X-Ray Crystallography Complement Each Other journal, September 2016

Identification of Secondary Structure Elements in Intermediate-Resolution Density Maps journal, January 2007

A Structural-informatics Approach for Tracing β-Sheets: Building Pseudo-Cα Traces for β-Strands in Intermediate-resolution Density Maps journal, May 2004

Three-dimensional pattern recognition: An approach to automated interpretation of electron density maps of proteins journal, January 1974

The Buccaneer software for automated model building. 1. Tracing protein chains
journal, August 2006

A note on two problems in connexion with graphs
journal, December 1959

EMDataBank unified data resource for 3DEM
journal, November 2015

Measuring the optimal exposure for single particle cryo-EM using a 2.6 Å reconstruction of rotavirus VP6
journal, May 2015

RosettaES: a sampling strategy enabling automated interpretation of difficult cryo-EM maps
journal, June 2017

Bridging the information gap: computational tools for intermediate resolution structure interpretation
journal, May 2001

The Resolution Revolution
journal, March 2014

Features and development of Coot
journal, March 2010

De novo protein structure determination from near-atomic-resolution cryo-EM maps
journal, February 2015

Structure of -galactosidase at 3.2-A resolution obtained by cryo-electron microscopy
journal, July 2014

EM-Fold: De Novo Atomic-Detail Protein Structure Determination from Medium-Resolution Density Maps
journal, March 2012

The crystal structure of the bacterial chaperonln GroEL at 2.8 Å
journal, October 1994

Accurate model annotation of a near-atomic resolution cryo-EM map
journal, March 2017

Fast procedure for reconstruction of full-atom protein models from reduced representations
journal, January 2008

Tertiary templates for proteins
journal, February 1987

A fully automatic method yielding initial models from high-resolution cryo-electron microscopy maps
journal, October 2018

Overview and future of single particle electron cryomicroscopy
journal, September 2015

A Structural-informatics Approach for Mining β-Sheets: Locating Sheets in Intermediate-resolution Density Maps
journal, September 2003

Subunit conformational variation within individual GroEL oligomers resolved by Cryo-EM
journal, July 2017

Automated main-chain model building by template matching and iterative fragment extension
journal, December 2002

Cryo-EM structures of the human endolysosomal TRPML3 channel in three distinct states
journal, November 2017

Modeling protein structure at near atomic resolutions with Gorgon
journal, May 2011

The Protein Data Bank
journal, January 2000

A Multi-model Approach to Assessing Local and Global Cryo-EM Map Quality
journal, February 2019

De Novo modeling in cryo-EM density maps with Pathwalking
journal, December 2016

Structure of the E. coli ribosome–EF-Tu complex at <3 Å resolution by Cs-corrected cryo-EM
journal, February 2015

De novo main-chain modeling for EM maps using MAINMAST
journal, April 2018

Advances in the molecular dynamics flexible fitting method for cryo-EM modeling
journal, May 2016

EMBuilder: A Template Matching-based Automatic Model-building Program for High-resolution Cryo-Electron Microscopy Maps
journal, June 2017

How Good Can Single-Particle Cryo-EM Become? What Remains Before It Approaches Its Physical Limits?
journal, May 2019

The development of cryo-EM into a mainstream structural biology technique
journal, December 2015

UCSF Chimera?A visualization system for exploratory research and analysis
journal, January 2004

How cryo-electron microscopy and X-ray crystallography complement each other: Cryo-EM and X-Ray Crystallography Complement Each Other
journal, September 2016

Identification of Secondary Structure Elements in Intermediate-Resolution Density Maps
journal, January 2007

A Structural-informatics Approach for Tracing β-Sheets: Building Pseudo-Cα Traces for β-Strands in Intermediate-resolution Density Maps
journal, May 2004

Three-dimensional pattern recognition: An approach to automated interpretation of electron density maps of proteins
journal, January 1974