Accurate prediction of chemical shifts for aqueous protein structure on “Real World” data

Li, Jie; Bennett, Kochise C.; Liu, Yuchen; Martin, Michael V.; Head-Gordon, Teresa

doi:10.1039/C9SC06561J

Title: Accurate prediction of chemical shifts for aqueous protein structure on “Real World” data

Abstract

UCBShift predicts NMR chemical shifts of proteins that exceeds accuracy of other popular chemical shift predictors on real-world data sets.

Authors:

^[1]; Bennett, Kochise C. ^[1]; Liu, Yuchen ^[1]; Martin, Michael V. ^[2];

^[1]

Pitzer Center for Theoretical Chemistry, University of California, Berkeley, USA, Department of Chemistry
Department of Bioengineering, University of California, Berkeley, USA

Publication Date:: 2020-03-25

Sponsoring Org.:: USDOE

OSTI Identifier:: 1603712

Grant/Contract Number:: AC02-05CH11231

Resource Type:: Published Article

Journal Name:: Chemical Science

Additional Journal Information:: Journal Name: Chemical Science Journal Volume: 11 Journal Issue: 12; Journal ID: ISSN 2041-6520

Publisher:: Royal Society of Chemistry (RSC)

Country of Publication:: United Kingdom

Language:: English

Citation Formats


                    Li, Jie, Bennett, Kochise C., Liu, Yuchen, Martin, Michael V., and Head-Gordon, Teresa. Accurate prediction of chemical shifts for aqueous protein structure on “Real World” data.  United Kingdom: N. p., 2020. 
Web.  doi:10.1039/C9SC06561J.

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                    Li, Jie, Bennett, Kochise C., Liu, Yuchen, Martin, Michael V., & Head-Gordon, Teresa. Accurate prediction of chemical shifts for aqueous protein structure on “Real World” data.  United Kingdom.  https://doi.org/10.1039/C9SC06561J

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                    Li, Jie, Bennett, Kochise C., Liu, Yuchen, Martin, Michael V., and Head-Gordon, Teresa. Wed .  
"Accurate prediction of chemical shifts for aqueous protein structure on “Real World” data".  United Kingdom.  https://doi.org/10.1039/C9SC06561J.

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@article{osti_1603712,

  title        = {Accurate prediction of chemical shifts for aqueous protein structure on “Real World” data},

  author       = {Li, Jie and Bennett, Kochise C. and Liu, Yuchen and Martin, Michael V. and Head-Gordon, Teresa},

  abstractNote = {UCBShift predicts NMR chemical shifts of proteins that exceeds accuracy of other popular chemical shift predictors on real-world data sets.},

  doi          = {10.1039/C9SC06561J},

  journal      = {Chemical Science},

  number       = 12,

  volume       = 11,

  place        = {United Kingdom},

  year         = {2020},

  month        = {3}

}

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Works referenced in this record:

Empirical correlation between protein backbone conformation and C.alpha. and C.beta. 13C nuclear magnetic resonance chemical shifts
journal, July 1991

Spera, Silvia; Bax, Ad
Journal of the American Chemical Society, Vol. 113, Issue 14
DOI: 10.1021/ja00014a071

A probabilistic approach for validating protein NMR chemical shift assignments
journal, May 2010

Wang, Bowei; Wang, Yunjun; Wishart, David S.
Journal of Biomolecular NMR, Vol. 47, Issue 2
DOI: 10.1007/s10858-010-9407-y

Water–protein interactions from high–resolution protein crystallography
journal, August 2004

Nakasako, Masayoshi
Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, Vol. 359, Issue 1448
DOI: 10.1098/rstb.2004.1498

SHIFTX2: significantly improved protein chemical shift prediction
journal, March 2011

Han, Beomsoo; Liu, Yifeng; Ginzinger, Simon W.
Journal of Biomolecular NMR, Vol. 50, Issue 1
DOI: 10.1007/s10858-011-9478-4

Relationship between chemical shift value and accessible surface area for all amino acid atoms
journal, January 2009

Vranken, Wim F.; Rieping, Wolfgang
BMC Structural Biology, Vol. 9, Issue 1
DOI: 10.1186/1472-6807-9-20

1H, 13C and 15N random coil NMR chemical shifts of the common amino acids. I. Investigations of nearest-neighbor effects
journal, January 1995

Wishart, David S.; Bigam, Colin G.; Holm, Arne
Journal of Biomolecular NMR, Vol. 5, Issue 1
DOI: 10.1007/BF00227471

Multiresolution 3D-DenseNet for Chemical Shift Prediction in NMR Crystallography
journal, July 2019

Liu, Shuai; Li, Jie; Bennett, Kochise C.
The Journal of Physical Chemistry Letters, Vol. 10, Issue 16
DOI: 10.1021/acs.jpclett.9b01570

Coupled prediction of protein secondary and tertiary structure
journal, October 2003

Meiler, J.; Baker, D.
Proceedings of the National Academy of Sciences, Vol. 100, Issue 21
DOI: 10.1073/pnas.1831973100

An amino acid has two sides: A new 2D measure provides a different view of solvent exposure
journal, February 2005

Hamelryck, Thomas
Proteins: Structure, Function, and Bioinformatics, Vol. 59, Issue 1
DOI: 10.1002/prot.20379

Machine Learning Predictions of Molecular Properties: Accurate Many-Body Potentials and Nonlocality in Chemical Space
journal, June 2015

Hansen, Katja; Biegler, Franziska; Ramakrishnan, Raghunathan
The Journal of Physical Chemistry Letters, Vol. 6, Issue 12
DOI: 10.1021/acs.jpclett.5b00831

Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology
journal, July 2007

Shen, Yang; Bax, Ad
Journal of Biomolecular NMR, Vol. 38, Issue 4
DOI: 10.1007/s10858-007-9166-6

Secondary-structure dependent chemical shifts in proteins
journal, August 1990

Williamson, Michael P.
Biopolymers, Vol. 29, Issue 10-11
DOI: 10.1002/bip.360291009

Experimental Inferential Structure Determination of Ensembles for Intrinsically Disordered Proteins
journal, March 2016

Brookes, David H.; Head-Gordon, Teresa
Journal of the American Chemical Society, Vol. 138, Issue 13
DOI: 10.1021/jacs.6b00351

Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding
journal, February 1996

Müller, Cw; Schlauderer, Gj; Reinstein, J.
Structure, Vol. 4, Issue 2
DOI: 10.1016/S0969-2126(96)00018-4

A Simple Method To Predict Protein Flexibility Using Secondary Chemical Shifts
journal, November 2005

Berjanskii, Mark V.; Wishart, David S.
Journal of the American Chemical Society, Vol. 127, Issue 43
DOI: 10.1021/ja054842f

Hydrogen bond length and proton NMR chemical shifts in proteins
journal, September 1983

Wagner, Gerhard; Pardi, Arthur; Wuethrich, Kurt
Journal of the American Chemical Society, Vol. 105, Issue 18
DOI: 10.1021/ja00356a056

Consistent blind protein structure generation from NMR chemical shift data
journal, March 2008

Shen, Y.; Lange, O.; Delaglio, F.
Proceedings of the National Academy of Sciences, Vol. 105, Issue 12
DOI: 10.1073/pnas.0800256105

PPM: a side-chain and backbone chemical shift predictor for the assessment of protein conformational ensembles
journal, September 2012

Li, Da-Wei; Brüschweiler, Rafael
Journal of Biomolecular NMR, Vol. 54, Issue 3
DOI: 10.1007/s10858-012-9668-8

SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network
journal, July 2010

Shen, Yang; Bax, Ad
Journal of Biomolecular NMR, Vol. 48, Issue 1
DOI: 10.1007/s10858-010-9433-9

Chemical Shifts in the Nuclear Magnetic Resonance Spectra of Molecules Containing Polar Groups
journal, February 1960

Buckingham, A. D.
Canadian Journal of Chemistry, Vol. 38, Issue 2
DOI: 10.1139/v60-040

Water molecules as structural determinants among prions of low sequence identity
journal, April 2006

De Simone, Alfonso; Dodson, Guy G.; Fraternali, Franca
FEBS Letters, Vol. 580, Issue 10
DOI: 10.1016/j.febslet.2006.02.083

Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation 1 1Edited by J. Thornton
journal, January 1999

Word, J. Michael; Lovell, Simon C.; Richardson, Jane S.
Journal of Molecular Biology, Vol. 285, Issue 4
DOI: 10.1006/jmbi.1998.2401

Calibration of ring-current effects in proteins and nucleic acids
journal, December 1995

Case, DavidA.
Journal of Biomolecular NMR, Vol. 6, Issue 4
DOI: 10.1007/BF00197633

Chemical shifts in biomolecules
journal, April 2013

Case, David A.
Current Opinion in Structural Biology, Vol. 23, Issue 2
DOI: 10.1016/j.sbi.2013.01.007

Protein Structure Validation and Refinement Using Amide Proton Chemical Shifts Derived from Quantum Mechanics
journal, December 2013

Christensen, Anders S.; Linnet, Troels E.; Borg, Mikael
PLoS ONE, Vol. 8, Issue 12
DOI: 10.1371/journal.pone.0084123

Fast and Accurate Predictions of Protein NMR Chemical Shifts from Interatomic Distances
journal, October 2009

Kohlhoff, Kai J.; Robustelli, Paul; Cavalli, Andrea
Journal of the American Chemical Society, Vol. 131, Issue 39
DOI: 10.1021/ja903772t

Extremely randomized trees
journal, March 2006

Geurts, Pierre; Ernst, Damien; Wehenkel, Louis
Machine Learning, Vol. 63, Issue 1
DOI: 10.1007/s10994-006-6226-1

Solution structure of the DNA-binding domain of the yeast transcriptional activator protein GCN4
journal, January 1990

Saudek, Vladimir; Pastore, Annalisa; Morelli, Maria A. Castiglione
"Protein Engineering, Design and Selection", Vol. 4, Issue 1
DOI: 10.1093/protein/4.1.3

3DRobot: automated generation of diverse and well-packed protein structure decoys
journal, October 2015

Deng, Haiyou; Jia, Ya; Zhang, Yang
Bioinformatics, Vol. 32, Issue 3
DOI: 10.1093/bioinformatics/btv601

mTM-align: an algorithm for fast and accurate multiple protein structure alignment
journal, December 2017

Dong, Runze; Peng, Zhenling; Zhang, Yang
Bioinformatics, Vol. 34, Issue 10
DOI: 10.1093/bioinformatics/btx828

Decoys ‘R’ Us: A database of incorrect conformations to improve protein structure prediction
journal, January 2000

Samudrala, Ram; Levitt, Michael
Protein Science, Vol. 9, Issue 7
DOI: 10.1110/ps.9.7.1399

Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
journal, January 2012

Nielsen, Jakob T.; Eghbalnia, Hamid R.; Nielsen, Niels Chr.
Progress in Nuclear Magnetic Resonance Spectroscopy, Vol. 60
DOI: 10.1016/j.pnmrs.2011.05.002

Contact Model for the Prediction of NMR N−H Order Parameters in Globular Proteins
journal, October 2002

Zhang, Fengli; Brüschweiler, Rafael
Journal of the American Chemical Society, Vol. 124, Issue 43
DOI: 10.1021/ja027847a

Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
journal, December 1983

Kabsch, Wolfgang; Sander, Christian
Biopolymers, Vol. 22, Issue 12
DOI: 10.1002/bip.360221211

Molecular Dynamics and NMR Spin Relaxation in Proteins
journal, June 2002

Case, David A.
Accounts of Chemical Research, Vol. 35, Issue 6
DOI: 10.1021/ar010020l

A general method applicable to the search for similarities in the amino acid sequence of two proteins
journal, March 1970

Needleman, Saul B.; Wunsch, Christian D.
Journal of Molecular Biology, Vol. 48, Issue 3, p. 443-453
DOI: 10.1016/0022-2836(70)90057-4

Basic local alignment search tool
journal, October 1990

Altschul, Stephen F.; Gish, Warren; Miller, Webb
Journal of Molecular Biology, Vol. 215, Issue 3, p. 403-410
DOI: 10.1016/S0022-2836(05)80360-2

Amino acid substitution matrices from protein blocks.
journal, November 1992

Henikoff, S.; Henikoff, J. G.
Proceedings of the National Academy of Sciences, Vol. 89, Issue 22, p. 10915-10919
DOI: 10.1073/pnas.89.22.10915

Generalized Neural-Network Representation of High-Dimensional Potential-Energy Surfaces
journal, April 2007

Behler, Jörg; Parrinello, Michele
Physical Review Letters, Vol. 98, Issue 14
DOI: 10.1103/PhysRevLett.98.146401

BioMagResBank
journal, December 2007

Ulrich, E. L.; Akutsu, H.; Doreleijers, J. F.
Nucleic Acids Research, Vol. 36, Issue Database
DOI: 10.1093/nar/gkm957

Unfolded Proteins and Protein Folding Studied by NMR
journal, August 2004

Dyson, H. Jane; Wright, Peter E.
Chemical Reviews, Vol. 104, Issue 8
DOI: 10.1021/cr030403s

Chemical shifts in molecular solids by machine learning
journal, October 2018

Paruzzo, Federico M.; Hofstetter, Albert; Musil, Félix
Nature Communications, Vol. 9, Issue 1
DOI: 10.1038/s41467-018-06972-x

The Protein Data Bank
journal, January 2000

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

Relationship between nuclear magnetic resonance chemical shift and protein secondary structure
journal, November 1991

Wishart, D. S.; Sykes, B. D.; Richards, F. M.
Journal of Molecular Biology, Vol. 222, Issue 2
DOI: 10.1016/0022-2836(91)90214-Q

Protein chemical shift analysis: a practical guide
journal, May 1998

Wishart, David S.; Nip, Alex M.
Biochemistry and Cell Biology, Vol. 76, Issue 2-3
DOI: 10.1139/o98-038

Experimentally determined hydrophobicity scale for proteins at membrane interfaces
journal, October 1996

Wimley, William C.; White, Stephen H.
Nature Structural & Molecular Biology, Vol. 3, Issue 10
DOI: 10.1038/nsb1096-842

Crystal structures of two mutants of adenylate kinase fromEscherichia coli that modify the Gly-loop
journal, January 1993

Müller, Christoph W.; Schulz, Georg E.
Proteins: Structure, Function, and Genetics, Vol. 15, Issue 1
DOI: 10.1002/prot.340150106

Ring current theories in nuclear magnetic resonance
journal, January 1979

Haigh, C. W.; Mallion, R. B.
Progress in Nuclear Magnetic Resonance Spectroscopy, Vol. 13, Issue 4
DOI: 10.1016/0079-6565(79)80010-2

Random Forests
journal, January 2001

Breiman, Leo
Machine Learning, Vol. 45, Issue 1, p. 5-32
DOI: 10.1023/A:1010933404324

PPM_One: a static protein structure based chemical shift predictor
journal, June 2015

Li, Dawei; Brüschweiler, Rafael
Journal of Biomolecular NMR, Vol. 62, Issue 3
DOI: 10.1007/s10858-015-9958-z

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Title: Accurate prediction of chemical shifts for aqueous protein structure on “Real World” data

Abstract

Citation Formats

Empirical correlation between protein backbone conformation and C.alpha. and C.beta. 13C nuclear magnetic resonance chemical shifts journal, July 1991

A probabilistic approach for validating protein NMR chemical shift assignments journal, May 2010

Water–protein interactions from high–resolution protein crystallography journal, August 2004

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Relationship between chemical shift value and accessible surface area for all amino acid atoms journal, January 2009

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Multiresolution 3D-DenseNet for Chemical Shift Prediction in NMR Crystallography journal, July 2019

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Secondary-structure dependent chemical shifts in proteins journal, August 1990

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A Simple Method To Predict Protein Flexibility Using Secondary Chemical Shifts journal, November 2005

Hydrogen bond length and proton NMR chemical shifts in proteins journal, September 1983

Consistent blind protein structure generation from NMR chemical shift data journal, March 2008

PPM: a side-chain and backbone chemical shift predictor for the assessment of protein conformational ensembles journal, September 2012

SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network journal, July 2010

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Water molecules as structural determinants among prions of low sequence identity journal, April 2006

Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation 1 1Edited by J. Thornton journal, January 1999

Calibration of ring-current effects in proteins and nucleic acids journal, December 1995

Chemical shifts in biomolecules journal, April 2013

Protein Structure Validation and Refinement Using Amide Proton Chemical Shifts Derived from Quantum Mechanics journal, December 2013

Fast and Accurate Predictions of Protein NMR Chemical Shifts from Interatomic Distances journal, October 2009

Extremely randomized trees journal, March 2006

Solution structure of the DNA-binding domain of the yeast transcriptional activator protein GCN4 journal, January 1990

3DRobot: automated generation of diverse and well-packed protein structure decoys journal, October 2015

mTM-align: an algorithm for fast and accurate multiple protein structure alignment journal, December 2017

Decoys ‘R’ Us: A database of incorrect conformations to improve protein structure prediction journal, January 2000

Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field journal, January 2012

Contact Model for the Prediction of NMR N−H Order Parameters in Globular Proteins journal, October 2002

Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features journal, December 1983

Molecular Dynamics and NMR Spin Relaxation in Proteins journal, June 2002

A general method applicable to the search for similarities in the amino acid sequence of two proteins journal, March 1970

Basic local alignment search tool journal, October 1990

Amino acid substitution matrices from protein blocks. journal, November 1992

Generalized Neural-Network Representation of High-Dimensional Potential-Energy Surfaces journal, April 2007

BioMagResBank journal, December 2007

Unfolded Proteins and Protein Folding Studied by NMR journal, August 2004

Chemical shifts in molecular solids by machine learning journal, October 2018

The Protein Data Bank journal, January 2000

Relationship between nuclear magnetic resonance chemical shift and protein secondary structure journal, November 1991

Protein chemical shift analysis: a practical guide journal, May 1998

Experimentally determined hydrophobicity scale for proteins at membrane interfaces journal, October 1996

Crystal structures of two mutants of adenylate kinase fromEscherichia coli that modify the Gly-loop journal, January 1993

Ring current theories in nuclear magnetic resonance journal, January 1979

Random Forests journal, January 2001

PPM_One: a static protein structure based chemical shift predictor journal, June 2015

Empirical correlation between protein backbone conformation and C.alpha. and C.beta. 13C nuclear magnetic resonance chemical shifts
journal, July 1991

A probabilistic approach for validating protein NMR chemical shift assignments
journal, May 2010

Water–protein interactions from high–resolution protein crystallography
journal, August 2004

SHIFTX2: significantly improved protein chemical shift prediction
journal, March 2011

Relationship between chemical shift value and accessible surface area for all amino acid atoms
journal, January 2009

1H, 13C and 15N random coil NMR chemical shifts of the common amino acids. I. Investigations of nearest-neighbor effects
journal, January 1995

Multiresolution 3D-DenseNet for Chemical Shift Prediction in NMR Crystallography
journal, July 2019

Coupled prediction of protein secondary and tertiary structure
journal, October 2003

An amino acid has two sides: A new 2D measure provides a different view of solvent exposure
journal, February 2005

Machine Learning Predictions of Molecular Properties: Accurate Many-Body Potentials and Nonlocality in Chemical Space
journal, June 2015

Protein backbone chemical shifts predicted from searching a database for torsion angle and sequence homology
journal, July 2007

Secondary-structure dependent chemical shifts in proteins
journal, August 1990

Experimental Inferential Structure Determination of Ensembles for Intrinsically Disordered Proteins
journal, March 2016

Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding
journal, February 1996

A Simple Method To Predict Protein Flexibility Using Secondary Chemical Shifts
journal, November 2005

Hydrogen bond length and proton NMR chemical shifts in proteins
journal, September 1983

Consistent blind protein structure generation from NMR chemical shift data
journal, March 2008

PPM: a side-chain and backbone chemical shift predictor for the assessment of protein conformational ensembles
journal, September 2012

SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network
journal, July 2010

Chemical Shifts in the Nuclear Magnetic Resonance Spectra of Molecules Containing Polar Groups
journal, February 1960

Water molecules as structural determinants among prions of low sequence identity
journal, April 2006

Asparagine and glutamine: using hydrogen atom contacts in the choice of side-chain amide orientation 1 1Edited by J. Thornton
journal, January 1999

Calibration of ring-current effects in proteins and nucleic acids
journal, December 1995

Chemical shifts in biomolecules
journal, April 2013

Protein Structure Validation and Refinement Using Amide Proton Chemical Shifts Derived from Quantum Mechanics
journal, December 2013

Fast and Accurate Predictions of Protein NMR Chemical Shifts from Interatomic Distances
journal, October 2009

Extremely randomized trees
journal, March 2006

Solution structure of the DNA-binding domain of the yeast transcriptional activator protein GCN4
journal, January 1990

3DRobot: automated generation of diverse and well-packed protein structure decoys
journal, October 2015

mTM-align: an algorithm for fast and accurate multiple protein structure alignment
journal, December 2017

Decoys ‘R’ Us: A database of incorrect conformations to improve protein structure prediction
journal, January 2000

Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field
journal, January 2012

Contact Model for the Prediction of NMR N−H Order Parameters in Globular Proteins
journal, October 2002

Dictionary of protein secondary structure: Pattern recognition of hydrogen-bonded and geometrical features
journal, December 1983

Molecular Dynamics and NMR Spin Relaxation in Proteins
journal, June 2002

A general method applicable to the search for similarities in the amino acid sequence of two proteins
journal, March 1970

Basic local alignment search tool
journal, October 1990

Amino acid substitution matrices from protein blocks.
journal, November 1992

Generalized Neural-Network Representation of High-Dimensional Potential-Energy Surfaces
journal, April 2007

BioMagResBank
journal, December 2007

Unfolded Proteins and Protein Folding Studied by NMR
journal, August 2004

Chemical shifts in molecular solids by machine learning
journal, October 2018

The Protein Data Bank
journal, January 2000

Relationship between nuclear magnetic resonance chemical shift and protein secondary structure
journal, November 1991

Protein chemical shift analysis: a practical guide
journal, May 1998

Experimentally determined hydrophobicity scale for proteins at membrane interfaces
journal, October 1996

Crystal structures of two mutants of adenylate kinase fromEscherichia coli that modify the Gly-loop
journal, January 1993

Ring current theories in nuclear magnetic resonance
journal, January 1979

Random Forests
journal, January 2001

PPM_One: a static protein structure based chemical shift predictor
journal, June 2015