Publications by authors named "Harold A Scheraga"

100Publications

The structure of protein dynamic space.

Proc Natl Acad Sci U S A 2020 08 5;117(33):19938-19942. Epub 2020 Aug 5.

Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, NY 14853;

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http://dx.doi.org/10.1073/pnas.2008873117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7443874PMC
August 2020

Curvature and Torsion of Protein Main Chain as Local Order Parameters of Protein Unfolding.

J Phys Chem B 2020 Jun 24;124(22):4391-4398. Epub 2020 May 24.

Laboratoire Interdisciplinaire Carnot de Bourgogne, UMR 6303, CNRS, Université de Bourgogne Franche-Comté, 9 Av. A. Savary, BP 47 870, F-21078 Cedex Dijon, France.

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http://dx.doi.org/10.1021/acs.jpcb.0c01230DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7362589PMC
June 2020

New Insights into Folding, Misfolding, and Nonfolding Dynamics of a WW Domain.

J Phys Chem B 2020 May 1;124(19):3855-3872. Epub 2020 May 1.

Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca 14853-1301, New York, United States.

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http://dx.doi.org/10.1021/acs.jpcb.0c00628DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7228858PMC
May 2020

Assessing the One-Bond C-H Spin-Spin Coupling Constants in Proteins: Pros and Cons of Different Approaches.

J Phys Chem B 2020 02 23;124(5):735-741. Epub 2020 Jan 23.

IMASL-CONICET, Universidad Nacional de San Luis , Ejército de Los Andes 950 , 5700 San Luis , Argentina.

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http://dx.doi.org/10.1021/acs.jpcb.9b10123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7082799PMC
February 2020

A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields.

J Comput Chem 2018 10 11;39(28):2360-2370. Epub 2018 Oct 11.

Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland.

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http://doi.wiley.com/10.1002/jcc.25571
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http://dx.doi.org/10.1002/jcc.25571DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6487257PMC
October 2018

Dependence of the Formation of Tau and Aβ Peptide Mixed Aggregates on the Secondary Structure of the N-Terminal Region of Aβ.

J Phys Chem B 2018 07 10;122(28):7049-7056. Epub 2018 Jul 10.

Baker Laboratory of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853 , United States.

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http://dx.doi.org/10.1021/acs.jpcb.8b04647DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6524542PMC
July 2018

From a Highly Disordered to a Metastable State: Uncovering Insights of α-Synuclein.

ACS Chem Neurosci 2018 05 26;9(5):1051-1065. Epub 2018 Feb 26.

Baker Laboratory of Chemistry and Chemical Biology , Cornell University , Ithaca , New York 14853-1301 , United States.

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http://dx.doi.org/10.1021/acschemneuro.7b00446DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5955826PMC
May 2018

Statistical Model To Decipher Protein Folding/Unfolding at a Local Scale.

J Phys Chem B 2018 04 28;122(13):3540-3549. Epub 2018 Feb 28.

Laboratoire Interdisciplinaire Carnot de Bourgogne , UMR 6303 CNRS-Univ. de Bourgogne Franche-Comté , 9 Av. A. Savary, BP 47 870 , F-21078 Dijon Cedex , France.

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http://dx.doi.org/10.1021/acs.jpcb.7b10733DOI Listing
April 2018

Dynamics of Disulfide-Bond Disruption and Formation in the Thermal Unfolding of Ribonuclease A.

J Chem Theory Comput 2017 Nov 9;13(11):5721-5730. Epub 2017 Oct 9.

Baker Laboratory of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853-1301, United States.

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http://pubs.acs.org/doi/10.1021/acs.jctc.7b00724
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http://dx.doi.org/10.1021/acs.jctc.7b00724DOI Listing
November 2017

Limiting Values of the one-bond C-H Spin-Spin Coupling Constants of the Imidazole Ring of Histidine at High-pH.

J Mol Struct 2017 Apr 8;1134:576-581. Epub 2017 Jan 8.

Baker Laboratory of Chemistry, Cornell University, Ithaca, NY, USA.

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http://dx.doi.org/10.1016/j.molstruc.2017.01.022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5596661PMC
April 2017

A comprehensive analysis of the computed tautomer fractions of the imidazole ring of histidines in Loligo vulgaris.

J Biomol Struct Dyn 2018 Sep 25;36(12):3094-3105. Epub 2017 Sep 25.

d IMASL-CONICET , Universidad Nacional de San Luis , Ejército de Los Andes 950, 5700 San Luis , Argentina.

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http://dx.doi.org/10.1080/07391102.2017.1377636DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6102090PMC
September 2018

Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics.

J Chem Inf Model 2017 09 5;57(9):2364-2377. Epub 2017 Sep 5.

Faculty of Chemistry, University of Gdańsk , ul. Wita Stwosza 63, 80-308 Gdańsk, Poland.

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http://dx.doi.org/10.1021/acs.jcim.7b00254DOI Listing
September 2017

Sequence-, structure-, and dynamics-based comparisons of structurally homologous CheY-like proteins.

Proc Natl Acad Sci U S A 2017 02 31;114(7):1578-1583. Epub 2017 Jan 31.

Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853;

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http://dx.doi.org/10.1073/pnas.1621344114DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5321002PMC
February 2017

Coupled molecular dynamics and continuum electrostatic method to compute the ionization pKa's of proteins as a function of pH. Test on a large set of proteins.

J Biomol Struct Dyn 2018 02 24;36(3):561-574. Epub 2017 Feb 24.

d IMASL-CONICET, Universidad Nacional de San Luis , Ejército de Los Andes 950, San Luis 5700 , Argentina.

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http://dx.doi.org/10.1080/07391102.2017.1288169DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6191177PMC
February 2018

Elucidating Important Sites and the Mechanism for Amyloid Fibril Formation by Coarse-Grained Molecular Dynamics.

ACS Chem Neurosci 2017 01 18;8(1):201-209. Epub 2016 Nov 18.

Baker Laboratory of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853-1301, United States.

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http://dx.doi.org/10.1021/acschemneuro.6b00331DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5245180PMC
January 2017

Simple Physics-Based Analytical Formulas for the Potentials of Mean Force of the Interaction of Amino Acid Side Chains in Water. VII. Charged-Hydrophobic/Polar and Polar-Hydrophobic/Polar Side Chains.

J Phys Chem B 2017 01 5;121(2):379-390. Epub 2017 Jan 5.

Baker laboratory of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853-1301, United States.

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http://dx.doi.org/10.1021/acs.jpcb.6b08541DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5367159PMC
January 2017

Eliminating a Protein Folding Intermediate by Tuning a Local Hydrophobic Contact.

J Phys Chem B 2017 04 29;121(15):3276-3284. Epub 2016 Sep 29.

Baker Laboratory of Chemistry and Chemical Biology, Cornell University , Ithaca, New York 14853-1301, United States.

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http://dx.doi.org/10.1021/acs.jpcb.6b07250DOI Listing
April 2017

Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction.

J Chem Phys 2016 May;144(18):184110

Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, USA.

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http://dx.doi.org/10.1063/1.4948710DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4866947PMC
May 2016

Global informatics and physical property selection in protein sequences.

Proc Natl Acad Sci U S A 2016 Feb 1;113(7):1808-10. Epub 2016 Feb 1.

Department of Chemistry and Chemical Biology, Baker Laboratory, Cornell University, Ithaca, NY 14853; Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029

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http://dx.doi.org/10.1073/pnas.1525745113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4763726PMC
February 2016

George Hess: A scientific appreciation.

Proc Natl Acad Sci U S A 2016 Feb 25;113(6):1466-7. Epub 2016 Jan 25.

Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853

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http://dx.doi.org/10.1073/pnas.1524997113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4760801PMC
February 2016

Optimization of a Nucleic Acids united-RESidue 2-Point model (NARES-2P) with a maximum-likelihood approach.

J Chem Phys 2015 Dec;143(24):243111

Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA.

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http://aip.scitation.org/doi/10.1063/1.4932082
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http://dx.doi.org/10.1063/1.4932082DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4608961PMC
December 2015

Preventing fibril formation of a protein by selective mutation.

Proc Natl Acad Sci U S A 2015 Nov 19;112(44):13549-54. Epub 2015 Oct 19.

Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301;

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http://dx.doi.org/10.1073/pnas.1518298112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4640778PMC
November 2015

Theoretical Studies of Interactions between O-Phosphorylated and Standard Amino-Acid Side-Chain Models in Water.

J Phys Chem B 2015 Jul 30;119(27):8526-34. Epub 2015 Jun 30.

†Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland.

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http://dx.doi.org/10.1021/acs.jpcb.5b04782DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4664056PMC
July 2015

My 65 years in protein chemistry.

Q Rev Biophys 2015 May 8;48(2):117-77. Epub 2015 Apr 8.

Baker Laboratory of Chemistry,Cornell University,Ithaca,NY 14853-1301,USA.

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http://dx.doi.org/10.1017/S0033583514000134DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4450725PMC
May 2015

Alternative approach to protein structure prediction based on sequential similarity of physical properties.

Proc Natl Acad Sci U S A 2015 Apr 6;112(16):5029-32. Epub 2015 Apr 6.

Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853; and

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http://www.pnas.org/content/112/16/5029.full.pdf
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http://www.pnas.org/lookup/doi/10.1073/pnas.1504806112
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http://dx.doi.org/10.1073/pnas.1504806112DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4413275PMC
April 2015

Folding kinetics of WW domains with the united residue force field for bridging microscopic motions and experimental measurements.

Proc Natl Acad Sci U S A 2014 Dec 8;111(51):18243-8. Epub 2014 Dec 8.

Laboratory of Molecular Modeling, Faculty of Chemistry, University of Gdańsk, 80-308 Gdańsk, Poland;

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http://dx.doi.org/10.1073/pnas.1420914111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4280612PMC
December 2014

Common functionally important motions of the nucleotide-binding domain of Hsp70.

Proteins 2015 Feb 18;83(2):282-99. Epub 2014 Dec 18.

Faculty of Chemistry, University of Gdańsk, 80-308, Gdańsk, Poland.

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http://dx.doi.org/10.1002/prot.24731DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4300246PMC
February 2015

DNA Duplex Formation with a Coarse-Grained Model.

J Chem Theory Comput 2014 Nov 22;10(11):5020-5035. Epub 2014 Sep 22.

Baker Laboratory of Chemistry, Cornell University , Ithaca, New York 14850, United States.

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http://dx.doi.org/10.1021/ct4006689DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4230386PMC
November 2014

Factors affecting the computation of the 13C shielding in disaccharides.

J Comput Chem 2014 Sep 28;35(25):1854-64. Epub 2014 Jul 28.

IMASL-CONICET, Universidad Nacional de San Luis, Italia 1556, 5700-San Luis, Argentina.

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http://dx.doi.org/10.1002/jcc.23697DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383045PMC
September 2014

Accounting for a mirror-image conformation as a subtle effect in protein folding.

Proc Natl Acad Sci U S A 2014 Jun 27;111(23):8458-63. Epub 2014 May 27.

Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301;

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http://www.pnas.org/cgi/doi/10.1073/pnas.1407837111
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http://dx.doi.org/10.1073/pnas.1407837111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4060689PMC
June 2014

Revised Backbone-Virtual-Bond-Angle Potentials to Treat the l- and d-Amino Acid Residues in the Coarse-Grained United Residue (UNRES) Force Field.

J Chem Theory Comput 2014 May 15;10(5):2194-2203. Epub 2014 Apr 15.

Faculty of Chemistry, University of Gdańsk , Wita Stwosza 63, 80-308 Gdańsk, Poland.

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http://dx.doi.org/10.1021/ct500119rDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4020588PMC
May 2014

Homolog detection using global sequence properties suggests an alternate view of structural encoding in protein sequences.

Proc Natl Acad Sci U S A 2014 Apr 24;111(14):5225-9. Epub 2014 Mar 24.

Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853.

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http://dx.doi.org/10.1073/pnas.1403599111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3986189PMC
April 2014

Kinks, loops, and protein folding, with protein A as an example.

J Chem Phys 2014 Jan;140(2):025101

Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, USA.

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http://dx.doi.org/10.1063/1.4855735DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3899063PMC
January 2014

Are accurate computations of the 13C' shielding feasible at the DFT level of theory?

J Comput Chem 2014 Feb 3;35(4):309-12. Epub 2013 Dec 3.

IMASL-CONICET, Universidad Nacional de San Luis, Italia 1556, 5700-San Luis, Argentina; Department of Chemistry and Chemical Biology, Cornell University, Ithaca, NY, 14853.

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http://dx.doi.org/10.1002/jcc.23499DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3902030PMC
February 2014

Physics-based method to validate and repair flaws in protein structures.

Proc Natl Acad Sci U S A 2013 Oct 30;110(42):16826-31. Epub 2013 Sep 30.

Instituto de Matemática Aplicada San Luis, Consejo Nacional de Investigaciones Científicas y Técnicas de Argentina, Departamento de Física, Universidad Nacional de San Luis, 5700 San Luis, Argentina.

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http://dx.doi.org/10.1073/pnas.1315525110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3801053PMC
October 2013

Local vs global motions in protein folding.

J Chem Theory Comput 2013 Jul;9(7):2907-2921

Baker Laboratory of Chemistry and Chemical Biology, Cornell University Ithaca, New York 14853-1301.

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http://pubs.acs.org/doi/10.1021/ct4001558
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http://dx.doi.org/10.1021/ct4001558DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3727290PMC
July 2013

Mean-field interactions between nucleic-acid-base dipoles can drive the formation of a double helix.

Phys Rev Lett 2013 Mar 28;110(9):098101. Epub 2013 Feb 28.

Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3627500PMC
http://dx.doi.org/10.1103/PhysRevLett.110.098101DOI Listing
March 2013

A generalized G-SFED continuum solvation free energy calculation model.

Proc Natl Acad Sci U S A 2013 Feb 1;110(8):E662-7. Epub 2013 Feb 1.

Department of Biotechnology, Yonsei University, Seoul 120-749, Korea.

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http://dx.doi.org/10.1073/pnas.1221940110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3581891PMC
February 2013

Influence of the Length of the Alanine Spacer on the Acidic-Basic Properties of the Ac-Lys-(Ala)(n)-Lys-NH(2) Peptides (n = 0, 1, 2, …, 5).

J Solution Chem 2012 Nov 13;41(10):1738-1746. Epub 2012 Oct 13.

Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland ; Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301 USA.

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http://dx.doi.org/10.1007/s10953-012-9903-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3510421PMC
November 2012

Extension of UNRES force field to treat polypeptide chains with D-amino-acid residues.

J Chem Theory Comput 2012 Nov;8(11):4746-4757

Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland.

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http://dx.doi.org/10.1021/ct3005563DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3982868PMC
November 2012

CheShift-2 resolves a local inconsistency between two X-ray crystal structures.

J Biomol NMR 2012 Oct 4;54(2):193-8. Epub 2012 Sep 4.

Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.

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http://dx.doi.org/10.1007/s10858-012-9663-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3471536PMC
October 2012

Coexistence of phases in a protein heterodimer.

J Chem Phys 2012 Jul;137(3):035101

Department of Physics and Astronomy and Science for Life Laboratory, Uppsala University, P.O. Box 803, S-75108 Uppsala, Sweden.

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http://dx.doi.org/10.1063/1.4734019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3411598PMC
July 2012

Simulation of the opening and closing of Hsp70 chaperones by coarse-grained molecular dynamics.

J Chem Theory Comput 2012 May 15;8(5):1750-1764. Epub 2012 Mar 15.

Faculty of Chemistry, University of Gdánsk, Sobieskiego 18, 80-952 Gdánsk, Poland.

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http://dx.doi.org/10.1021/ct200680gDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3380372PMC
May 2012

Hidden protein folding pathways in free-energy landscapes uncovered by network analysis.

J Chem Theory Comput 2012 Apr 24;8(4):1176-1189. Epub 2012 Feb 24.

Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, 14850-1301.

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http://dx.doi.org/10.1021/ct200806nDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3376395PMC
April 2012

Anomalous diffusion and dynamical correlation between the side chains and the main chain of proteins in their native state.

Proc Natl Acad Sci U S A 2012 Jun 11;109(26):10346-51. Epub 2012 Jun 11.

Laboratoire Interdisciplinaire Carnot de Bourgogne, Unité Mixte de Recherche 6303 Centre National de la Recherche Scientifique-Université de Bourgogne, 9 Avenue A Savary, BP 47 870, F-21078 Dijon Cedex, France.

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http://dx.doi.org/10.1073/pnas.1207083109DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3387131PMC
June 2012

Effects of mutation, truncation, and temperature on the folding kinetics of a WW domain.

J Mol Biol 2012 Jul 2;420(4-5):350-65. Epub 2012 May 2.

Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.

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http://dx.doi.org/10.1016/j.jmb.2012.04.027DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3586707PMC
July 2012

CheShift-2: graphic validation of protein structures.

Bioinformatics 2012 Jun 11;28(11):1538-9. Epub 2012 Apr 11.

Universidad Nacional de San Luis, IMASL-CONICET, Ejército de Los Andes, San Luis, Argentina.

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http://dx.doi.org/10.1093/bioinformatics/bts179DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3356844PMC
June 2012

Like-charged residues at the ends of oligoalanine sequences might induce a chain reversal.

Biopolymers 2012 Apr 9;97(4):240-9. Epub 2011 Dec 9.

Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland.

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http://dx.doi.org/10.1002/bip.22013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3371584PMC
April 2012

Identification of formation of initial native structure in onconase from an unfolded state.

Biochemistry 2012 Jan 14;51(1):521-32. Epub 2011 Dec 14.

Baker Laboratory of Chemistry, Cornell University, Ithaca, New York 14853-1301, United States.

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http://dx.doi.org/10.1021/bi201168dDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3254794PMC
January 2012

A study of the α-helical intermediate preceding the aggregation of the amino-terminal fragment of the β amyloid peptide (Aβ(1-28)).

J Phys Chem B 2011 Nov 18;115(44):12978-83. Epub 2011 Oct 18.

Baker Laboratory of Chemistry, Department of Chemistry and Chemical Biology, Cornell Universty, Ithaca, New York 14853-1301, United States.

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http://dx.doi.org/10.1021/jp2050993DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3236598PMC
November 2011

Coarse-grained force field: general folding theory.

Phys Chem Chem Phys 2011 Oct 3;13(38):16890-901. Epub 2011 Jun 3.

Faculty of Chemistry, University of Gdansk, ul. Sobieskiego 18, 80-952 Gdansk, Poland.

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http://dx.doi.org/10.1039/c1cp20752kDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3362049PMC
October 2011

Respice, adspice, and prospice.

Annu Rev Biophys 2011 ;40:1-39

Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.

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http://dx.doi.org/10.1146/annurev-biophys-042910-155334DOI Listing
September 2011

Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. V. Like-charged side chains.

J Phys Chem B 2011 May 18;115(19):6119-29. Epub 2011 Apr 18.

Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland.

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http://dx.doi.org/10.1021/jp111258pDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3099398PMC
May 2011

Simple physics-based analytical formulas for the potentials of mean force of the interaction of amino-acid side chains in water. VI. Oppositely charged side chains.

J Phys Chem B 2011 May 18;115(19):6130-7. Epub 2011 Apr 18.

Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland.

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http://dx.doi.org/10.1021/jp111259eDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3093716PMC
May 2011

Assessing the fractions of tautomeric forms of the imidazole ring of histidine in proteins as a function of pH.

Proc Natl Acad Sci U S A 2011 Apr 21;108(14):5602-7. Epub 2011 Mar 21.

Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.

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http://dx.doi.org/10.1073/pnas.1102373108DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3078339PMC
April 2011

PDZ binding to the BAR domain of PICK1 is elucidated by coarse-grained molecular dynamics.

J Mol Biol 2011 Jan 2;405(1):298-314. Epub 2010 Nov 2.

Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, USA.

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https://linkinghub.elsevier.com/retrieve/pii/S00222836100118
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http://dx.doi.org/10.1016/j.jmb.2010.10.051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3008210PMC
January 2011

Nonexponential decay of internal rotational correlation functions of native proteins and self-similar structural fluctuations.

Proc Natl Acad Sci U S A 2010 Nov 2;107(46):19844-9. Epub 2010 Nov 2.

Laboratoire Interdisciplinaire Carnot de Bourgogne, Unité Mixte de Recherche 5209 Centre National de la Recherche Scientifique-Université de Bourgogne, 9 Avenue A. Savary, BP 47 870, F-21078 Dijon Cedex, France.

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http://www.pnas.org/cgi/doi/10.1073/pnas.1013674107
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http://dx.doi.org/10.1073/pnas.1013674107DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2993386PMC
November 2010

Mechanism of fiber assembly: treatment of Aβ peptide aggregation with a coarse-grained united-residue force field.

J Mol Biol 2010 Dec 1;404(3):537-52. Epub 2010 Oct 1.

Department of Physics and Astronomy, Louisiana State University, Baton Rouge, LA 70803, USA.

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http://dx.doi.org/10.1016/j.jmb.2010.09.057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2981693PMC
December 2010

Sequential nearest-neighbor effects on computed 13Calpha chemical shifts.

J Biomol NMR 2010 Sep 20;48(1):23-30. Epub 2010 Jul 20.

Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.

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http://dx.doi.org/10.1007/s10858-010-9435-7DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2970923PMC
September 2010

Evidence, from simulations, of a single state with residual native structure at the thermal denaturation midpoint of a small globular protein.

J Am Chem Soc 2010 Jul;132(27):9444-52

Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, USA.

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http://dx.doi.org/10.1021/ja1031503DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2910365PMC
July 2010

beta-hairpin-forming peptides; models of early stages of protein folding.

Biophys Chem 2010 Sep 6;151(1-2):1-9. Epub 2010 May 6.

University of Gdańsk and Medical University of Gdańsk, Poland.

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http://dx.doi.org/10.1016/j.bpc.2010.05.001DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2906654PMC
September 2010

Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field.

J Phys Chem A 2010 Apr;114(13):4471-85

Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, USA.

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https://pubs.acs.org/doi/10.1021/jp9117776
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2849147PMC
April 2010

Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with alpha and alpha+beta Proteins.

J Chem Theory Comput 2009 Mar;5(3):627-640

Baker Laboratory of Chemisty and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, and, Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland.

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http://dx.doi.org/10.1021/ct800397zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2790289PMC
March 2009

Relation between free energy landscapes of proteins and dynamics.

J Chem Theory Comput 2010 Feb;6(2):583-595

Baker Laboratory of Chemistry and Chemical Biology, Cornell University Ithaca, New York 14853-1301.

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http://dx.doi.org/10.1021/ct9005745DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3633568PMC
February 2010

Analysis of 13Calpha and 13Cbeta chemical shifts of cysteine and cystine residues in proteins: a quantum chemical approach.

J Biomol NMR 2010 Mar 21;46(3):217-25. Epub 2010 Jan 21.

Instituto de Matemática Aplicada San Luis, Universidad Nacional de San Luis, CONICET, Ejército de Los Andes 950, 5700, San Luis, Argentina.

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http://dx.doi.org/10.1007/s10858-010-9396-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2864455PMC
March 2010

Role of the surface loop on the structure and biological activity of angiogenin.

BMB Rep 2009 Dec;42(12):829-33

Department of Bioinformatics and Life Science, and CAMDRC, Soongsil University, Seoul 156-743, Korea.

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http://dx.doi.org/10.5483/bmbrep.2009.42.12.829DOI Listing
December 2009

Potential of mean force of association of large hydrophobic particles: toward the nanoscale limit.

J Phys Chem B 2010 Jan;114(2):993-1003

Faculty of Chemistry, University of Gdańsk, ul. Sobieskiego 18, 80-952 Gdańsk, Poland.

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http://dx.doi.org/10.1021/jp907794hDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2826153PMC
January 2010

Coarse-grained model of nucleic acid bases.

J Comput Chem 2010 Jun;31(8):1644-55

Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, USA.

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http://dx.doi.org/10.1002/jcc.21448DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7219547PMC
June 2010

Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. III. Dynamics of long-range hydrophobic interactions.

Proteins 2010 Feb;78(3):723-37

Laboratory of Biopolymer Structure, Intercollegiate Faculty of Biotechnology, University of Gdańsk, Medical University of Gdańsk, Kładki 24, 80-822 Gdańsk, Poland.

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http://doi.wiley.com/10.1002/prot.22605
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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3074100PMC
February 2010

Quantum-mechanics-derived 13Calpha chemical shift server (CheShift) for protein structure validation.

Proc Natl Acad Sci U S A 2009 Oct 8;106(40):16972-7. Epub 2009 Sep 8.

Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca NY, 14853-1301, USA.

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http://dx.doi.org/10.1073/pnas.0908833106DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2761357PMC
October 2009

How adequate are one- and two-dimensional free energy landscapes for protein folding dynamics?

Phys Rev Lett 2009 Jun 12;102(23):238102. Epub 2009 Jun 12.

Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760970PMC
http://dx.doi.org/10.1103/PhysRevLett.102.238102DOI Listing
June 2009

Assessing the accuracy of protein structures by quantum mechanical computations of 13C(alpha) chemical shifts.

Acc Chem Res 2009 Oct;42(10):1545-53

Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, USA.

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http://dx.doi.org/10.1021/ar900068sDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3396562PMC
October 2009

What can we learn by computing 13Calpha chemical shifts for X-ray protein models?

Acta Crystallogr D Biol Crystallogr 2009 Jul 20;65(Pt 7):697-703. Epub 2009 Jun 20.

Baker Laboratory of Chemistry and Chemical Biology, Cornell University, Ithaca, NY 14853-1301, USA.

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http://dx.doi.org/10.1107/S0907444909012086DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2703576PMC
July 2009

Towards temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. I: molecular dynamics study of a pair of methane molecules in water at various temperatures.

Protein Eng Des Sel 2009 Sep 25;22(9):547-52. Epub 2009 Jun 25.

Laboratory of Biopolymer Structure, Intercollegiate Faculty of Biotechnology, University of Gdańsk, Medical University of Gdańsk, Kładki 24, 80-822 Gdańsk.

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http://dx.doi.org/10.1093/protein/gzp028DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2909823PMC
September 2009

Exploring the parameter space of the coarse-grained UNRES force field by random search: selecting a transferable medium-resolution force field.

J Comput Chem 2009 Oct;30(13):2127-35

Biomolecular Physics and Modeling Group, School of Physics, Huazhong University of Science and Technology, Wuhan 430074, China.

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http://dx.doi.org/10.1002/jcc.21215DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2760447PMC
October 2009