Publications by authors named "Adam Liwo"

100Publications

UNRES-Dock - protein-protein and peptide-protein docking by coarse-grained replica-exchange MD simulations.

Bioinformatics 2020 Oct 18. Epub 2020 Oct 18.

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

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http://dx.doi.org/10.1093/bioinformatics/btaa897DOI Listing
October 2020

Hydrophobic hydration and pairwise hydrophobic interaction of Lennard-Jones and Mie particles in different water models.

Phys Chem Chem Phys 2020 Feb;22(8):4758-4771

Department of Science and Technology, University of Sannio, Via Francesco de Sanctis snc, 82100 Benevento, Italy.

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http://dx.doi.org/10.1039/c9cp06627fDOI Listing
February 2020

Extension of the force-matching method to coarse-grained models with axially symmetric sites to produce transferable force fields: Application to the UNRES model of proteins.

J Chem Phys 2020 Feb;152(5):054902

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

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http://dx.doi.org/10.1063/1.5138991DOI Listing
February 2020

Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment.

Authors:
Marc F Lensink Guillaume Brysbaert Nurul Nadzirin Sameer Velankar Raphaël A G Chaleil Tereza Gerguri Paul A Bates Elodie Laine Alessandra Carbone Sergei Grudinin Ren Kong Ran-Ran Liu Xi-Ming Xu Hang Shi Shan Chang Miriam Eisenstein Agnieszka Karczynska Cezary Czaplewski Emilia Lubecka Agnieszka Lipska Paweł Krupa Magdalena Mozolewska Łukasz Golon Sergey Samsonov Adam Liwo Silvia Crivelli Guillaume Pagès Mikhail Karasikov Maria Kadukova Yumeng Yan Sheng-You Huang Mireia Rosell Luis A Rodríguez-Lumbreras Miguel Romero-Durana Lucía Díaz-Bueno Juan Fernandez-Recio Charles Christoffer Genki Terashi Woong-Hee Shin Tunde Aderinwale Sai Raghavendra Maddhuri Venkata Subraman Daisuke Kihara Dima Kozakov Sandor Vajda Kathryn Porter Dzmitry Padhorny Israel Desta Dmitri Beglov Mikhail Ignatov Sergey Kotelnikov Iain H Moal David W Ritchie Isaure Chauvot de Beauchêne Bernard Maigret Marie-Dominique Devignes Maria E Ruiz Echartea Didier Barradas-Bautista Zhen Cao Luigi Cavallo Romina Oliva Yue Cao Yang Shen Minkyung Baek Taeyong Park Hyeonuk Woo Chaok Seok Merav Braitbard Lirane Bitton Dina Scheidman-Duhovny Justas Dapkūnas Kliment Olechnovič Česlovas Venclovas Petras J Kundrotas Saveliy Belkin Devlina Chakravarty Varsha D Badal Ilya A Vakser Thom Vreven Sweta Vangaveti Tyler Borrman Zhiping Weng Johnathan D Guest Ragul Gowthaman Brian G Pierce Xianjin Xu Rui Duan Liming Qiu Jie Hou Benjamin Ryan Merideth Zhiwei Ma Jianlin Cheng Xiaoqin Zou Panagiotis I Koukos Jorge Roel-Touris Francesco Ambrosetti Cunliang Geng Jörg Schaarschmidt Mikael E Trellet Adrien S J Melquiond Li Xue Brian Jiménez-García Charlotte W van Noort Rodrigo V Honorato Alexandre M J J Bonvin Shoshana J Wodak

Proteins 2019 12 25;87(12):1200-1221. Epub 2019 Oct 25.

VIB Structural Biology Research Center, VUB, Brussels, Belgium.

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http://dx.doi.org/10.1002/prot.25838DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7274794PMC
December 2019

Extension of the UNRES Coarse-Grained Force Field to Membrane Proteins in the Lipid Bilayer.

J Phys Chem B 2019 09 10;123(37):7829-7839. Epub 2019 Sep 10.

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.9b06700DOI Listing
September 2019

Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment.

J Mol Graph Model 2019 11 26;92:154-166. Epub 2019 Jul 26.

Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308, Gdańsk, Poland; School of Computational Sciences, Korea Institute for Advanced Study, 85 Hoegiro, Dongdaemun-gu, 130-722, Seoul, Republic of Korea. Electronic address:

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http://dx.doi.org/10.1016/j.jmgm.2019.07.013DOI Listing
November 2019

Introduction of Phosphorylated Residues into the UNRES Coarse-Grained Model: Toward Modeling of Signaling Processes.

J Phys Chem B 2019 07 26;123(27):5721-5729. Epub 2019 Jun 26.

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.jpcb.9b03799DOI Listing
July 2019

The molecular mechanism of structural changes in the antimicrobial peptide CM15 upon complex formation with drug molecule suramin: a computational analysis.

Phys Chem Chem Phys 2019 May 13;21(20):10644-10659. Epub 2019 May 13.

Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Magyar tudósok körútja 2, H-1117 Budapest, Hungary. and Department of Chemical and Biological Engineering, Physical Chemistry, Chalmers University of Technology, SE-412 96 Göteborg, Sweden.

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http://dx.doi.org/10.1039/c9cp00471hDOI Listing
May 2019

Introduction of a bounded penalty function in contact-assisted simulations of protein structures to omit false restraints.

J Comput Chem 2019 09 29;40(25):2164-2178. Epub 2019 Apr 29.

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

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http://dx.doi.org/10.1002/jcc.25847DOI Listing
September 2019

Local and long range potentials for heparin-protein systems for coarse-grained simulations.

Biopolymers 2019 Aug 13;110(8):e23269. Epub 2019 Mar 13.

Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland.

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http://dx.doi.org/10.1002/bip.23269DOI Listing
August 2019

Reoptimized UNRES Potential for Protein Model Quality Assessment.

Genes (Basel) 2018 Dec 3;9(12). Epub 2018 Dec 3.

Battelle Center for Mathematical Medicine, Nationwide Children's Hospital, Columbus, OH 43215, USA.

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http://dx.doi.org/10.3390/genes9120601DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6315818PMC
December 2018

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

Insights into the structure and dynamics of lysyl oxidase propeptide, a flexible protein with numerous partners.

Sci Rep 2018 08 6;8(1):11768. Epub 2018 Aug 6.

Univ Lyon, University Claude Bernard Lyon 1, CNRS, INSA Lyon, CPE, Institute of Molecular and Supramolecular Chemistry and Biochemistry, UMR 5246, F-69622, Villeurbanne cedex, France.

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http://dx.doi.org/10.1038/s41598-018-30190-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6078952PMC
August 2018

Protein-Ligand Interaction Energy-Based Entropy Calculations: Fundamental Challenges For Flexible Systems.

J Phys Chem B 2018 08 8;122(32):7821-7827. Epub 2018 Aug 8.

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.jpcb.8b03658DOI Listing
August 2018

Prediction of DNA and RNA structure with the NARES-2P force field and conformational space annealing.

Phys Chem Chem Phys 2018 Jul;20(29):19656-19663

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

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http://dx.doi.org/10.1039/c8cp03018aDOI Listing
July 2018

An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12.

Sci Rep 2018 07 2;8(1):9939. Epub 2018 Jul 2.

Lawrence Berkeley National Laboratory, Berkeley, CA, USA.

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http://dx.doi.org/10.1038/s41598-018-26812-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6028396PMC
July 2018

UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics.

Nucleic Acids Res 2018 07;46(W1):W304-W309

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

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http://dx.doi.org/10.1093/nar/gky328DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6031057PMC
July 2018

Prediction of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information.

Proteins 2018 03 29;86 Suppl 1:228-239. Epub 2017 Nov 29.

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

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http://dx.doi.org/10.1002/prot.25421DOI Listing
March 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

Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins.

J Comput Chem 2017 12 22;38(31):2730-2746. Epub 2017 Sep 22.

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

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http://dx.doi.org/10.1002/jcc.25070DOI Listing
December 2017

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

In situ data analytics and indexing of protein trajectories.

J Comput Chem 2017 06 17;38(16):1419-1430. Epub 2017 Jan 17.

Department of Computer and Information Sciences, University of Delaware, Newark, DE 19711, USA.

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http://dx.doi.org/10.1002/jcc.24729DOI Listing
June 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

Use of Restraints from Consensus Fragments of Multiple Server Models To Enhance Protein-Structure Prediction Capability of the UNRES Force Field.

J Chem Inf Model 2016 11 28;56(11):2263-2279. Epub 2016 Oct 28.

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

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http://dx.doi.org/10.1021/acs.jcim.6b00189DOI Listing
November 2016

Role of the sulfur to α-carbon thioether bridges in thurincin H.

J Biomol Struct Dyn 2017 Oct 5;35(13):2868-2879. Epub 2016 Oct 5.

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

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http://dx.doi.org/10.1080/07391102.2016.1234414DOI Listing
October 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

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

A Maximum-Likelihood Approach to Force-Field Calibration.

J Chem Inf Model 2015 Sep 20;55(9):2050-70. Epub 2015 Aug 20.

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.5b00395DOI Listing
September 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

Prediction of Protein Structure by Template-Based Modeling Combined with the UNRES Force Field.

J Chem Inf Model 2015 Jun 22;55(6):1271-81. Epub 2015 May 22.

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

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http://dx.doi.org/10.1021/acs.jcim.5b00117DOI Listing
June 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

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

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

Folding and self-assembly of a small protein complex.

J Chem Theory Comput 2012 Sep;8(9):3416-3422

Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland ; Department of Chemistry and Biochemistry, Oklahoma University, Norman, OK, 73019, U.S.A.

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http://dx.doi.org/10.1021/ct300528rDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3771543PMC
September 2012

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

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

Multiple β-sheet molecular dynamics of amyloid formation from two ABl-SH3 domain peptides.

Biopolymers 2012 ;98(6):557-66

Latvian Institute of Organic Synthesis, Riga, LV1006, Latvia.

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http://dx.doi.org/10.1002/bip.22161DOI Listing
April 2013

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

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

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

Conformational dynamics of the trp-cage miniprotein at its folding temperature.

J Phys Chem B 2012 Jun 22;116(23):6898-907. Epub 2012 Apr 22.

Laboratory of Biopolymer Structure, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Kładki 24, 80-922 Gdańsk, Poland.

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http://dx.doi.org/10.1021/jp212630yDOI Listing
June 2012

Toward temperature-dependent coarse-grained potentials of side-chain interactions for protein folding simulations. II. Molecular dynamics study of pairs of different types of interactions in water at various temperatures.

J Phys Chem B 2012 Jun 16;116(23):6844-53. Epub 2012 Apr 16.

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://dx.doi.org/10.1021/jp212593hDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3376214PMC
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

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

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

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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http://dx.doi.org/10.1016/j.jmb.2010.10.051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3008210PMC
January 2011

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

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://www.ncbi.nlm.nih.gov/pmc/articles/PMC3633568PMC
February 2010

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

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://dx.doi.org/10.1103/PhysRevLett.102.238102DOI Listing
June 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

Dynamics study on single and multiple beta-sheets.

Adv Exp Med Biol 2009 ;611:293-4

Latvian Institute of Organic Synthesis, Riga, LV1006, Latvia.

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http://dx.doi.org/10.1007/978-0-387-73657-0_131DOI Listing
June 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

Mechanism of formation of the C-terminal beta-hairpin of the B3 domain of the immunoglobulin binding protein G from Streptococcus. I. Importance of hydrophobic interactions in stabilization of beta-hairpin structure.

Proteins 2009 Jun;75(4):931-53

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

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http://dx.doi.org/10.1002/prot.22304DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2791351PMC
June 2009

Principal component analysis for protein folding dynamics.

J Mol Biol 2009 Jan 15;385(1):312-29. Epub 2008 Oct 15.

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.2008.10.018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2652707PMC
January 2009

Conformational studies of the C-terminal 16-amino-acid-residue fragment of the B3 domain of the immunoglobulin binding protein G from Streptococcus.

Biopolymers 2009 Jan;91(1):37-51

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://dx.doi.org/10.1002/bip.21080DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2766666PMC
January 2009

Influence of charge and size of terminal amino-acid residues on local conformational states and shape of alanine-based peptides.

Biopolymers 2008 ;90(6):772-82

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

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February 2009