Literature DB >> 34845623

Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field.

Adam K Sieradzan1, Cezary Czaplewski1, Paweł Krupa2, Magdalena A Mozolewska3, Agnieszka S Karczyńska1, Agnieszka G Lipska1, Emilia A Lubecka4, Ewa Gołaś2, Tomasz Wirecki5, Mariusz Makowski1, Stanisław Ołdziej6, Adam Liwo7.   

Abstract

The physics-based united-residue (UNRES) model of proteins ( www.unres.pl ) has been designed to carry out large-scale simulations of protein folding. The force field has been derived and parameterized based on the principles of statistical-mechanics, which makes it independent of structural databases and applicable to treat nonstandard situations such as, proteins that contain D-amino-acid residues. Powered by Langevin dynamics and its replica-exchange extensions, UNRES has found a variety of applications, including ab initio and database-assisted protein-structure prediction, simulating protein-folding pathways, exploring protein free-energy landscapes, and solving biological problems. This chapter provides a summary of UNRES and a guide for potential users regarding the application of the UNRES package in a variety of research tasks.
© 2022. Springer Science+Business Media, LLC, part of Springer Nature.

Entities:  

Keywords:  Coarse graining; Molecular dynamics simulations; Protein dynamics; Protein folding; Protein–structure prediction

Mesh：

Substances：

Year:  2022        PMID： 34845623     DOI： 10.1007/978-1-0716-1716-8_23

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN： 1064-3745


  44 in total

1.  Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains.

Authors:  Adam Liwo; Mey Khalili; Harold A Scheraga
Journal:  Proc Natl Acad Sci U S A       Date:  2005-01-26       Impact factor: 11.205

2.  Lessons from application of the UNRES force field to predictions of structures of CASP10 targets.

Authors:  Yi He; Magdalena A Mozolewska; Pawel Krupa; Adam K Sieradzan; Tomasz K Wirecki; Adam Liwo; Khatuna Kachlishvili; Shalom Rackovsky; Dawid Jagiela; Rafał Ślusarz; Cezary R Czaplewski; Stanisław Ołdziej; Harold A Scheraga
Journal:  Proc Natl Acad Sci U S A       Date:  2013-08-26       Impact factor: 11.205

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

Authors:  Emilia A Lubecka; Agnieszka S Karczyńska; Agnieszka G Lipska; Adam K Sieradzan; Karolina Ziȩba; Celina Sikorska; Urszula Uciechowska; Sergey A Samsonov; Paweł Krupa; Magdalena A Mozolewska; Łukasz Golon; Artur Giełdoń; Cezary Czaplewski; Rafał Ślusarz; Magdalena Ślusarz; Silvia N Crivelli; Adam Liwo
Journal:  J Mol Graph Model       Date:  2019-07-26       Impact factor: 2.518

Review 4.  Coarse-Grained Protein Models and Their Applications.

Authors:  Sebastian Kmiecik; Dominik Gront; Michal Kolinski; Lukasz Wieteska; Aleksandra Elzbieta Dawid; Andrzej Kolinski
Journal:  Chem Rev       Date:  2016-06-22       Impact factor: 60.622

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

Authors:  Agnieszka S Karczyńska; Magdalena A Mozolewska; Paweł Krupa; Artur Giełdoń; Adam Liwo; Cezary Czaplewski
Journal:  Proteins       Date:  2017-11-29

6.  WeFold: a coopetition for protein structure prediction.

Authors:  George A Khoury; Adam Liwo; Firas Khatib; Hongyi Zhou; Gaurav Chopra; Jaume Bacardit; Leandro O Bortot; Rodrigo A Faccioli; Xin Deng; Yi He; Pawel Krupa; Jilong Li; Magdalena A Mozolewska; Adam K Sieradzan; James Smadbeck; Tomasz Wirecki; Seth Cooper; Jeff Flatten; Kefan Xu; David Baker; Jianlin Cheng; Alexandre C B Delbem; Christodoulos A Floudas; Chen Keasar; Michael Levitt; Zoran Popović; Harold A Scheraga; Jeffrey Skolnick; Silvia N Crivelli
Journal:  Proteins       Date:  2014-07-08

7.  The MARTINI Coarse-Grained Force Field: Extension to Proteins.

Authors:  Luca Monticelli; Senthil K Kandasamy; Xavier Periole; Ronald G Larson; D Peter Tieleman; Siewert-Jan Marrink
Journal:  J Chem Theory Comput       Date:  2008-05       Impact factor: 6.006

8.  A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. I. Backbone potentials of coarse-grained polypeptide chains.

Authors:  Adam K Sieradzan; Mariusz Makowski; Antoni Augustynowicz; Adam Liwo
Journal:  J Chem Phys       Date:  2017-03-28       Impact factor: 3.488

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

Authors:  Gia G Maisuradze; Patrick Senet; Cezary Czaplewski; Adam Liwo; Harold A Scheraga
Journal:  J Phys Chem A       Date:  2010-04-08       Impact factor: 2.781

10.  Improved Consensus-Fragment Selection in Template-Assisted Prediction of Protein Structures with the UNRES Force Field in CASP13.

Authors:  Agnieszka S Karczyńska; Karolina Ziȩba; Urszula Uciechowska; Magdalena A Mozolewska; Paweł Krupa; Emilia A Lubecka; Agnieszka G Lipska; Celina Sikorska; Sergey A Samsonov; Adam K Sieradzan; Artur Giełdoń; Adam Liwo; Rafał Ślusarz; Magdalena Ślusarz; Jooyoung Lee; Keehyoung Joo; Cezary Czaplewski
Journal:  J Chem Inf Model       Date:  2020-02-11       Impact factor: 4.956
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  2 in total

1.  Automated Protein Secondary Structure Assignment from Cα Positions Using Neural Networks.

Authors:  Mohammad N Saqib; Justyna D Kryś; Dominik Gront
Journal:  Biomolecules       Date:  2022-06-17

2.  Prediction of Aggregation of Biologically-Active Peptides with the UNRES Coarse-Grained Model.

Authors:  Iga Biskupek; Cezary Czaplewski; Justyna Sawicka; Emilia Iłowska; Maria Dzierżyńska; Sylwia Rodziewicz-Motowidło; Adam Liwo
Journal:  Biomolecules       Date:  2022-08-18
  2 in total

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