These tools will no longer be maintained as of December 31, 2024. Archived website can be found here. PubMed4Hh GitHub repository can be found here. Contact NLM Customer Service if you have questions.
134 related articles for article (PubMed ID: 20011673)
1. Implementation of a Serial Replica Exchange Method in a Physics-Based United-Residue (UNRES) Force Field. Shen H; Czaplewski C; Liwo A; Scheraga HA J Chem Theory Comput; 2008 Aug; 4(8):1386-1400. PubMed ID: 20011673 [TBL] [Abstract][Full Text] [Related]
2. Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins. Liwo A; Khalili M; Czaplewski C; Kalinowski S; Ołdziej S; Wachucik K; Scheraga HA J Phys Chem B; 2007 Jan; 111(1):260-85. PubMed ID: 17201450 [TBL] [Abstract][Full Text] [Related]
3. An improved functional form for the temperature scaling factors of the components of the mesoscopic UNRES force field for simulations of protein structure and dynamics. Shen H; Liwo A; Scheraga HA J Phys Chem B; 2009 Jun; 113(25):8738-44. PubMed ID: 19480420 [TBL] [Abstract][Full Text] [Related]
4. Replica Exchange and Multicanonical Algorithms with the coarse-grained UNRES force field. Nanias M; Czaplewski C; Scheraga HA J Chem Theory Comput; 2006; 2(3):513-528. PubMed ID: 18797518 [TBL] [Abstract][Full Text] [Related]
5. Application of Multiplexed Replica Exchange Molecular Dynamics to the UNRES Force Field: Tests with alpha and alpha+beta Proteins. Czaplewski C; Kalinowski S; Liwo A; Scheraga HA J Chem Theory Comput; 2009 Mar; 5(3):627-640. PubMed ID: 20161452 [TBL] [Abstract][Full Text] [Related]
6. Revised Backbone-Virtual-Bond-Angle Potentials to Treat the l- and d-Amino Acid Residues in the Coarse-Grained United Residue (UNRES) Force Field. Sieradzan AK; Niadzvedtski A; Scheraga HA; Liwo A J Chem Theory Comput; 2014 May; 10(5):2194-2203. PubMed ID: 24839411 [TBL] [Abstract][Full Text] [Related]
7. Physics-based potentials for the coupling between backbone- and side-chain-local conformational states in the UNited RESidue (UNRES) force field for protein simulations. Sieradzan AK; Krupa P; Scheraga HA; Liwo A; Czaplewski C J Chem Theory Comput; 2015 Feb; 11(2):817-31. PubMed ID: 25691834 [TBL] [Abstract][Full Text] [Related]
8. Investigation of protein folding by coarse-grained molecular dynamics with the UNRES force field. Maisuradze GG; Senet P; Czaplewski C; Liwo A; Scheraga HA J Phys Chem A; 2010 Apr; 114(13):4471-85. PubMed ID: 20166738 [TBL] [Abstract][Full Text] [Related]
9. Serial replica exchange. Hagen M; Kim B; Liu P; Friesner RA; Berne BJ J Phys Chem B; 2007 Feb; 111(6):1416-23. PubMed ID: 17249714 [TBL] [Abstract][Full Text] [Related]
10. Molecular dynamics with the united-residue model of polypeptide chains. II. Langevin and Berendsen-bath dynamics and tests on model alpha-helical systems. Khalili M; Liwo A; Jagielska A; Scheraga HA J Phys Chem B; 2005 Jul; 109(28):13798-810. PubMed ID: 16852728 [TBL] [Abstract][Full Text] [Related]
12. Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field. Sieradzan AK; Czaplewski C; Krupa P; Mozolewska MA; Karczyńska AS; Lipska AG; Lubecka EA; Gołaś E; Wirecki T; Makowski M; Ołdziej S; Liwo A Methods Mol Biol; 2022; 2376():399-416. PubMed ID: 34845623 [TBL] [Abstract][Full Text] [Related]
13. Ab initio simulations of protein-folding pathways by molecular dynamics with the united-residue model of polypeptide chains. Liwo A; Khalili M; Scheraga HA Proc Natl Acad Sci U S A; 2005 Feb; 102(7):2362-7. PubMed ID: 15677316 [TBL] [Abstract][Full Text] [Related]
14. UNRES server for physics-based coarse-grained simulations and prediction of protein structure, dynamics and thermodynamics. Czaplewski C; Karczynska A; Sieradzan AK; Liwo A Nucleic Acids Res; 2018 Jul; 46(W1):W304-W309. PubMed ID: 29718313 [TBL] [Abstract][Full Text] [Related]
15. A general method for the derivation of the functional forms of the effective energy terms in coarse-grained energy functions of polymers. III. Determination of scale-consistent backbone-local and correlation potentials in the UNRES force field and force-field calibration and validation. Liwo A; Sieradzan AK; Lipska AG; Czaplewski C; Joung I; Żmudzińska W; Hałabis A; Ołdziej S J Chem Phys; 2019 Apr; 150(15):155104. PubMed ID: 31005069 [TBL] [Abstract][Full Text] [Related]
16. Performance of protein-structure predictions with the physics-based UNRES force field in CASP11. Krupa P; Mozolewska MA; Wiśniewska M; Yin Y; He Y; Sieradzan AK; Ganzynkowicz R; Lipska AG; Karczyńska A; Ślusarz M; Ślusarz R; Giełdoń A; Czaplewski C; Jagieła D; Zaborowski B; Scheraga HA; Liwo A Bioinformatics; 2016 Nov; 32(21):3270-3278. PubMed ID: 27378298 [TBL] [Abstract][Full Text] [Related]
17. Implementation of molecular dynamics and its extensions with the coarse-grained UNRES force field on massively parallel systems; towards millisecond-scale simulations of protein structure, dynamics, and thermodynamics. Liwo A; Ołdziej S; Czaplewski C; Kleinerman DS; Blood P; Scheraga HA J Chem Theory Comput; 2010 Mar; 6(3):890-909. PubMed ID: 20305729 [TBL] [Abstract][Full Text] [Related]
18. Simple and Effective Conformational Sampling Strategy for Intrinsically Disordered Proteins Using the UNRES Web Server. Li T; Hendrix E; He Y J Phys Chem B; 2023 Mar; 127(10):2177-2186. PubMed ID: 36827446 [TBL] [Abstract][Full Text] [Related]
19. Simulated Tempering Distributed Replica Sampling, Virtual Replica Exchange, and Other Generalized-Ensemble Methods for Conformational Sampling. Rauscher S; Neale C; Pomès R J Chem Theory Comput; 2009 Oct; 5(10):2640-62. PubMed ID: 26631779 [TBL] [Abstract][Full Text] [Related]
20. Coarse-grained force field: general folding theory. Liwo A; He Y; Scheraga HA Phys Chem Chem Phys; 2011 Oct; 13(38):16890-901. PubMed ID: 21643583 [TBL] [Abstract][Full Text] [Related] [Next] [New Search]