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.
192 related articles for article (PubMed ID: 31454484)
1. Extension of the UNRES Coarse-Grained Force Field to Membrane Proteins in the Lipid Bilayer. Ziȩba K; Ślusarz M; Ślusarz R; Liwo A; Czaplewski C; Sieradzan AK J Phys Chem B; 2019 Sep; 123(37):7829-7839. PubMed ID: 31454484 [TBL] [Abstract][Full Text] [Related]
2. A new protein nucleic-acid coarse-grained force field based on the UNRES and NARES-2P force fields. Sieradzan AK; Giełdoń A; Yin Y; He Y; Scheraga HA; Liwo A J Comput Chem; 2018 Oct; 39(28):2360-2370. PubMed ID: 30306573 [TBL] [Abstract][Full Text] [Related]
3. 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. Liwo A; Czaplewski C J Chem Phys; 2020 Feb; 152(5):054902. PubMed ID: 32035448 [TBL] [Abstract][Full Text] [Related]
4. Extension of coarse-grained UNRES force field to treat carbon nanotubes. Sieradzan AK; Mozolewska MA J Mol Model; 2018 Apr; 24(5):121. PubMed ID: 29700628 [TBL] [Abstract][Full Text] [Related]
5. Reconciling structural and thermodynamic predictions using all-atom and coarse-grain force fields: the case of charged oligo-arginine translocation into DMPC bilayers. Hu Y; Sinha SK; Patel S J Phys Chem B; 2014 Oct; 118(41):11973-92. PubMed ID: 25290376 [TBL] [Abstract][Full Text] [Related]
6. 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]
7. 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]
8. Introduction of steered molecular dynamics into UNRES coarse-grained simulations package. Sieradzan AK; Jakubowski R J Comput Chem; 2017 Mar; 38(8):553-562. PubMed ID: 28074486 [TBL] [Abstract][Full Text] [Related]
9. 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]
10. Parameterization of a coarse-grained model of cholesterol with point-dipole electrostatics. Siani P; Khandelia H; Orsi M; Dias LG J Comput Aided Mol Des; 2018 Nov; 32(11):1259-1271. PubMed ID: 30259387 [TBL] [Abstract][Full Text] [Related]
11. Interaction of monotopic membrane enzymes with a lipid bilayer: a coarse-grained MD simulation study. Balali-Mood K; Bond PJ; Sansom MS Biochemistry; 2009 Mar; 48(10):2135-45. PubMed ID: 19161285 [TBL] [Abstract][Full Text] [Related]
13. Coarse-grained simulation: a high-throughput computational approach to membrane proteins. Sansom MS; Scott KA; Bond PJ Biochem Soc Trans; 2008 Feb; 36(Pt 1):27-32. PubMed ID: 18208379 [TBL] [Abstract][Full Text] [Related]
14. Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics. Krupa P; Hałabis A; Żmudzińska W; Ołdziej S; Scheraga HA; Liwo A J Chem Inf Model; 2017 Sep; 57(9):2364-2377. PubMed ID: 28809487 [TBL] [Abstract][Full Text] [Related]
15. Spontaneous adsorption of coiled-coil model peptides K and E to a mixed lipid bilayer. Pluhackova K; Wassenaar TA; Kirsch S; Böckmann RA J Phys Chem B; 2015 Mar; 119(12):4396-408. PubMed ID: 25719673 [TBL] [Abstract][Full Text] [Related]
16. 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]
17. An overview of molecular dynamics simulations of oxidized lipid systems, with a comparison of ELBA and MARTINI force fields for coarse grained lipid simulations. Siani P; de Souza RM; Dias LG; Itri R; Khandelia H Biochim Biophys Acta; 2016 Oct; 1858(10):2498-2511. PubMed ID: 27058982 [TBL] [Abstract][Full Text] [Related]
18. Coarse-grained MD simulations of membrane protein-bilayer self-assembly. Scott KA; Bond PJ; Ivetac A; Chetwynd AP; Khalid S; Sansom MS Structure; 2008 Apr; 16(4):621-30. PubMed ID: 18400182 [TBL] [Abstract][Full Text] [Related]
19. A coarse-grained approach to studying the interactions of the antimicrobial peptides aurein 1.2 and maculatin 1.1 with POPG/POPE lipid mixtures. Balatti GE; Martini MF; Pickholz M J Mol Model; 2018 Jul; 24(8):208. PubMed ID: 30019106 [TBL] [Abstract][Full Text] [Related]