3301 related articles for article (PubMed ID: 16200636)
1. The Amber biomolecular simulation programs.
Case DA; Cheatham TE; Darden T; Gohlke H; Luo R; Merz KM; Onufriev A; Simmerling C; Wang B; Woods RJ
J Comput Chem; 2005 Dec; 26(16):1668-88. PubMed ID: 16200636
[TBL] [Abstract][Full Text] [Related]
2. CHARMM: the biomolecular simulation program.
Brooks BR; Brooks CL; Mackerell AD; Nilsson L; Petrella RJ; Roux B; Won Y; Archontis G; Bartels C; Boresch S; Caflisch A; Caves L; Cui Q; Dinner AR; Feig M; Fischer S; Gao J; Hodoscek M; Im W; Kuczera K; Lazaridis T; Ma J; Ovchinnikov V; Paci E; Pastor RW; Post CB; Pu JZ; Schaefer M; Tidor B; Venable RM; Woodcock HL; Wu X; Yang W; York DM; Karplus M
J Comput Chem; 2009 Jul; 30(10):1545-614. PubMed ID: 19444816
[TBL] [Abstract][Full Text] [Related]
3. Advances in biomolecular simulations: methodology and recent applications.
Norberg J; Nilsson L
Q Rev Biophys; 2003 Aug; 36(3):257-306. PubMed ID: 15029826
[TBL] [Abstract][Full Text] [Related]
4. Empirical force fields for biological macromolecules: overview and issues.
Mackerell AD
J Comput Chem; 2004 Oct; 25(13):1584-604. PubMed ID: 15264253
[TBL] [Abstract][Full Text] [Related]
5. Comparison of protein force fields for molecular dynamics simulations.
Guvench O; MacKerell AD
Methods Mol Biol; 2008; 443():63-88. PubMed ID: 18446282
[TBL] [Abstract][Full Text] [Related]
6. GROMACS: fast, flexible, and free.
Van Der Spoel D; Lindahl E; Hess B; Groenhof G; Mark AE; Berendsen HJ
J Comput Chem; 2005 Dec; 26(16):1701-18. PubMed ID: 16211538
[TBL] [Abstract][Full Text] [Related]
7. Force Field X: A computational microscope to study genetic variation and organic crystals using theory and experiment.
Gogal RA; Nessler AJ; Thiel AC; Bernabe HV; Corrigan Grove RA; Cousineau LM; Litman JM; Miller JM; Qi G; Speranza MJ; Tollefson MR; Fenn TD; Michaelson JJ; Okada O; Piquemal JP; Ponder JW; Shen J; Smith RJH; Yang W; Ren P; Schnieders MJ
J Chem Phys; 2024 Jul; 161(1):. PubMed ID: 38958156
[TBL] [Abstract][Full Text] [Related]
8. The GROMOS software for biomolecular simulation: GROMOS05.
Christen M; Hünenberger PH; Bakowies D; Baron R; Bürgi R; Geerke DP; Heinz TN; Kastenholz MA; Kräutler V; Oostenbrink C; Peter C; Trzesniak D; van Gunsteren WF
J Comput Chem; 2005 Dec; 26(16):1719-51. PubMed ID: 16211540
[TBL] [Abstract][Full Text] [Related]
9. Potential energy functions.
Halgren TA
Curr Opin Struct Biol; 1995 Apr; 5(2):205-10. PubMed ID: 7648322
[TBL] [Abstract][Full Text] [Related]
10. Force field validation for nucleic acid simulations: comparing energies and dynamics of a DNA dodecamer.
Jha S; Coveney PV; Laughton CA
J Comput Chem; 2005 Nov; 26(15):1617-27. PubMed ID: 16170796
[TBL] [Abstract][Full Text] [Related]
11. RedMD--reduced molecular dynamics package.
Górecki A; Szypowski M; Długosz M; Trylska J
J Comput Chem; 2009 Nov; 30(14):2364-73. PubMed ID: 19247989
[TBL] [Abstract][Full Text] [Related]
12. Identification of tunnels in proteins, nucleic acids, inorganic materials and molecular ensembles.
Damborský J; Petrek M; Banás P; Otyepka M
Biotechnol J; 2007 Jan; 2(1):62-7. PubMed ID: 17183511
[TBL] [Abstract][Full Text] [Related]
13. The perspectives of computational chemistry modeling.
Tetko IV
J Comput Aided Mol Des; 2012 Jan; 26(1):135-6. PubMed ID: 22160554
[TBL] [Abstract][Full Text] [Related]
14. Theoretical methods for the simulation of nucleic acids.
Orozco M; Pérez A; Noy A; Luque FJ
Chem Soc Rev; 2003 Nov; 32(6):350-64. PubMed ID: 14671790
[TBL] [Abstract][Full Text] [Related]
15. Geometric and potential driving formation and evolution of biomolecular surfaces.
Bates PW; Chen Z; Sun Y; Wei GW; Zhao S
J Math Biol; 2009 Aug; 59(2):193-231. PubMed ID: 18941751
[TBL] [Abstract][Full Text] [Related]
16. Carbohydrate-protein interactions: molecular modeling insights.
Pérez S; Tvaroška I
Adv Carbohydr Chem Biochem; 2014; 71():9-136. PubMed ID: 25480504
[TBL] [Abstract][Full Text] [Related]
17. A topical issue: NMR investigations of molecular dynamics.
Palmer AG
J Biomol NMR; 2009 Sep; 45(1-2):1-4. PubMed ID: 19669621
[No Abstract] [Full Text] [Related]
18. MoViES: molecular vibrations evaluation server for analysis of fluctuational dynamics of proteins and nucleic acids.
Cao ZW; Xue Y; Han LY; Xie B; Zhou H; Zheng CJ; Lin HH; Chen YZ
Nucleic Acids Res; 2004 Jul; 32(Web Server issue):W679-85. PubMed ID: 15215475
[TBL] [Abstract][Full Text] [Related]
19. Force field parameters for rotation around chi torsion axis in nucleic acids.
Ode H; Matsuo Y; Neya S; Hoshino T
J Comput Chem; 2008 Nov; 29(15):2531-42. PubMed ID: 18470965
[TBL] [Abstract][Full Text] [Related]
20. Molecular modeling of nucleic acid structure.
Galindo-Murillo R; Bergonzo C; Cheatham TE
Curr Protoc Nucleic Acid Chem; 2013 Oct; 54():7.5.1-7.5.13. PubMed ID: 24510799
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]