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Items: 1 to 20 of 142

1.

CHARMM: the biomolecular simulation program.

Brooks BR, Brooks CL 3rd, Mackerell AD Jr, 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;30(10):1545-614. doi: 10.1002/jcc.21287. Review.

2.

CHARMM additive and polarizable force fields for biophysics and computer-aided drug design.

Vanommeslaeghe K, MacKerell AD Jr.

Biochim Biophys Acta. 2015 May;1850(5):861-71. doi: 10.1016/j.bbagen.2014.08.004. Epub 2014 Aug 19. Review.

3.

CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields.

Vanommeslaeghe K, Hatcher E, Acharya C, Kundu S, Zhong S, Shim J, Darian E, Guvench O, Lopes P, Vorobyov I, Mackerell AD Jr.

J Comput Chem. 2010 Mar;31(4):671-90. doi: 10.1002/jcc.21367.

4.

The Amber biomolecular simulation programs.

Case DA, Cheatham TE 3rd, Darden T, Gohlke H, Luo R, Merz KM Jr, Onufriev A, Simmerling C, Wang B, Woods RJ.

J Comput Chem. 2005 Dec;26(16):1668-88.

5.

Comparison of protein force fields for molecular dynamics simulations.

Guvench O, MacKerell AD Jr.

Methods Mol Biol. 2008;443:63-88. doi: 10.1007/978-1-59745-177-2_4. Review.

PMID:
18446282
7.

Integrated Modeling Program, Applied Chemical Theory (IMPACT).

Banks JL, Beard HS, Cao Y, Cho AE, Damm W, Farid R, Felts AK, Halgren TA, Mainz DT, Maple JR, Murphy R, Philipp DM, Repasky MP, Zhang LY, Berne BJ, Friesner RA, Gallicchio E, Levy RM.

J Comput Chem. 2005 Dec;26(16):1752-80. Review.

8.

Some practical approaches to treating electrostatic polarization of proteins.

Ji C, Mei Y.

Acc Chem Res. 2014 Sep 16;47(9):2795-803. doi: 10.1021/ar500094n. Epub 2014 Jun 2.

PMID:
24883956
9.

Empirical force fields for biological macromolecules: overview and issues.

Mackerell AD Jr.

J Comput Chem. 2004 Oct;25(13):1584-604. Review.

PMID:
15264253
10.

Advances in biomolecular simulations: methodology and recent applications.

Norberg J, Nilsson L.

Q Rev Biophys. 2003 Aug;36(3):257-306. Review.

PMID:
15029826
11.

CHARMM additive all-atom force field for glycosidic linkages in carbohydrates involving furanoses.

Raman EP, Guvench O, MacKerell AD Jr.

J Phys Chem B. 2010 Oct 14;114(40):12981-94. doi: 10.1021/jp105758h.

12.

Development of CHARMM polarizable force field for nucleic acid bases based on the classical Drude oscillator model.

Baker CM, Anisimov VM, MacKerell AD Jr.

J Phys Chem B. 2011 Jan 27;115(3):580-96. doi: 10.1021/jp1092338. Epub 2010 Dec 17.

13.

Molecular dynamics and quantum mechanics of RNA: conformational and chemical change we can believe in.

Ditzler MA, Otyepka M, Sponer J, Walter NG.

Acc Chem Res. 2010 Jan 19;43(1):40-7. doi: 10.1021/ar900093g.

14.

MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology.

Feig M, Karanicolas J, Brooks CL 3rd.

J Mol Graph Model. 2004 May;22(5):377-95.

PMID:
15099834
15.

Potential energy functions.

Halgren TA.

Curr Opin Struct Biol. 1995 Apr;5(2):205-10. Review.

PMID:
7648322
16.
17.

Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).

Foffi G, Pastore A, Piazza F, Temussi PA.

Phys Biol. 2013 Aug 2;10(4):040301. [Epub ahead of print]

PMID:
23912807
18.

Scalable molecular dynamics with NAMD.

Phillips JC, Braun R, Wang W, Gumbart J, Tajkhorshid E, Villa E, Chipot C, Skeel RD, Kalé L, Schulten K.

J Comput Chem. 2005 Dec;26(16):1781-802.

19.

Enhanced sampling techniques in molecular dynamics simulations of biological systems.

Bernardi RC, Melo MC, Schulten K.

Biochim Biophys Acta. 2015 May;1850(5):872-7. doi: 10.1016/j.bbagen.2014.10.019. Epub 2014 Oct 23. Review.

20.

PEACH 4 with ABINIT-MP: a general platform for classical and quantum simulations of biological molecules.

Komeiji Y, Inadomi Y, Nakano T.

Comput Biol Chem. 2004 Apr;28(2):155-61.

PMID:
15185673
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