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Items: 1 to 20 of 109

1.

Rapid parameterization of small molecules using the Force Field Toolkit.

Mayne CG, Saam J, Schulten K, Tajkhorshid E, Gumbart JC.

J Comput Chem. 2013 Dec 15;34(32):2757-70. doi: 10.1002/jcc.23422. Epub 2013 Sep 2.

2.

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.

3.

Optimized Lennard-Jones Parameters for Druglike Small Molecules.

Boulanger E, Huang L, Rupakheti C, MacKerell AD Jr, Roux B.

J Chem Theory Comput. 2018 Jun 12;14(6):3121-3131. doi: 10.1021/acs.jctc.8b00172. Epub 2018 May 7.

4.

Automation of the CHARMM General Force Field (CGenFF) II: assignment of bonded parameters and partial atomic charges.

Vanommeslaeghe K, Raman EP, MacKerell AD Jr.

J Chem Inf Model. 2012 Dec 21;52(12):3155-68. doi: 10.1021/ci3003649. Epub 2012 Nov 28.

5.

Parametrization of macrolide antibiotics using the force field toolkit.

Pavlova A, Gumbart JC.

J Comput Chem. 2015 Oct 15;36(27):2052-63. doi: 10.1002/jcc.24043. Epub 2015 Aug 17.

6.

SwissParam: a fast force field generation tool for small organic molecules.

Zoete V, Cuendet MA, Grosdidier A, Michielin O.

J Comput Chem. 2011 Aug;32(11):2359-68. doi: 10.1002/jcc.21816. Epub 2011 May 3.

PMID:
21541964
7.

Automatic GROMACS topology generation and comparisons of force fields for solvation free energy calculations.

Lundborg M, Lindahl E.

J Phys Chem B. 2015 Jan 22;119(3):810-23. doi: 10.1021/jp505332p. Epub 2014 Nov 7.

PMID:
25343332
8.

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;10(4):040301. Epub 2013 Aug 2.

PMID:
23912807
9.

CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules.

Kim S, Lee J, Jo S, Brooks CL 3rd, Lee HS, Im W.

J Comput Chem. 2017 Jun 5;38(21):1879-1886. doi: 10.1002/jcc.24829. Epub 2017 May 11.

10.
11.

Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes.

Knight JL, Yesselman JD, Brooks CL 3rd.

J Comput Chem. 2013 Apr 30;34(11):893-903. doi: 10.1002/jcc.23199. Epub 2013 Jan 7.

12.

CHARMM force field parameters for 2'-hydroxybiphenyl-2-sulfinate, 2-hydroxybiphenyl, and related analogs.

Yu Y, Fursule IA, Mills LC, Englert DL, Berron BJ, Payne CM.

J Mol Graph Model. 2017 Mar;72:32-42. doi: 10.1016/j.jmgm.2016.12.005. Epub 2016 Dec 15.

PMID:
28027509
13.

Extension of the CHARMM General Force Field to sulfonyl-containing compounds and its utility in biomolecular simulations.

Yu W, He X, Vanommeslaeghe K, MacKerell AD Jr.

J Comput Chem. 2012 Dec 5;33(31):2451-68. doi: 10.1002/jcc.23067. Epub 2012 Jul 23.

14.

Automation of the CHARMM General Force Field (CGenFF) I: bond perception and atom typing.

Vanommeslaeghe K, MacKerell AD Jr.

J Chem Inf Model. 2012 Dec 21;52(12):3144-54. doi: 10.1021/ci300363c. Epub 2012 Nov 28.

15.

Paramfit: automated optimization of force field parameters for molecular dynamics simulations.

Betz RM, Walker RC.

J Comput Chem. 2015 Jan 15;36(2):79-87. doi: 10.1002/jcc.23775. Epub 2014 Nov 21.

PMID:
25413259
16.

TopoGromacs: Automated Topology Conversion from CHARMM to GROMACS within VMD.

Vermaas JV, Hardy DJ, Stone JE, Tajkhorshid E, Kohlmeyer A.

J Chem Inf Model. 2016 Jun 27;56(6):1112-6. doi: 10.1021/acs.jcim.6b00103. Epub 2016 Jun 1.

17.

AMBER-DYES: Characterization of Charge Fluctuations and Force Field Parameterization of Fluorescent Dyes for Molecular Dynamics Simulations.

Graen T, Hoefling M, Grubm├╝ller H.

J Chem Theory Comput. 2014 Dec 9;10(12):5505-12. doi: 10.1021/ct500869p. Epub 2014 Dec 1.

PMID:
26583233
18.

Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field.

Shivakumar D, Williams J, Wu Y, Damm W, Shelley J, Sherman W.

J Chem Theory Comput. 2010 May 11;6(5):1509-19. doi: 10.1021/ct900587b. Epub 2010 Apr 14.

PMID:
26615687
19.

Parameterization of aromatic azido groups: application as photoaffinity probes in molecular dynamics studies.

Pieffet G, Petukhov PA.

J Mol Model. 2009 Nov;15(11):1291-7. doi: 10.1007/s00894-009-0488-z. Epub 2009 Mar 14.

20.

CHARMM force field parameterization protocol for self-assembling peptide amphiphiles: the Fmoc moiety.

Ramos Sasselli I, Ulijn RV, Tuttle T.

Phys Chem Chem Phys. 2016 Feb 14;18(6):4659-67. doi: 10.1039/c5cp06770g.

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