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Items: 1 to 20 of 104

1.

Escaping Atom Types in Force Fields Using Direct Chemical Perception.

Mobley DL, Bannan CC, Rizzi A, Bayly CI, Chodera JD, Lim VT, Lim NM, Beauchamp KA, Slochower DR, Shirts MR, Gilson MK, Eastman PK.

J Chem Theory Comput. 2018 Nov 13;14(11):6076-6092. doi: 10.1021/acs.jctc.8b00640. Epub 2018 Oct 30.

PMID:
30351006
2.

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.

3.

MATCH: an atom-typing toolset for molecular mechanics force fields.

Yesselman JD, Price DJ, Knight JL, Brooks CL 3rd.

J Comput Chem. 2012 Jan 15;33(2):189-202. doi: 10.1002/jcc.21963. Epub 2011 Nov 1.

4.

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.

5.

Hierarchical atom type definitions and extensible all-atom force fields.

Jin Z, Yang C, Cao F, Li F, Jing Z, Chen L, Shen Z, Xin L, Tong S, Sun H.

J Comput Chem. 2016 Mar 15;37(7):653-64. doi: 10.1002/jcc.24244. Epub 2015 Nov 5.

PMID:
26537332
6.

Comparison of Methods to Obtain Force-Field Parameters for Metal Sites.

Hu L, Ryde U.

J Chem Theory Comput. 2011 Aug 9;7(8):2452-63. doi: 10.1021/ct100725a. Epub 2011 Jul 20.

PMID:
26606619
7.

Biomolecular Force Field Parameterization via Atoms-in-Molecule Electron Density Partitioning.

Cole DJ, Vilseck JZ, Tirado-Rives J, Payne MC, Jorgensen WL.

J Chem Theory Comput. 2016 May 10;12(5):2312-23. doi: 10.1021/acs.jctc.6b00027. Epub 2016 Apr 21.

8.

Atom-atom partitioning of total (super)molecular energy: the hidden terms of classical force fields.

Rafat M, Popelier PL.

J Comput Chem. 2007 Jan 15;28(1):292-301.

PMID:
17109431
9.

Rational design of ion force fields based on thermodynamic solvation properties.

Horinek D, Mamatkulov SI, Netz RR.

J Chem Phys. 2009 Mar 28;130(12):124507. doi: 10.1063/1.3081142.

PMID:
19334851
10.

Engineering Aspects of Olfaction.

Persaud KC.

In: Persaud KC, Marco S, Gutiérrez-Gálvez A, editors. Neuromorphic Olfaction. Boca Raton (FL): CRC Press/Taylor & Francis; 2013. Chapter 1.

11.
12.

New-generation amber united-atom force field.

Yang L, Tan CH, Hsieh MJ, Wang J, Duan Y, Cieplak P, Caldwell J, Kollman PA, Luo R.

J Phys Chem B. 2006 Jul 6;110(26):13166-76.

PMID:
16805629
13.

Theoretical modeling of large molecular systems. Advances in the local self consistent field method for mixed quantum mechanics/molecular mechanics calculations.

Monari A, Rivail JL, Assfeld X.

Acc Chem Res. 2013 Feb 19;46(2):596-603. doi: 10.1021/ar300278j. Epub 2012 Dec 18.

PMID:
23249409
14.

Optimizing Protein-Protein van der Waals Interactions for the AMBER ff9x/ff12 Force Field.

Chapman DE, Steck JK, Nerenberg PS.

J Chem Theory Comput. 2014 Jan 14;10(1):273-81. doi: 10.1021/ct400610x. Epub 2013 Dec 3.

PMID:
26579910
15.

Discrete Derivatives for Atom-Pairs as a Novel Graph-Theoretical Invariant for Generating New Molecular Descriptors: Orthogonality, Interpretation and QSARs/QSPRs on Benchmark Databases.

Martínez-Santiago O, Millán-Cabrera R, Marrero-Ponce Y, Barigye SJ, Martínez-López Y, Torrens F, Pérez-Giménez F.

Mol Inform. 2014 May;33(5):343-68. doi: 10.1002/minf.201300173. Epub 2014 May 12.

PMID:
27485891
16.

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.

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.

Force field development for organic molecules: modifying dihedral and 1-n pair interaction parameters.

Chen S, Yi S, Gao W, Zuo C, Hu Z.

J Comput Chem. 2015 Mar 5;36(6):376-84. doi: 10.1002/jcc.23808. Epub 2014 Dec 8.

PMID:
25487650
19.

Translational Metabolomics of Head Injury: Exploring Dysfunctional Cerebral Metabolism with Ex Vivo NMR Spectroscopy-Based Metabolite Quantification.

Wolahan SM, Hirt D, Glenn TC.

In: Kobeissy FH, editor. Brain Neurotrauma: Molecular, Neuropsychological, and Rehabilitation Aspects. Boca Raton (FL): CRC Press/Taylor & Francis; 2015. Chapter 25.

20.

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