Log in

Relevant bibliographies by topics / CHARMM / Journal articles

To see the other types of publications on this topic, follow the link: CHARMM.

Journal articles on the topic 'CHARMM'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles

Select a source type:

Consult the top 50 journal articles for your research on the topic 'CHARMM.'

Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.

You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.

Browse journal articles on a wide variety of disciplines and organise your bibliography correctly.

1

Jo, Sunhwan, Taehoon Kim, Vidyashankara G. Iyer, and Wonpil Im. "CHARMM-GUI: A web-based graphical user interface for CHARMM." Journal of Computational Chemistry 29, no. 11 (2008): 1859–65. http://dx.doi.org/10.1002/jcc.20945.

Full text

APA, Harvard, Vancouver, ISO, and other styles

2

Brooks, B., and R. Venable. "CHARMM for Molecular Simulations." ACM SIGBIO Newsletter 8, no. 3 (1986): 30–34. http://dx.doi.org/10.1145/16297.992728.

Full text

APA, Harvard, Vancouver, ISO, and other styles

3

Shaw, Robert A., Tristan Johnston-Wood, Benjamin Ambrose, Timothy D. Craggs, and J. Grant Hill. "CHARMM-DYES: Parameterization of Fluorescent Dyes for Use with the CHARMM Force Field." Journal of Chemical Theory and Computation 16, no. 12 (2020): 7817–24. http://dx.doi.org/10.1021/acs.jctc.0c00721.

Full text

APA, Harvard, Vancouver, ISO, and other styles

4

Nguyen, Trang Truc, Man Hoang Viet, and Mai Suan Li. "Effects of Water Models on Binding Affinity: Evidence from All-Atom Simulation of Binding of Tamiflu to A/H5N1 Neuraminidase." Scientific World Journal 2014 (2014): 1–14. http://dx.doi.org/10.1155/2014/536084.

Full text

Abstract:

The influence of water models SPC, SPC/E, TIP3P, and TIP4P on ligand binding affinity is examined by calculating the binding free energyΔGbindof oseltamivir carboxylate (Tamiflu) to the wild type of glycoprotein neuraminidase from the pandemic A/H5N1 virus.ΔGbindis estimated by the Molecular Mechanic-Poisson Boltzmann Surface Area method and all-atom simulations with different combinations of these aqueous models and four force fields AMBER99SB, CHARMM27, GROMOS96 43a1, and OPLS-AA/L. It is shown that there is no correlation between the binding free energy and the water density in the binding

APA, Harvard, Vancouver, ISO, and other styles

5

Park, Sang-Jun, Hugo Guterres, Han Zhang, and Wonpil Im. "CHARMM-GUI high-throughput simulator." Biophysical Journal 121, no. 3 (2022): 531a. http://dx.doi.org/10.1016/j.bpj.2021.11.2800.

Full text

APA, Harvard, Vancouver, ISO, and other styles

6

Cheng, Xi, Yifei Qi, Jumin Lee, Sunhwan Jo, and Wonpil Im. "CHARMM Gui Membrane Builder Updates." Biophysical Journal 108, no. 2 (2015): 159a. http://dx.doi.org/10.1016/j.bpj.2014.11.877.

Full text

APA, Harvard, Vancouver, ISO, and other styles

7

Brooks, B. R., C. L. Brooks, A. D. Mackerell, et al. "CHARMM: The biomolecular simulation program." Journal of Computational Chemistry 30, no. 10 (2009): 1545–614. http://dx.doi.org/10.1002/jcc.21287.

Full text

APA, Harvard, Vancouver, ISO, and other styles

8

Park, Sang-Jun, Hyuntae Na, and Wonpil Im. "CHARMM-GUI normal mode analyzer." Biophysical Journal 123, no. 3 (2024): 283a. http://dx.doi.org/10.1016/j.bpj.2023.11.1759.

Full text

APA, Harvard, Vancouver, ISO, and other styles

9

Kim, Seonghoon, Jumin Lee, Sunhwan Jo, Charles L. Brooks, Hui Sun Lee, and Wonpil Im. "CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules." Journal of Computational Chemistry 38, no. 21 (2017): 1879–86. http://dx.doi.org/10.1002/jcc.24829.

Full text

APA, Harvard, Vancouver, ISO, and other styles

10

Kim, Seonghoon, Jumin Lee, Sunhwan Jo, and Wonpil Im. "CHARMM-GUI Ligand Reader & Modeler." Biophysical Journal 112, no. 3 (2017): 289a. http://dx.doi.org/10.1016/j.bpj.2016.11.1564.

Full text

APA, Harvard, Vancouver, ISO, and other styles

11

Hansson, Anders, Paulo C. T. Souza, Rodrigo L. Silveira, Leandro Martínez, and Munir S. Skaf. "CHARMM force field parameterization of rosiglitazone." International Journal of Quantum Chemistry 111, no. 7-8 (2011): 1346–54. http://dx.doi.org/10.1002/qua.22638.

Full text

APA, Harvard, Vancouver, ISO, and other styles

12

Beu, Titus Adrian, Andrada-Elena Ailenei, and Alexandra Farcaş. "CHARMM force field for protonated polyethyleneimine." Journal of Computational Chemistry 39, no. 31 (2018): 2564–75. http://dx.doi.org/10.1002/jcc.25637.

Full text

APA, Harvard, Vancouver, ISO, and other styles

13

Hynninen, Antti‐Pekka, and Michael F. Crowley. "New faster CHARMM molecular dynamics engine." Journal of Computational Chemistry 35, no. 5 (2013): 406–13. http://dx.doi.org/10.1002/jcc.23501.

Full text

APA, Harvard, Vancouver, ISO, and other styles

14

Cournia, Zoe, A. C. Vaiana, G. M. Ullmann, and J. C. Smith. "Derivation of a molecular mechanics force field for cholesterol." Pure and Applied Chemistry 76, no. 1 (2004): 189–96. http://dx.doi.org/10.1351/pac200476010189.

Full text

Abstract:

As a necessary step toward realistic cholesterol:biomembrane simulations, we have derived CHARMM molecular mechanics force-field parameters for cholesterol. For the parametrization we use an automated method that involves fitting the molecular mechanics potential to both vibrational frequencies and eigenvector projections derived from quantum chemical calculations. Results for another polycyclic molecule, rhodamine 6G, are also given. The usefulness of the method is thus demonstrated by the use of reference data from two molecules at different levels of theory. The frequency-matching plots for

APA, Harvard, Vancouver, ISO, and other styles

15

Hénin, Jérôme, Wataru Shinoda, and Michael L. Klein. "United-Atom Acyl Chains for CHARMM Phospholipids." Journal of Physical Chemistry B 112, no. 23 (2008): 7008–15. http://dx.doi.org/10.1021/jp800687p.

Full text

APA, Harvard, Vancouver, ISO, and other styles

16

Lee, Jumin, Manuel Hitzenberger, Manuel Rieger, Nathan R. Kern, Martin Zacharias, and Wonpil Im. "CHARMM-GUI supports the Amber force fields." Journal of Chemical Physics 153, no. 3 (2020): 035103. http://dx.doi.org/10.1063/5.0012280.

Full text

APA, Harvard, Vancouver, ISO, and other styles

17

Pourmousa, Mohsen, Richard M. Venable, and Richard W. Pastor. "Calcium Parameters in CHARMM Force Field Revisited." Biophysical Journal 110, no. 3 (2016): 327a—328a. http://dx.doi.org/10.1016/j.bpj.2015.11.1761.

Full text

APA, Harvard, Vancouver, ISO, and other styles

18

Suárez, María, Pablo Tortosa, and Alfonso Jaramillo. "PROTDES: CHARMM toolbox for computational protein design." Systems and Synthetic Biology 2, no. 3-4 (2008): 105–13. http://dx.doi.org/10.1007/s11693-009-9026-7.

Full text

APA, Harvard, Vancouver, ISO, and other styles

19

Wu, Emilia L., Xi Cheng, Sunhwan Jo, et al. "CHARMM-GUIMembrane Buildertoward realistic biological membrane simulations." Journal of Computational Chemistry 35, no. 27 (2014): 1997–2004. http://dx.doi.org/10.1002/jcc.23702.

Full text

APA, Harvard, Vancouver, ISO, and other styles

20

Teo, Ruijie D., and D. Peter Tieleman. "Evaluation of all-atom force fields in viral capsid simulations and properties." RSC Advances 12, no. 1 (2022): 216–20. http://dx.doi.org/10.1039/d1ra08431c.

Full text

APA, Harvard, Vancouver, ISO, and other styles

21

Barden, Daniel Ryan, and Harish Vashisth. "Parameterization and atomistic simulations of biomimetic membranes." Faraday Discussions 209 (2018): 161–78. http://dx.doi.org/10.1039/c8fd00047f.

Full text

Abstract:

We have developed CHARMM force-field compatible parameters and conducted all-atom explicit-solvent MD simulations of biomimetic membranes composed of block copolymers of poly(butadiene), poly(isoprene), and poly(ethylene oxide).

APA, Harvard, Vancouver, ISO, and other styles

22

Lee, Jumin, Xi Cheng, Jason M. Swails, et al. "CHARMM-GUI Input Generator for NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM Simulations Using the CHARMM36 Additive Force Field." Journal of Chemical Theory and Computation 12, no. 1 (2015): 405–13. http://dx.doi.org/10.1021/acs.jctc.5b00935.

Full text

APA, Harvard, Vancouver, ISO, and other styles

23

Lee, Jumin, Xi Cheng, Sunhwan Jo, Alexander D. MacKerell, Jeffery B. Klauda, and Wonpil Im. "CHARMM-GUI Input Generator for NAMD, Gromacs, Amber, Openmm, and CHARMM/OpenMM Simulations using the CHARMM36 Additive Force Field." Biophysical Journal 110, no. 3 (2016): 641a. http://dx.doi.org/10.1016/j.bpj.2015.11.3431.

Full text

APA, Harvard, Vancouver, ISO, and other styles

24

Ecker, János. "Generating CHARMM compatible force field parameters for atrazine." Journal of Universal Science Online 3, no. 1 (2016): 1–8. http://dx.doi.org/10.17202/juso.2016.3.1.

Full text

Abstract:

There are many synthetic, drug-like molecules whose interactions with large biomolecules could be partly described by molecular dynamics studies. The parameters necessary to perform an MD simulation are available for biomolecules (proteins, nucleic acids, lipids, carbohydrates) and for many other small chemical compounds with biological relevance. In case of uncharacterized molecules, parameter sets can be calculated using quantummechanical calculations. The optimized geometry, van der Waals, charge, bond, angle and torsion parameters for the photosystem II-inhibitor herbicide, atrazine, were

APA, Harvard, Vancouver, ISO, and other styles

25

Yu, Yalun, Jeffery B. Klauda, Alexander D. MacKerell, Benoit Roux, and Richard W. Pastor. "Recent Updates to the Charmm Lipid Force Fields." Biophysical Journal 120, no. 3 (2021): 325a. http://dx.doi.org/10.1016/j.bpj.2020.11.2050.

Full text

APA, Harvard, Vancouver, ISO, and other styles

26

Pastor, R. W., and A. D. MacKerell. "Development of the CHARMM Force Field for Lipids." Journal of Physical Chemistry Letters 2, no. 13 (2011): 1526–32. http://dx.doi.org/10.1021/jz200167q.

Full text

APA, Harvard, Vancouver, ISO, and other styles

27

Miller, Benjamin T., Rishi P. Singh, Jeffery B. Klauda, Milan Hodošček, Bernard R. Brooks, and H. Lee Woodcock. "CHARMMing: A New, Flexible Web Portal for CHARMM." Journal of Chemical Information and Modeling 48, no. 9 (2008): 1920–29. http://dx.doi.org/10.1021/ci800133b.

Full text

APA, Harvard, Vancouver, ISO, and other styles

28

Klauda, Jeffery B., and Bernard R. Brooks. "CHARMM Force Field Parameters for Nitroalkanes and Nitroarenes." Journal of Chemical Theory and Computation 4, no. 1 (2007): 107–15. http://dx.doi.org/10.1021/ct700191v.

Full text

APA, Harvard, Vancouver, ISO, and other styles

29

Lee, Jumin, Göran Widmalm, Jeffery B. Klauda, and Wonpil Im. "Charmm-GUI Membrane Builder with Glycolipids and Lipopolysaccharides." Biophysical Journal 114, no. 3 (2018): 344a. http://dx.doi.org/10.1016/j.bpj.2017.11.1920.

Full text

APA, Harvard, Vancouver, ISO, and other styles

30

Qi, Yifei, Xi Cheng, and Wonpil Im. "CHARMM-GUI Martini Maker for Coarse-Grained Simulations." Biophysical Journal 108, no. 2 (2015): 161a. http://dx.doi.org/10.1016/j.bpj.2014.11.888.

Full text

APA, Harvard, Vancouver, ISO, and other styles

31

Kav, Batuhan, and Birgit Strodel. "Does the inclusion of electronic polarisability lead to a better modelling of peptide aggregation?" RSC Advances 12, no. 32 (2022): 20829–37. http://dx.doi.org/10.1039/d2ra01478e.

Full text

Abstract:

Simulating the process of amyloid aggregation is a hard task. We test whether the inclusion of electronic polarisability as done in CHARMM-Drude improves the modelling of Aβ16–22 aggregation and find it does not. Reasons for the failure are given.

APA, Harvard, Vancouver, ISO, and other styles

32

Kyo Choi, Yeol, Shasha Feng, Nathan R. Kern, and Wonpil Im. "CHARMM-GUI Nanomaterial Modeler: extension to ligand-protected nanomaterials." Biophysical Journal 121, no. 3 (2022): 273a—274a. http://dx.doi.org/10.1016/j.bpj.2021.11.1373.

Full text

APA, Harvard, Vancouver, ISO, and other styles

33

Lim, Joseph B., Brent Rogaski, and Jeffery B. Klauda. "Update of the Cholesterol Force Field Parameters in CHARMM." Journal of Physical Chemistry B 116, no. 1 (2011): 203–10. http://dx.doi.org/10.1021/jp207925m.

Full text

APA, Harvard, Vancouver, ISO, and other styles

34

Jo, Sunhwan, and Wonpil Im. "CHARMM-GUI: Brining Advanced Computational Techniques to Web Interface." Biophysical Journal 98, no. 3 (2010): 568a. http://dx.doi.org/10.1016/j.bpj.2009.12.3078.

Full text

APA, Harvard, Vancouver, ISO, and other styles

35

Vermaas, Josh V., Loukas Petridis, Gregg T. Beckham, and Michael F. Crowley. "Systematic Parameterization of Lignin for the Charmm Force Field." Biophysical Journal 112, no. 3 (2017): 449a. http://dx.doi.org/10.1016/j.bpj.2016.11.2405.

Full text

APA, Harvard, Vancouver, ISO, and other styles

36

Beaven, Andrew H., Alexander J. Sodt, Richard W. Pastor, and Wonpil Im. "Protocol and Validation of CHARMM-GUI Hex Phase Builder." Biophysical Journal 112, no. 3 (2017): 73a—74a. http://dx.doi.org/10.1016/j.bpj.2016.11.442.

Full text

APA, Harvard, Vancouver, ISO, and other styles

37

Jo, Sunhwan, and Wonpil Im. "CHARMM-GUI: Brining Advanced Computational Techniques to Web Interface." Biophysical Journal 100, no. 3 (2011): 156a. http://dx.doi.org/10.1016/j.bpj.2010.12.1067.

Full text

APA, Harvard, Vancouver, ISO, and other styles

38

Vermaas, Josh V., Loukas Petridis, John Ralph, Michael F. Crowley, and Gregg T. Beckham. "Systematic parameterization of lignin for the CHARMM force field." Green Chemistry 21, no. 1 (2019): 109–22. http://dx.doi.org/10.1039/c8gc03209b.

Full text

Abstract:

We develop a comprehensive molecular mechanics force field for lignin and evaluate its performance in terms of thermodynamics and structure with respect to experimental observables. The developed force field can be used to model lignin polymers, including their covalent linkages to carbohydrates, and their interaction with other biomolecules.

APA, Harvard, Vancouver, ISO, and other styles

39

Xu, You, Lennart Nilsson, and Alexander D. MacKerrel. "An Additive Charmm Force Field for Modified Nucleic Acids." Biophysical Journal 108, no. 2 (2015): 235a—236a. http://dx.doi.org/10.1016/j.bpj.2014.11.1302.

Full text

APA, Harvard, Vancouver, ISO, and other styles

40

Kern, Nathan R., Jumin Lee, Morgan Fine-Morris, et al. "CHARMM-GUI Lecture Series on Molecular Modeling and Simulation." Biophysical Journal 114, no. 3 (2018): 184a. http://dx.doi.org/10.1016/j.bpj.2017.11.1027.

Full text

APA, Harvard, Vancouver, ISO, and other styles

41

Im, Wonpil. "CHARMM-GUI 10 Years for Biomolecular Modeling and Simulation." Biophysical Journal 110, no. 3 (2016): 328a. http://dx.doi.org/10.1016/j.bpj.2015.11.1764.

Full text

APA, Harvard, Vancouver, ISO, and other styles

42

Zhu, Xiao, Pedro E. M. Lopes, and Alexander D. MacKerell. "Recent developments and applications of the CHARMM force fields." WIREs Computational Molecular Science 2, no. 1 (2011): 167–85. http://dx.doi.org/10.1002/wcms.74.

Full text

APA, Harvard, Vancouver, ISO, and other styles

43

Xu, You, Kenno Vanommeslaeghe, Alexey Aleksandrov, Alexander D. MacKerell, and Lennart Nilsson. "Additive CHARMM force field for naturally occurring modified ribonucleotides." Journal of Computational Chemistry 37, no. 10 (2016): 896–912. http://dx.doi.org/10.1002/jcc.24307.

Full text

APA, Harvard, Vancouver, ISO, and other styles

44

Jo, Sunhwan, Xi Cheng, Jumin Lee, et al. "CHARMM-GUI 10 years for biomolecular modeling and simulation." Journal of Computational Chemistry 38, no. 15 (2016): 1114–24. http://dx.doi.org/10.1002/jcc.24660.

Full text

APA, Harvard, Vancouver, ISO, and other styles

45

Nicklaus, Marc C. "Conformational energies calculated by the molecular mechanics program CHARMm." Journal of Computational Chemistry 18, no. 8 (1997): 1056–60. http://dx.doi.org/10.1002/(sici)1096-987x(199706)18:8<1056::aid-jcc9>3.0.co;2-s.

Full text

APA, Harvard, Vancouver, ISO, and other styles

46

Sohn, Christopher J. "Devlopment and Application of Bicelle Builder in Charmm-Gui." Biophysical Journal 116, no. 3 (2019): 90a. http://dx.doi.org/10.1016/j.bpj.2018.11.527.

Full text

APA, Harvard, Vancouver, ISO, and other styles

47

Plazinski, Wojciech, and Anita Plazinska. "Molecular dynamics simulations of hexopyranose ring distortion in different force fields." Pure and Applied Chemistry 89, no. 9 (2017): 1283–94. http://dx.doi.org/10.1515/pac-2016-0922.

Full text

Abstract:

Abstract:The four classical, biomolecular force fields designed to study hexopyranose-based carbohydrates (GROMOS 56a6CARBO/56a6CARBO_R, GROMOS 53a6GLYC, CHARMM and GLYCAM06) have been tested in the context of ring-inversion properties. These properties were evaluated for both unfunctionalized monomers of all hexopyranoses of the d series and for residues in a chain composed of uniform units connected by α(1→4) and β(1→4) glycosidic linkages. The results indicate that the tested force fields differ in their predictions of the ring-inversion properties of both monomers and residues in a chain.

APA, Harvard, Vancouver, ISO, and other styles

48

Alpízar-Pedraza, Daniel, Yessica Roque-Diaz, Hilda Garay-Pérez, Frank Rosenau, Ludger Ständker, and Vivian Montero-Alejo. "Insights into the Adsorption Mechanisms of the Antimicrobial Peptide CIDEM-501 on Membrane Models." Antibiotics 13, no. 2 (2024): 167. http://dx.doi.org/10.3390/antibiotics13020167.

Full text

Abstract:

CIDEM-501 is a hybrid antimicrobial peptide rationally designed based on the structure of panusin and panulirin template peptides. The new peptide exhibits significant antibacterial activity against multidrug-resistant pathogens (MIC = 2–4 μM) while conserving no toxicity in human cell lines. We conducted molecular dynamics (MD) simulations using the CHARMM-36 force field to explore the CIDEM-501 adsorption mechanism with different membrane compositions. Several parameters that characterize these interactions were analyzed to elucidate individual residues’ structural and thermodynamic contribu

APA, Harvard, Vancouver, ISO, and other styles

49

Golopentia, Sanda. "Towards a pragmatic study of magic poetry." Linguistic Approaches to Poetry 15 (December 31, 2001): 53–73. http://dx.doi.org/10.1075/bjl.15.05gol.

Full text

Abstract:

In this paper, we introduce the basic concepts needed for a pragmatic analysis of a specific kind of magic poetry, viz. Romanian love charms. We first distinguish between five types of charms: charms for love and beauty; charms for knowing one’s fated spouse; charms for bringing one’s fated spouse; charms for hate; charms for undoing hate. Our study concentrates on charm scenarios, i.e. on the instructions transmitted by charm-performers. Each charm scenario combines two sets of textual data: charm formulas (verses or poems) and charm techniques. The technique texts contain prose directions co

APA, Harvard, Vancouver, ISO, and other styles

50

Besombes, S., D. Robert, J. P. Utille, F. R. Taravel та K. Mazeau. "Molecular Modeling of Lignin β-O-4 Model Compounds. Comparative Study of the Computed and Experimental Conformational Properties for a Guaiacyl β-O-4 Dimer". Holzforschung 57, № 3 (2003): 266–74. http://dx.doi.org/10.1515/hf.2003.040.

Full text

Abstract:

SummaryThe conformational preferences of thethreoanderythrodiastereomeric forms of a guaiacyl β-O-4 dimer have been investigated by molecular modeling using the CHARMM force field. Many low energy conformations have been identified for each diastereomer, showing that β-O-4 dimers can adopt a large variety of shapes. A consistent structural model has emerged that indicates different conformational behavior for thethreoanderythroforms, corresponding to a preferential extended overall shape for thethreoform. All the low energy conformers are stabilized by intramolecular H-bonds. In particular, th

APA, Harvard, Vancouver, ISO, and other styles

We offer discounts on all premium plans for authors whose works are included in thematic literature selections. Contact us to get a unique promo code!