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A potential for molecular simulation of compounds with linear moieties.

The Journal of chemical physics

van der Spoel D, Henschel H, van Maaren PJ, Ghahremanpour MM, Costa LT.
PMID: 32872881
J Chem Phys. 2020 Aug 28;153(8):084503. doi: 10.1063/5.0015184.

The harmonic angle bending potential is used in many force fields for (bio)molecular simulation. The force associated with this potential is discontinuous at angles close to 180°, which can lead to numeric instabilities. Angle bending of linear groups, such...

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van der Spoel D, Henschel H, van Maaren PJ, et al. A potential for molecular simulation of compounds with linear moieties. J Chem Phys. 2020;153(8):084503doi: 10.1063/5.0015184.
van der Spoel, D., Henschel, H., van Maaren, P. J., Ghahremanpour, M. M., & Costa, L. T. (2020). A potential for molecular simulation of compounds with linear moieties. The Journal of chemical physics, 153(8), 084503. https://doi.org/10.1063/5.0015184
van der Spoel, David, et al. "A potential for molecular simulation of compounds with linear moieties." The Journal of chemical physics vol. 153,8 (2020): 084503. doi: https://doi.org/10.1063/5.0015184
van der Spoel D, Henschel H, van Maaren PJ, Ghahremanpour MM, Costa LT. A potential for molecular simulation of compounds with linear moieties. J Chem Phys. 2020 Aug 28;153(8):084503. doi: 10.1063/5.0015184. PMID: 32872881.
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Small Molecule Thermochemistry: A Tool for Empirical Force Field Development.

The journal of physical chemistry. A

van der Spoel D, Ghahremanpour MM, Lemkul JA.
PMID: 30362355
J Phys Chem A. 2018 Nov 15;122(45):8982-8988. doi: 10.1021/acs.jpca.8b09867. Epub 2018 Nov 06.

Spectroscopic analysis of compounds is typically combined with density functional theory, for instance, for assigning vibrational frequencies, limiting application to relatively small compounds. Accurate classical force fields could, in principle, complement these quantum-chemical tools. A relatively simple way to...

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van der Spoel D, Ghahremanpour MM, Lemkul JA. Small Molecule Thermochemistry: A Tool for Empirical Force Field Development. J Phys Chem A. 2018;122(45):8982-8988doi: 10.1021/acs.jpca.8b09867.
van der Spoel, D., Ghahremanpour, M. M., & Lemkul, J. A. (2018). Small Molecule Thermochemistry: A Tool for Empirical Force Field Development. The journal of physical chemistry. A, 122(45), 8982-8988. https://doi.org/10.1021/acs.jpca.8b09867
van der Spoel, David, et al. "Small Molecule Thermochemistry: A Tool for Empirical Force Field Development." The journal of physical chemistry. A vol. 122,45 (2018): 8982-8988. doi: https://doi.org/10.1021/acs.jpca.8b09867
van der Spoel D, Ghahremanpour MM, Lemkul JA. Small Molecule Thermochemistry: A Tool for Empirical Force Field Development. J Phys Chem A. 2018 Nov 15;122(45):8982-8988. doi: 10.1021/acs.jpca.8b09867. Epub 2018 Nov 06. PMID: 30362355.
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The Alexandria library, a quantum-chemical database of molecular properties for force field development.

Scientific data

Ghahremanpour MM, van Maaren PJ, van der Spoel D.
PMID: 29633987
Sci Data. 2018 Apr 10;5:180062. doi: 10.1038/sdata.2018.62.

Data quality as well as library size are crucial issues for force field development. In order to predict molecular properties in a large chemical space, the foundation to build force fields on needs to encompass a large variety of...

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Ghahremanpour MM, van Maaren PJ, van der Spoel D. The Alexandria library, a quantum-chemical database of molecular properties for force field development. Sci Data. 2018;5:180062doi: 10.1038/sdata.2018.62.
Ghahremanpour, M. M., van Maaren, P. J., & van der Spoel, D. (2018). The Alexandria library, a quantum-chemical database of molecular properties for force field development. Scientific data, 5180062. https://doi.org/10.1038/sdata.2018.62
Ghahremanpour, Mohammad M, et al. "The Alexandria library, a quantum-chemical database of molecular properties for force field development." Scientific data vol. 5 (2018): 180062. doi: https://doi.org/10.1038/sdata.2018.62
Ghahremanpour MM, van Maaren PJ, van der Spoel D. The Alexandria library, a quantum-chemical database of molecular properties for force field development. Sci Data. 2018 Apr 10;5:180062. doi: 10.1038/sdata.2018.62. PMID: 29633987; PMCID: PMC5892371.
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Phase-Transferable Force Field for Alkali Halides.

Journal of chemical theory and computation

Walz MM, Ghahremanpour MM, van Maaren PJ, van der Spoel D.
PMID: 30300552
J Chem Theory Comput. 2018 Nov 13;14(11):5933-5948. doi: 10.1021/acs.jctc.8b00507. Epub 2018 Oct 22.

A longstanding goal of computational chemistry is to predict the state of materials in all phases with a single model. This is particularly relevant for materials that are difficult or dangerous to handle or compounds that have not yet...

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Walz MM, Ghahremanpour MM, van Maaren PJ, et al. Phase-Transferable Force Field for Alkali Halides. J Chem Theory Comput. 2018;14(11):5933-5948doi: 10.1021/acs.jctc.8b00507.
Walz, M. M., Ghahremanpour, M. M., van Maaren, P. J., & van der Spoel, D. (2018). Phase-Transferable Force Field for Alkali Halides. Journal of chemical theory and computation, 14(11), 5933-5948. https://doi.org/10.1021/acs.jctc.8b00507
Walz, Marie-Madeleine, et al. "Phase-Transferable Force Field for Alkali Halides." Journal of chemical theory and computation vol. 14,11 (2018): 5933-5948. doi: https://doi.org/10.1021/acs.jctc.8b00507
Walz MM, Ghahremanpour MM, van Maaren PJ, van der Spoel D. Phase-Transferable Force Field for Alkali Halides. J Chem Theory Comput. 2018 Nov 13;14(11):5933-5948. doi: 10.1021/acs.jctc.8b00507. Epub 2018 Oct 22. PMID: 30300552.
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Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2.

ACS medicinal chemistry letters

Ghahremanpour MM, Tirado-Rives J, Deshmukh M, Ippolito JA, Zhang CH, Cabeza de Vaca I, Liosi ME, Anderson KS, Jorgensen WL.
PMID: 33324471
ACS Med Chem Lett. 2020 Oct 25;11(12):2526-2533. doi: 10.1021/acsmedchemlett.0c00521. eCollection 2020 Dec 10.

A consensus virtual screening protocol has been applied to ca. 2000 approved drugs to seek inhibitors of the main protease (M

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Ghahremanpour MM, Tirado-Rives J, Deshmukh M, et al. Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2. ACS Med Chem Lett. 2020;11(12):2526-2533doi: 10.1021/acsmedchemlett.0c00521.
Ghahremanpour, M. M., Tirado-Rives, J., Deshmukh, M., Ippolito, J. A., Zhang, C. H., Cabeza de Vaca, I., Liosi, M. E., Anderson, K. S., & Jorgensen, W. L. (2020). Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2. ACS medicinal chemistry letters, 11(12), 2526-2533. https://doi.org/10.1021/acsmedchemlett.0c00521
Ghahremanpour, Mohammad M, et al. "Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2." ACS medicinal chemistry letters vol. 11,12 (2020): 2526-2533. doi: https://doi.org/10.1021/acsmedchemlett.0c00521
Ghahremanpour MM, Tirado-Rives J, Deshmukh M, Ippolito JA, Zhang CH, Cabeza de Vaca I, Liosi ME, Anderson KS, Jorgensen WL. Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2. ACS Med Chem Lett. 2020 Oct 25;11(12):2526-2533. doi: 10.1021/acsmedchemlett.0c00521. eCollection 2020 Dec 10. PMID: 33324471; PMCID: PMC7605328.
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Polarizable Drude Model with s-Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields.

Journal of chemical theory and computation

Ghahremanpour MM, van Maaren PJ, Caleman C, Hutchison GR, van der Spoel D.
PMID: 30281307
J Chem Theory Comput. 2018 Nov 13;14(11):5553-5566. doi: 10.1021/acs.jctc.8b00430. Epub 2018 Oct 17.

Gas-phase electric properties of molecules can be computed routinely using wave function methods or density functional theory (DFT). However, these methods remain computationally expensive for high-throughput screening of the vast chemical space of virtual compounds. Therefore, empirical force fields...

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Ghahremanpour MM, van Maaren PJ, Caleman C, et al. Polarizable Drude Model with s-Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields. J Chem Theory Comput. 2018;14(11):5553-5566doi: 10.1021/acs.jctc.8b00430.
Ghahremanpour, M. M., van Maaren, P. J., Caleman, C., Hutchison, G. R., & van der Spoel, D. (2018). Polarizable Drude Model with s-Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields. Journal of chemical theory and computation, 14(11), 5553-5566. https://doi.org/10.1021/acs.jctc.8b00430
Ghahremanpour, Mohammad Mehdi, et al. "Polarizable Drude Model with s-Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields." Journal of chemical theory and computation vol. 14,11 (2018): 5553-5566. doi: https://doi.org/10.1021/acs.jctc.8b00430
Ghahremanpour MM, van Maaren PJ, Caleman C, Hutchison GR, van der Spoel D. Polarizable Drude Model with s-Type Gaussian or Slater Charge Density for General Molecular Mechanics Force Fields. J Chem Theory Comput. 2018 Nov 13;14(11):5553-5566. doi: 10.1021/acs.jctc.8b00430. Epub 2018 Oct 17. PMID: 30281307.
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Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV-2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations.

ACS central science

Zhang CH, Stone EA, Deshmukh M, Ippolito JA, Ghahremanpour MM, Tirado-Rives J, Spasov KA, Zhang S, Takeo Y, Kudalkar SN, Liang Z, Isaacs F, Lindenbach B, Miller SJ, Anderson KS, Jorgensen WL.
PMID: 33786375
ACS Cent Sci. 2021 Mar 24;7(3):467-475. doi: 10.1021/acscentsci.1c00039. Epub 2021 Feb 22.

Starting from our previous finding of 14 known drugs as inhibitors of the main protease (M

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Zhang CH, Stone EA, Deshmukh M, et al. Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV-2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations. ACS Cent Sci. 2021;7(3):467-475doi: 10.1021/acscentsci.1c00039.
Zhang, C. H., Stone, E. A., Deshmukh, M., Ippolito, J. A., Ghahremanpour, M. M., Tirado-Rives, J., Spasov, K. A., Zhang, S., Takeo, Y., Kudalkar, S. N., Liang, Z., Isaacs, F., Lindenbach, B., Miller, S. J., Anderson, K. S., & Jorgensen, W. L. (2021). Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV-2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations. ACS central science, 7(3), 467-475. https://doi.org/10.1021/acscentsci.1c00039
Zhang, Chun-Hui, et al. "Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV-2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations." ACS central science vol. 7,3 (2021): 467-475. doi: https://doi.org/10.1021/acscentsci.1c00039
Zhang CH, Stone EA, Deshmukh M, Ippolito JA, Ghahremanpour MM, Tirado-Rives J, Spasov KA, Zhang S, Takeo Y, Kudalkar SN, Liang Z, Isaacs F, Lindenbach B, Miller SJ, Anderson KS, Jorgensen WL. Potent Noncovalent Inhibitors of the Main Protease of SARS-CoV-2 from Molecular Sculpting of the Drug Perampanel Guided by Free Energy Perturbation Calculations. ACS Cent Sci. 2021 Mar 24;7(3):467-475. doi: 10.1021/acscentsci.1c00039. Epub 2021 Feb 22. PMID: 33786375; PMCID: PMC7931627.
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Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2.

bioRxiv : the preprint server for biology

Ghahremanpour MM, Tirado-Rives J, Deshmukh M, Ippolito JA, Zhang CH, de Vaca IC, Liosi ME, Anderson KS, Jorgensen WL.
PMID: 32869018
bioRxiv. 2020 Aug 28; doi: 10.1101/2020.08.28.271957.

A consensus virtual screening protocol has been applied to ca. 2000 approved drugs to seek inhibitors of the main protease (M

Cite
Ghahremanpour MM, Tirado-Rives J, Deshmukh M, et al. Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2. bioRxiv. 2020;doi: 10.1101/2020.08.28.271957.
Ghahremanpour, M. M., Tirado-Rives, J., Deshmukh, M., Ippolito, J. A., Zhang, C. H., de Vaca, I. C., Liosi, M. E., Anderson, K. S., & Jorgensen, W. L. (2020). Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2. bioRxiv : the preprint server for biology, . https://doi.org/10.1101/2020.08.28.271957
Ghahremanpour, Mohammad M, et al. "Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2." bioRxiv : the preprint server for biology vol. (2020). doi: https://doi.org/10.1101/2020.08.28.271957
Ghahremanpour MM, Tirado-Rives J, Deshmukh M, Ippolito JA, Zhang CH, de Vaca IC, Liosi ME, Anderson KS, Jorgensen WL. Identification of 14 Known Drugs as Inhibitors of the Main Protease of SARS-CoV-2. bioRxiv. 2020 Aug 28; doi: 10.1101/2020.08.28.271957. PMID: 32869018; PMCID: PMC7457600.
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Showing 1 to 8 of 8 entries