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A Simple PB/LIE Free Energy Function Accurately Predicts the Peptide Binding Specificity of the Tiam1 PDZ Domain.

Frontiers in molecular biosciences

Panel N, Sun YJ, Fuentes EJ, Simonson T.
PMID: 29018806
Front Mol Biosci. 2017 Sep 26;4:65. doi: 10.3389/fmolb.2017.00065. eCollection 2017.

PDZ domains generally bind short amino acid sequences at the C-terminus of target proteins, and short peptides can be used as inhibitors or model ligands. Here, we used experimental binding assays and molecular dynamics simulations to characterize 51 complexes...

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Panel N, Sun YJ, Fuentes EJ, et al. A Simple PB/LIE Free Energy Function Accurately Predicts the Peptide Binding Specificity of the Tiam1 PDZ Domain. Front Mol Biosci. 2017;4:65doi: 10.3389/fmolb.2017.00065.
Panel, N., Sun, Y. J., Fuentes, E. J., & Simonson, T. (2017). A Simple PB/LIE Free Energy Function Accurately Predicts the Peptide Binding Specificity of the Tiam1 PDZ Domain. Frontiers in molecular biosciences, 465. https://doi.org/10.3389/fmolb.2017.00065
Panel, Nicolas, et al. "A Simple PB/LIE Free Energy Function Accurately Predicts the Peptide Binding Specificity of the Tiam1 PDZ Domain." Frontiers in molecular biosciences vol. 4 (2017): 65. doi: https://doi.org/10.3389/fmolb.2017.00065
Panel N, Sun YJ, Fuentes EJ, Simonson T. A Simple PB/LIE Free Energy Function Accurately Predicts the Peptide Binding Specificity of the Tiam1 PDZ Domain. Front Mol Biosci. 2017 Sep 26;4:65. doi: 10.3389/fmolb.2017.00065. eCollection 2017. PMID: 29018806; PMCID: PMC5623046.
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An Overview of Electrostatic Free Energy Computations for Solutions and Proteins.

Journal of chemical theory and computation

Lin YL, Aleksandrov A, Simonson T, Roux B.
PMID: 26586504
J Chem Theory Comput. 2014 Jul 08;10(7):2690-709. doi: 10.1021/ct500195p. Epub 2014 Jun 05.

Free energy simulations for electrostatic and charging processes in complex molecular systems encounter specific difficulties owing to the long-range, 1/r Coulomb interaction. To calculate the solvation free energy of a simple ion, it is essential to take into account...

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Lin YL, Aleksandrov A, Simonson T, et al. An Overview of Electrostatic Free Energy Computations for Solutions and Proteins. J Chem Theory Comput. 2014;10(7):2690-709doi: 10.1021/ct500195p.
Lin, Y. L., Aleksandrov, A., Simonson, T., & Roux, B. (2014). An Overview of Electrostatic Free Energy Computations for Solutions and Proteins. Journal of chemical theory and computation, 10(7), 2690-709. https://doi.org/10.1021/ct500195p
Lin, Yen-Lin, et al. "An Overview of Electrostatic Free Energy Computations for Solutions and Proteins." Journal of chemical theory and computation vol. 10,7 (2014): 2690-709. doi: https://doi.org/10.1021/ct500195p
Lin YL, Aleksandrov A, Simonson T, Roux B. An Overview of Electrostatic Free Energy Computations for Solutions and Proteins. J Chem Theory Comput. 2014 Jul 08;10(7):2690-709. doi: 10.1021/ct500195p. Epub 2014 Jun 05. PMID: 26586504.
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A new electrocardiographic limb electrode.

American heart journal

SIMONSON E.
PMID: 14877738
Am Heart J. 1951 Sep;42(3):445-6. doi: 10.1016/0002-8703(51)90139-1.

No abstract available.

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SIMONSON E. A new electrocardiographic limb electrode. Am Heart J. 1951;42(3):445-6doi: 10.1016/0002-8703(51)90139-1.
SIMONSON, E. (1951). A new electrocardiographic limb electrode. American heart journal, 42(3), 445-6. https://doi.org/10.1016/0002-8703(51)90139-1
SIMONSON, E. "A new electrocardiographic limb electrode." American heart journal vol. 42,3 (1951): 445-6. doi: https://doi.org/10.1016/0002-8703(51)90139-1
SIMONSON E. A new electrocardiographic limb electrode. Am Heart J. 1951 Sep;42(3):445-6. doi: 10.1016/0002-8703(51)90139-1. PMID: 14877738.
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Implicit solvent models.

Biophysical chemistry

Roux B, Simonson T.
PMID: 17030302
Biophys Chem. 1999 Apr 05;78(1):1-20. doi: 10.1016/s0301-4622(98)00226-9.

Implicit solvent models for biomolecular simulations are reviewed and their underlying statistical mechanical basis is discussed. The fundamental quantity that implicit models seek to approximate is the solute potential of mean force, which determines the statistical weight of solute...

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Roux B, Simonson T. Implicit solvent models. Biophys Chem. 1999;78(1):1-20doi: 10.1016/s0301-4622(98)00226-9.
Roux, B., & Simonson, T. (1999). Implicit solvent models. Biophysical chemistry, 78(1), 1-20. https://doi.org/10.1016/s0301-4622(98)00226-9
Roux, B, and Simonson, T. "Implicit solvent models." Biophysical chemistry vol. 78,1 (1999): 1-20. doi: https://doi.org/10.1016/s0301-4622(98)00226-9
Roux B, Simonson T. Implicit solvent models. Biophys Chem. 1999 Apr 05;78(1):1-20. doi: 10.1016/s0301-4622(98)00226-9. PMID: 17030302.
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Variability of the electrocardiogram in normal young men.

American heart journal

SIMONSON E, BROZEK J, KEYS A.
PMID: 18135736
Am Heart J. 1949 Sep;38(3):407-22. doi: 10.1016/0002-8703(49)90852-2.

No abstract available.

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SIMONSON E, BROZEK J, KEYS A. Variability of the electrocardiogram in normal young men. Am Heart J. 1949;38(3):407-22doi: 10.1016/0002-8703(49)90852-2.
SIMONSON, E., BROZEK, J., & KEYS, A. (1949). Variability of the electrocardiogram in normal young men. American heart journal, 38(3), 407-22. https://doi.org/10.1016/0002-8703(49)90852-2
SIMONSON, E, et al. "Variability of the electrocardiogram in normal young men." American heart journal vol. 38,3 (1949): 407-22. doi: https://doi.org/10.1016/0002-8703(49)90852-2
SIMONSON E, BROZEK J, KEYS A. Variability of the electrocardiogram in normal young men. Am Heart J. 1949 Sep;38(3):407-22. doi: 10.1016/0002-8703(49)90852-2. PMID: 18135736.
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Antiplatelet therapy for secondary prevention of the complications of atherothrombotic disease.

The Consultant pharmacist : the journal of the American Society of Consultant Pharmacists

Simonson W, Beizer JL.
PMID: 16553498
Consult Pharm. 2004 Sep;19(9):813-23. doi: 10.4140/tcp.n.2004.813.

OBJECTIVE: To review and summarize key studies of secondary prevention of atherothrombotic events.DATA SOURCES: English language clinical trials and guidelines.STUDY SELECTION: Key clinical trials and guidelines were selected by the authors based on their perceived importance and relevance to...

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Simonson W, Beizer JL. Antiplatelet therapy for secondary prevention of the complications of atherothrombotic disease. Consult Pharm. 2004;19(9):813-23doi: 10.4140/tcp.n.2004.813.
Simonson, W., & Beizer, J. L. (2004). Antiplatelet therapy for secondary prevention of the complications of atherothrombotic disease. The Consultant pharmacist : the journal of the American Society of Consultant Pharmacists, 19(9), 813-23. https://doi.org/10.4140/tcp.n.2004.813
Simonson, William, and Beizer, Judith L. "Antiplatelet therapy for secondary prevention of the complications of atherothrombotic disease." The Consultant pharmacist : the journal of the American Society of Consultant Pharmacists vol. 19,9 (2004): 813-23. doi: https://doi.org/10.4140/tcp.n.2004.813
Simonson W, Beizer JL. Antiplatelet therapy for secondary prevention of the complications of atherothrombotic disease. Consult Pharm. 2004 Sep;19(9):813-23. doi: 10.4140/tcp.n.2004.813. PMID: 16553498.
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AN UNUSUAL CASE OF A-V NODAL RHYTHM WITH VARYING A-V BLOCK.

British heart journal

Simonson E, Enzer N.
PMID: 18609988
Br Heart J. 1945 Jan;7(1):45-8. doi: 10.1136/hrt.7.1.45.

No abstract available.

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Simonson E, Enzer N. AN UNUSUAL CASE OF A-V NODAL RHYTHM WITH VARYING A-V BLOCK. Br Heart J. 1945;7(1):45-8doi: 10.1136/hrt.7.1.45.
Simonson, E., & Enzer, N. (1945). AN UNUSUAL CASE OF A-V NODAL RHYTHM WITH VARYING A-V BLOCK. British heart journal, 7(1), 45-8. https://doi.org/10.1136/hrt.7.1.45
Simonson, E, and Enzer, N. "AN UNUSUAL CASE OF A-V NODAL RHYTHM WITH VARYING A-V BLOCK." British heart journal vol. 7,1 (1945): 45-8. doi: https://doi.org/10.1136/hrt.7.1.45
Simonson E, Enzer N. AN UNUSUAL CASE OF A-V NODAL RHYTHM WITH VARYING A-V BLOCK. Br Heart J. 1945 Jan;7(1):45-8. doi: 10.1136/hrt.7.1.45. PMID: 18609988; PMCID: PMC503536.
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Simple models for nonpolar solvation: Parameterization and testing.

Journal of computational chemistry

Michael E, Polydorides S, Simonson T, Archontis G.
PMID: 28786118
J Comput Chem. 2017 Nov 05;38(29):2509-2519. doi: 10.1002/jcc.24910. Epub 2017 Aug 07.

Implicit solvent models are important for many biomolecular simulations. The polarity of aqueous solvent is essential and qualitatively captured by continuum electrostatics methods like Generalized Born (GB). However, GB does not account for the solvent-induced interactions between exposed hydrophobic...

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Michael E, Polydorides S, Simonson T, et al. Simple models for nonpolar solvation: Parameterization and testing. J Comput Chem. 2017;38(29):2509-2519doi: 10.1002/jcc.24910.
Michael, E., Polydorides, S., Simonson, T., & Archontis, G. (2017). Simple models for nonpolar solvation: Parameterization and testing. Journal of computational chemistry, 38(29), 2509-2519. https://doi.org/10.1002/jcc.24910
Michael, Eleni, et al. "Simple models for nonpolar solvation: Parameterization and testing." Journal of computational chemistry vol. 38,29 (2017): 2509-2519. doi: https://doi.org/10.1002/jcc.24910
Michael E, Polydorides S, Simonson T, Archontis G. Simple models for nonpolar solvation: Parameterization and testing. J Comput Chem. 2017 Nov 05;38(29):2509-2519. doi: 10.1002/jcc.24910. Epub 2017 Aug 07. PMID: 28786118.
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Full Protein Sequence Redesign with an MMGBSA Energy Function.

Journal of chemical theory and computation

Gaillard T, Simonson T.
PMID: 28886244
J Chem Theory Comput. 2017 Oct 10;13(10):4932-4943. doi: 10.1021/acs.jctc.7b00202. Epub 2017 Sep 28.

Computational protein design aims to create proteins with novel properties. A key element is the energy or scoring function used to select the sequences and conformations. We study the performance of an "MMGBSA" energy function, which combines molecular mechanics...

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Gaillard T, Simonson T. Full Protein Sequence Redesign with an MMGBSA Energy Function. J Chem Theory Comput. 2017;13(10):4932-4943doi: 10.1021/acs.jctc.7b00202.
Gaillard, T., & Simonson, T. (2017). Full Protein Sequence Redesign with an MMGBSA Energy Function. Journal of chemical theory and computation, 13(10), 4932-4943. https://doi.org/10.1021/acs.jctc.7b00202
Gaillard, Thomas, and Simonson, Thomas. "Full Protein Sequence Redesign with an MMGBSA Energy Function." Journal of chemical theory and computation vol. 13,10 (2017): 4932-4943. doi: https://doi.org/10.1021/acs.jctc.7b00202
Gaillard T, Simonson T. Full Protein Sequence Redesign with an MMGBSA Energy Function. J Chem Theory Comput. 2017 Oct 10;13(10):4932-4943. doi: 10.1021/acs.jctc.7b00202. Epub 2017 Sep 28. PMID: 28886244.
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Correction to "Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg.

The journal of physical chemistry. A

Villa F, MacKerell AD, Roux B, Simonson T.
PMID: 30600990
J Phys Chem A. 2019 Jan 17;123(2):629. doi: 10.1021/acs.jpca.8b12337. Epub 2019 Jan 02.

No abstract available.

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Villa F, MacKerell AD, Roux B, et al. Correction to "Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg. J Phys Chem A. 2019;123(2):629doi: 10.1021/acs.jpca.8b12337.
Villa, F., MacKerell, A. D., Roux, B., & Simonson, T. (2019). Correction to "Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg. The journal of physical chemistry. A, 123(2), 629. https://doi.org/10.1021/acs.jpca.8b12337
Villa, Francesco, et al. "Correction to "Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg." The journal of physical chemistry. A vol. 123,2 (2019): 629. doi: https://doi.org/10.1021/acs.jpca.8b12337
Villa F, MacKerell AD, Roux B, Simonson T. Correction to "Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg. J Phys Chem A. 2019 Jan 17;123(2):629. doi: 10.1021/acs.jpca.8b12337. Epub 2019 Jan 02. PMID: 30600990; PMCID: PMC6483368.
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Hot topics in interventional cardiology: Proceedings from the society for cardiovascular angiography and interventions (SCAI) 2021 think tank.

Catheterization and cardiovascular interventions : official journal of the Society for Cardiac Angiography & Interventions

Naidu SS, Baron SJ, Eng MH, Sathanandam SK, Zidar DA, Feldman DN, Ing FF, Latif F, Lim MJ, Henry TD, Rao SV, Dangas GD, Hermiller JB, Daggubati R, Shah B, Ang L, Aronow HD, Banerjee S, Box LC, Caputo RP, Cohen MG, Coylewright M, Duffy PL, Goldsweig AM, Hagler DJ, Hawkins BM, Hijazi ZM, Jayasuriya S, Justino H, Klein AJ, Kliger C, Li J, Mahmud E, Messenger JC, Morray BH, Parikh SA, Reilly J, Secemsky E, Shishehbor MH, Szerlip M, Yakubov SJ, Grines CL, Alvarez-Breckenridge J, Baird C, Baker D, Berry C, Bhattacharya M, Bilazarian S, Bowen R, Brounstein K, Cameron C, Cavalcante R, Culbertson C, Diaz P, Emanuele S, Evans E, Fletcher R, Fortune T, Gaiha P, Govender D, Gutfinger D, Haggstrom K, Herzog A, Hite D, Kalich B, Kirkland A, Kohler T, Laurisden H, Livolsi K, Lombardi L, Lowe S, Marhenke K, Meikle J, Moat N, Mueller M, Patarca R, Popma J, Rangwala N, Simonton C, Stokes J, Taber M, Tieche C, Venditto J, West NEJ, Zinn L.
PMID: 34398509
Catheter Cardiovasc Interv. 2021 Nov 01;98(5):904-913. doi: 10.1002/ccd.29898. Epub 2021 Aug 16.

The Society for Cardiovascular Angiography and Interventions (SCAI) Think Tank is a collaborative venture that brings together interventional cardiologists, administrative partners, and select members of the cardiovascular industry community annually for high-level field-wide discussions. The 2021 Think Tank was...

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Naidu SS, Baron SJ, Eng MH, et al. Hot topics in interventional cardiology: Proceedings from the society for cardiovascular angiography and interventions (SCAI) 2021 think tank. Catheter Cardiovasc Interv. 2021;98(5):904-913doi: 10.1002/ccd.29898.
Naidu, S. S., Baron, S. J., Eng, M. H., Sathanandam, S. K., Zidar, D. A., Feldman, D. N., Ing, F. F., Latif, F., Lim, M. J., Henry, T. D., Rao, S. V., Dangas, G. D., Hermiller, J. B., Daggubati, R., Shah, B., Ang, L., Aronow, H. D., Banerjee, S., Box, L. C., Caputo, R. P., Cohen, M. G., Coylewright, M., Duffy, P. L., Goldsweig, A. M., Hagler, D. J., Hawkins, B. M., Hijazi, Z. M., Jayasuriya, S., Justino, H., Klein, A. J., Kliger, C., Li, J., Mahmud, E., Messenger, J. C., Morray, B. H., Parikh, S. A., Reilly, J., Secemsky, E., Shishehbor, M. H., Szerlip, M., Yakubov, S. J., Grines, C. L., Alvarez-Breckenridge, J., Baird, C., Baker, D., Berry, C., Bhattacharya, M., Bilazarian, S., Bowen, R., Brounstein, K., Cameron, C., Cavalcante, R., Culbertson, C., Diaz, P., Emanuele, S., Evans, E., Fletcher, R., Fortune, T., Gaiha, P., Govender, D., Gutfinger, D., Haggstrom, K., Herzog, A., Hite, D., Kalich, B., Kirkland, A., Kohler, T., Laurisden, H., Livolsi, K., Lombardi, L., Lowe, S., Marhenke, K., Meikle, J., Moat, N., Mueller, M., Patarca, R., Popma, J., Rangwala, N., Simonton, C., Stokes, J., Taber, M., Tieche, C., Venditto, J., West, N. E. J., & Zinn, L. (2021). Hot topics in interventional cardiology: Proceedings from the society for cardiovascular angiography and interventions (SCAI) 2021 think tank. Catheterization and cardiovascular interventions : official journal of the Society for Cardiac Angiography & Interventions, 98(5), 904-913. https://doi.org/10.1002/ccd.29898
Naidu, Srihari S, et al. "Hot topics in interventional cardiology: Proceedings from the society for cardiovascular angiography and interventions (SCAI) 2021 think tank." Catheterization and cardiovascular interventions : official journal of the Society for Cardiac Angiography & Interventions vol. 98,5 (2021): 904-913. doi: https://doi.org/10.1002/ccd.29898
Naidu SS, Baron SJ, Eng MH, Sathanandam SK, Zidar DA, Feldman DN, Ing FF, Latif F, Lim MJ, Henry TD, Rao SV, Dangas GD, Hermiller JB, Daggubati R, Shah B, Ang L, Aronow HD, Banerjee S, Box LC, Caputo RP, Cohen MG, Coylewright M, Duffy PL, Goldsweig AM, Hagler DJ, Hawkins BM, Hijazi ZM, Jayasuriya S, Justino H, Klein AJ, Kliger C, Li J, Mahmud E, Messenger JC, Morray BH, Parikh SA, Reilly J, Secemsky E, Shishehbor MH, Szerlip M, Yakubov SJ, Grines CL, Alvarez-Breckenridge J, Baird C, Baker D, Berry C, Bhattacharya M, Bilazarian S, Bowen R, Brounstein K, Cameron C, Cavalcante R, Culbertson C, Diaz P, Emanuele S, Evans E, Fletcher R, Fortune T, Gaiha P, Govender D, Gutfinger D, Haggstrom K, Herzog A, Hite D, Kalich B, Kirkland A, Kohler T, Laurisden H, Livolsi K, Lombardi L, Lowe S, Marhenke K, Meikle J, Moat N, Mueller M, Patarca R, Popma J, Rangwala N, Simonton C, Stokes J, Taber M, Tieche C, Venditto J, West NEJ, Zinn L. Hot topics in interventional cardiology: Proceedings from the society for cardiovascular angiography and interventions (SCAI) 2021 think tank. Catheter Cardiovasc Interv. 2021 Nov 01;98(5):904-913. doi: 10.1002/ccd.29898. Epub 2021 Aug 16. PMID: 34398509.
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Behavioral characterization, potential clinical relevance and mechanisms of latent pain sensitization.

Pharmacology & therapeutics

Gerum M, Simonin F.
PMID: 34763010
Pharmacol Ther. 2021 Nov 08;108032. doi: 10.1016/j.pharmthera.2021.108032. Epub 2021 Nov 08.

Chronic pain is a debilitating disorder that can occur as painful episodes that alternates with bouts of remission and occurs despite healing of the primary insult. Those episodes are often triggered by stressful events. In the last decades, a...

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Gerum M, Simonin F. Behavioral characterization, potential clinical relevance and mechanisms of latent pain sensitization. Pharmacol Ther. 2021;108032doi: 10.1016/j.pharmthera.2021.108032.
Gerum, M., & Simonin, F. (2021). Behavioral characterization, potential clinical relevance and mechanisms of latent pain sensitization. Pharmacology & therapeutics, 108032. https://doi.org/10.1016/j.pharmthera.2021.108032
Gerum, Manon, and Simonin, Frédéric. "Behavioral characterization, potential clinical relevance and mechanisms of latent pain sensitization." Pharmacology & therapeutics vol. (2021): 108032. doi: https://doi.org/10.1016/j.pharmthera.2021.108032
Gerum M, Simonin F. Behavioral characterization, potential clinical relevance and mechanisms of latent pain sensitization. Pharmacol Ther. 2021 Nov 08;108032. doi: 10.1016/j.pharmthera.2021.108032. Epub 2021 Nov 08. PMID: 34763010.
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Showing 1 to 12 of 112 entries