Alchemical prediction of hydration free energies for SAMPL
Abstract Hydration free energy calculations have become important tests of force fields. Alchemical free energy calculations based on molecular dynamics simulations provide a rigorous way to calculate these free energies for a particular force field, given sufficient sampling. Here, we report result...
Ausführliche Beschreibung
Autor*in: |
Mobley, David L. [verfasserIn] |
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Format: |
Artikel |
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Sprache: |
Englisch |
Erschienen: |
2011 |
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Schlagwörter: |
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Anmerkung: |
© Springer Science+Business Media B.V. 2012 |
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Übergeordnetes Werk: |
Enthalten in: Journal of computer aided molecular design - Springer Netherlands, 1987, 26(2011), 5 vom: 24. Dez., Seite 551-562 |
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Übergeordnetes Werk: |
volume:26 ; year:2011 ; number:5 ; day:24 ; month:12 ; pages:551-562 |
Links: |
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DOI / URN: |
10.1007/s10822-011-9528-8 |
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Katalog-ID: |
OLC2034738861 |
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520 | |a Abstract Hydration free energy calculations have become important tests of force fields. Alchemical free energy calculations based on molecular dynamics simulations provide a rigorous way to calculate these free energies for a particular force field, given sufficient sampling. Here, we report results of alchemical hydration free energy calculations for the set of small molecules comprising the 2011 Statistical Assessment of Modeling of Proteins and Ligands challenge. Our calculations are largely based on the Generalized Amber Force Field with several different charge models, and we achieved RMS errors in the 1.4–2.2 kcal/mol range depending on charge model, marginally higher than what we typically observed in previous studies (Mobley et al. in J Phys Chem B 111(9):2242–2254, 2007, J Chem Theory Comput 5(2):350–358, 2009, J Phys Chem B 115:1329–1332, 2011; Nicholls et al. in J Med Chem 51:769–779, 2008; Klimovich and Mobley in J Comput Aided Mol Design 24(4):307–316, 2010). The test set consists of ethane, biphenyl, and a dibenzyl dioxin, as well as a series of chlorinated derivatives of each. We found that, for this set, using high-quality partial charges from MP2/cc-PVTZ SCRF RESP fits provided marginally improved agreement with experiment over using AM1-BCC partial charges as we have more typically done, in keeping with our recent findings (Mobley et al. in J Phys Chem B 115:1329–1332, 2011). Switching to OPLS Lennard–Jones parameters with AM1-BCC charges also improves agreement with experiment. We also find a number of chemical trends within each molecular series which we can explain, but there are also some surprises, including some that are captured by the calculations and some that are not. | ||
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10.1007/s10822-011-9528-8 doi (DE-627)OLC2034738861 (DE-He213)s10822-011-9528-8-p DE-627 ger DE-627 rakwb eng 570 VZ 12 15,3 ssgn PHARM DE-84 fid BIODIV DE-30 fid Mobley, David L. verfasserin aut Alchemical prediction of hydration free energies for SAMPL 2011 Text txt rdacontent ohne Hilfsmittel zu benutzen n rdamedia Band nc rdacarrier © Springer Science+Business Media B.V. 2012 Abstract Hydration free energy calculations have become important tests of force fields. Alchemical free energy calculations based on molecular dynamics simulations provide a rigorous way to calculate these free energies for a particular force field, given sufficient sampling. Here, we report results of alchemical hydration free energy calculations for the set of small molecules comprising the 2011 Statistical Assessment of Modeling of Proteins and Ligands challenge. Our calculations are largely based on the Generalized Amber Force Field with several different charge models, and we achieved RMS errors in the 1.4–2.2 kcal/mol range depending on charge model, marginally higher than what we typically observed in previous studies (Mobley et al. in J Phys Chem B 111(9):2242–2254, 2007, J Chem Theory Comput 5(2):350–358, 2009, J Phys Chem B 115:1329–1332, 2011; Nicholls et al. in J Med Chem 51:769–779, 2008; Klimovich and Mobley in J Comput Aided Mol Design 24(4):307–316, 2010). The test set consists of ethane, biphenyl, and a dibenzyl dioxin, as well as a series of chlorinated derivatives of each. We found that, for this set, using high-quality partial charges from MP2/cc-PVTZ SCRF RESP fits provided marginally improved agreement with experiment over using AM1-BCC partial charges as we have more typically done, in keeping with our recent findings (Mobley et al. in J Phys Chem B 115:1329–1332, 2011). Switching to OPLS Lennard–Jones parameters with AM1-BCC charges also improves agreement with experiment. We also find a number of chemical trends within each molecular series which we can explain, but there are also some surprises, including some that are captured by the calculations and some that are not. Hydration Alchemical Free energy Molecular dynamics Liu, Shaui aut Cerutti, David S. aut Swope, William C. aut Rice, Julia E. aut Enthalten in Journal of computer aided molecular design Springer Netherlands, 1987 26(2011), 5 vom: 24. Dez., Seite 551-562 (DE-627)130644110 (DE-600)808166-9 (DE-576)018278221 0920-654X nnns volume:26 year:2011 number:5 day:24 month:12 pages:551-562 https://doi.org/10.1007/s10822-011-9528-8 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_OLC FID-PHARM FID-BIODIV SSG-OLC-MAT SSG-OLC-PHA SSG-OLC-DE-84 SSG-OPC-PHA GBV_ILN_20 GBV_ILN_70 GBV_ILN_2219 GBV_ILN_4012 AR 26 2011 5 24 12 551-562 |
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10.1007/s10822-011-9528-8 doi (DE-627)OLC2034738861 (DE-He213)s10822-011-9528-8-p DE-627 ger DE-627 rakwb eng 570 VZ 12 15,3 ssgn PHARM DE-84 fid BIODIV DE-30 fid Mobley, David L. verfasserin aut Alchemical prediction of hydration free energies for SAMPL 2011 Text txt rdacontent ohne Hilfsmittel zu benutzen n rdamedia Band nc rdacarrier © Springer Science+Business Media B.V. 2012 Abstract Hydration free energy calculations have become important tests of force fields. Alchemical free energy calculations based on molecular dynamics simulations provide a rigorous way to calculate these free energies for a particular force field, given sufficient sampling. Here, we report results of alchemical hydration free energy calculations for the set of small molecules comprising the 2011 Statistical Assessment of Modeling of Proteins and Ligands challenge. Our calculations are largely based on the Generalized Amber Force Field with several different charge models, and we achieved RMS errors in the 1.4–2.2 kcal/mol range depending on charge model, marginally higher than what we typically observed in previous studies (Mobley et al. in J Phys Chem B 111(9):2242–2254, 2007, J Chem Theory Comput 5(2):350–358, 2009, J Phys Chem B 115:1329–1332, 2011; Nicholls et al. in J Med Chem 51:769–779, 2008; Klimovich and Mobley in J Comput Aided Mol Design 24(4):307–316, 2010). The test set consists of ethane, biphenyl, and a dibenzyl dioxin, as well as a series of chlorinated derivatives of each. We found that, for this set, using high-quality partial charges from MP2/cc-PVTZ SCRF RESP fits provided marginally improved agreement with experiment over using AM1-BCC partial charges as we have more typically done, in keeping with our recent findings (Mobley et al. in J Phys Chem B 115:1329–1332, 2011). Switching to OPLS Lennard–Jones parameters with AM1-BCC charges also improves agreement with experiment. We also find a number of chemical trends within each molecular series which we can explain, but there are also some surprises, including some that are captured by the calculations and some that are not. Hydration Alchemical Free energy Molecular dynamics Liu, Shaui aut Cerutti, David S. aut Swope, William C. aut Rice, Julia E. aut Enthalten in Journal of computer aided molecular design Springer Netherlands, 1987 26(2011), 5 vom: 24. Dez., Seite 551-562 (DE-627)130644110 (DE-600)808166-9 (DE-576)018278221 0920-654X nnns volume:26 year:2011 number:5 day:24 month:12 pages:551-562 https://doi.org/10.1007/s10822-011-9528-8 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_OLC FID-PHARM FID-BIODIV SSG-OLC-MAT SSG-OLC-PHA SSG-OLC-DE-84 SSG-OPC-PHA GBV_ILN_20 GBV_ILN_70 GBV_ILN_2219 GBV_ILN_4012 AR 26 2011 5 24 12 551-562 |
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10.1007/s10822-011-9528-8 doi (DE-627)OLC2034738861 (DE-He213)s10822-011-9528-8-p DE-627 ger DE-627 rakwb eng 570 VZ 12 15,3 ssgn PHARM DE-84 fid BIODIV DE-30 fid Mobley, David L. verfasserin aut Alchemical prediction of hydration free energies for SAMPL 2011 Text txt rdacontent ohne Hilfsmittel zu benutzen n rdamedia Band nc rdacarrier © Springer Science+Business Media B.V. 2012 Abstract Hydration free energy calculations have become important tests of force fields. Alchemical free energy calculations based on molecular dynamics simulations provide a rigorous way to calculate these free energies for a particular force field, given sufficient sampling. Here, we report results of alchemical hydration free energy calculations for the set of small molecules comprising the 2011 Statistical Assessment of Modeling of Proteins and Ligands challenge. Our calculations are largely based on the Generalized Amber Force Field with several different charge models, and we achieved RMS errors in the 1.4–2.2 kcal/mol range depending on charge model, marginally higher than what we typically observed in previous studies (Mobley et al. in J Phys Chem B 111(9):2242–2254, 2007, J Chem Theory Comput 5(2):350–358, 2009, J Phys Chem B 115:1329–1332, 2011; Nicholls et al. in J Med Chem 51:769–779, 2008; Klimovich and Mobley in J Comput Aided Mol Design 24(4):307–316, 2010). The test set consists of ethane, biphenyl, and a dibenzyl dioxin, as well as a series of chlorinated derivatives of each. We found that, for this set, using high-quality partial charges from MP2/cc-PVTZ SCRF RESP fits provided marginally improved agreement with experiment over using AM1-BCC partial charges as we have more typically done, in keeping with our recent findings (Mobley et al. in J Phys Chem B 115:1329–1332, 2011). Switching to OPLS Lennard–Jones parameters with AM1-BCC charges also improves agreement with experiment. We also find a number of chemical trends within each molecular series which we can explain, but there are also some surprises, including some that are captured by the calculations and some that are not. Hydration Alchemical Free energy Molecular dynamics Liu, Shaui aut Cerutti, David S. aut Swope, William C. aut Rice, Julia E. aut Enthalten in Journal of computer aided molecular design Springer Netherlands, 1987 26(2011), 5 vom: 24. Dez., Seite 551-562 (DE-627)130644110 (DE-600)808166-9 (DE-576)018278221 0920-654X nnns volume:26 year:2011 number:5 day:24 month:12 pages:551-562 https://doi.org/10.1007/s10822-011-9528-8 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_OLC FID-PHARM FID-BIODIV SSG-OLC-MAT SSG-OLC-PHA SSG-OLC-DE-84 SSG-OPC-PHA GBV_ILN_20 GBV_ILN_70 GBV_ILN_2219 GBV_ILN_4012 AR 26 2011 5 24 12 551-562 |
allfieldsGer |
10.1007/s10822-011-9528-8 doi (DE-627)OLC2034738861 (DE-He213)s10822-011-9528-8-p DE-627 ger DE-627 rakwb eng 570 VZ 12 15,3 ssgn PHARM DE-84 fid BIODIV DE-30 fid Mobley, David L. verfasserin aut Alchemical prediction of hydration free energies for SAMPL 2011 Text txt rdacontent ohne Hilfsmittel zu benutzen n rdamedia Band nc rdacarrier © Springer Science+Business Media B.V. 2012 Abstract Hydration free energy calculations have become important tests of force fields. Alchemical free energy calculations based on molecular dynamics simulations provide a rigorous way to calculate these free energies for a particular force field, given sufficient sampling. Here, we report results of alchemical hydration free energy calculations for the set of small molecules comprising the 2011 Statistical Assessment of Modeling of Proteins and Ligands challenge. Our calculations are largely based on the Generalized Amber Force Field with several different charge models, and we achieved RMS errors in the 1.4–2.2 kcal/mol range depending on charge model, marginally higher than what we typically observed in previous studies (Mobley et al. in J Phys Chem B 111(9):2242–2254, 2007, J Chem Theory Comput 5(2):350–358, 2009, J Phys Chem B 115:1329–1332, 2011; Nicholls et al. in J Med Chem 51:769–779, 2008; Klimovich and Mobley in J Comput Aided Mol Design 24(4):307–316, 2010). The test set consists of ethane, biphenyl, and a dibenzyl dioxin, as well as a series of chlorinated derivatives of each. We found that, for this set, using high-quality partial charges from MP2/cc-PVTZ SCRF RESP fits provided marginally improved agreement with experiment over using AM1-BCC partial charges as we have more typically done, in keeping with our recent findings (Mobley et al. in J Phys Chem B 115:1329–1332, 2011). Switching to OPLS Lennard–Jones parameters with AM1-BCC charges also improves agreement with experiment. We also find a number of chemical trends within each molecular series which we can explain, but there are also some surprises, including some that are captured by the calculations and some that are not. Hydration Alchemical Free energy Molecular dynamics Liu, Shaui aut Cerutti, David S. aut Swope, William C. aut Rice, Julia E. aut Enthalten in Journal of computer aided molecular design Springer Netherlands, 1987 26(2011), 5 vom: 24. Dez., Seite 551-562 (DE-627)130644110 (DE-600)808166-9 (DE-576)018278221 0920-654X nnns volume:26 year:2011 number:5 day:24 month:12 pages:551-562 https://doi.org/10.1007/s10822-011-9528-8 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_OLC FID-PHARM FID-BIODIV SSG-OLC-MAT SSG-OLC-PHA SSG-OLC-DE-84 SSG-OPC-PHA GBV_ILN_20 GBV_ILN_70 GBV_ILN_2219 GBV_ILN_4012 AR 26 2011 5 24 12 551-562 |
allfieldsSound |
10.1007/s10822-011-9528-8 doi (DE-627)OLC2034738861 (DE-He213)s10822-011-9528-8-p DE-627 ger DE-627 rakwb eng 570 VZ 12 15,3 ssgn PHARM DE-84 fid BIODIV DE-30 fid Mobley, David L. verfasserin aut Alchemical prediction of hydration free energies for SAMPL 2011 Text txt rdacontent ohne Hilfsmittel zu benutzen n rdamedia Band nc rdacarrier © Springer Science+Business Media B.V. 2012 Abstract Hydration free energy calculations have become important tests of force fields. Alchemical free energy calculations based on molecular dynamics simulations provide a rigorous way to calculate these free energies for a particular force field, given sufficient sampling. Here, we report results of alchemical hydration free energy calculations for the set of small molecules comprising the 2011 Statistical Assessment of Modeling of Proteins and Ligands challenge. Our calculations are largely based on the Generalized Amber Force Field with several different charge models, and we achieved RMS errors in the 1.4–2.2 kcal/mol range depending on charge model, marginally higher than what we typically observed in previous studies (Mobley et al. in J Phys Chem B 111(9):2242–2254, 2007, J Chem Theory Comput 5(2):350–358, 2009, J Phys Chem B 115:1329–1332, 2011; Nicholls et al. in J Med Chem 51:769–779, 2008; Klimovich and Mobley in J Comput Aided Mol Design 24(4):307–316, 2010). The test set consists of ethane, biphenyl, and a dibenzyl dioxin, as well as a series of chlorinated derivatives of each. We found that, for this set, using high-quality partial charges from MP2/cc-PVTZ SCRF RESP fits provided marginally improved agreement with experiment over using AM1-BCC partial charges as we have more typically done, in keeping with our recent findings (Mobley et al. in J Phys Chem B 115:1329–1332, 2011). Switching to OPLS Lennard–Jones parameters with AM1-BCC charges also improves agreement with experiment. We also find a number of chemical trends within each molecular series which we can explain, but there are also some surprises, including some that are captured by the calculations and some that are not. Hydration Alchemical Free energy Molecular dynamics Liu, Shaui aut Cerutti, David S. aut Swope, William C. aut Rice, Julia E. aut Enthalten in Journal of computer aided molecular design Springer Netherlands, 1987 26(2011), 5 vom: 24. Dez., Seite 551-562 (DE-627)130644110 (DE-600)808166-9 (DE-576)018278221 0920-654X nnns volume:26 year:2011 number:5 day:24 month:12 pages:551-562 https://doi.org/10.1007/s10822-011-9528-8 lizenzpflichtig Volltext GBV_USEFLAG_A SYSFLAG_A GBV_OLC FID-PHARM FID-BIODIV SSG-OLC-MAT SSG-OLC-PHA SSG-OLC-DE-84 SSG-OPC-PHA GBV_ILN_20 GBV_ILN_70 GBV_ILN_2219 GBV_ILN_4012 AR 26 2011 5 24 12 551-562 |
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alchemical prediction of hydration free energies for sampl |
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Alchemical prediction of hydration free energies for SAMPL |
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Abstract Hydration free energy calculations have become important tests of force fields. Alchemical free energy calculations based on molecular dynamics simulations provide a rigorous way to calculate these free energies for a particular force field, given sufficient sampling. Here, we report results of alchemical hydration free energy calculations for the set of small molecules comprising the 2011 Statistical Assessment of Modeling of Proteins and Ligands challenge. Our calculations are largely based on the Generalized Amber Force Field with several different charge models, and we achieved RMS errors in the 1.4–2.2 kcal/mol range depending on charge model, marginally higher than what we typically observed in previous studies (Mobley et al. in J Phys Chem B 111(9):2242–2254, 2007, J Chem Theory Comput 5(2):350–358, 2009, J Phys Chem B 115:1329–1332, 2011; Nicholls et al. in J Med Chem 51:769–779, 2008; Klimovich and Mobley in J Comput Aided Mol Design 24(4):307–316, 2010). The test set consists of ethane, biphenyl, and a dibenzyl dioxin, as well as a series of chlorinated derivatives of each. We found that, for this set, using high-quality partial charges from MP2/cc-PVTZ SCRF RESP fits provided marginally improved agreement with experiment over using AM1-BCC partial charges as we have more typically done, in keeping with our recent findings (Mobley et al. in J Phys Chem B 115:1329–1332, 2011). Switching to OPLS Lennard–Jones parameters with AM1-BCC charges also improves agreement with experiment. We also find a number of chemical trends within each molecular series which we can explain, but there are also some surprises, including some that are captured by the calculations and some that are not. © Springer Science+Business Media B.V. 2012 |
abstractGer |
Abstract Hydration free energy calculations have become important tests of force fields. Alchemical free energy calculations based on molecular dynamics simulations provide a rigorous way to calculate these free energies for a particular force field, given sufficient sampling. Here, we report results of alchemical hydration free energy calculations for the set of small molecules comprising the 2011 Statistical Assessment of Modeling of Proteins and Ligands challenge. Our calculations are largely based on the Generalized Amber Force Field with several different charge models, and we achieved RMS errors in the 1.4–2.2 kcal/mol range depending on charge model, marginally higher than what we typically observed in previous studies (Mobley et al. in J Phys Chem B 111(9):2242–2254, 2007, J Chem Theory Comput 5(2):350–358, 2009, J Phys Chem B 115:1329–1332, 2011; Nicholls et al. in J Med Chem 51:769–779, 2008; Klimovich and Mobley in J Comput Aided Mol Design 24(4):307–316, 2010). The test set consists of ethane, biphenyl, and a dibenzyl dioxin, as well as a series of chlorinated derivatives of each. We found that, for this set, using high-quality partial charges from MP2/cc-PVTZ SCRF RESP fits provided marginally improved agreement with experiment over using AM1-BCC partial charges as we have more typically done, in keeping with our recent findings (Mobley et al. in J Phys Chem B 115:1329–1332, 2011). Switching to OPLS Lennard–Jones parameters with AM1-BCC charges also improves agreement with experiment. We also find a number of chemical trends within each molecular series which we can explain, but there are also some surprises, including some that are captured by the calculations and some that are not. © Springer Science+Business Media B.V. 2012 |
abstract_unstemmed |
Abstract Hydration free energy calculations have become important tests of force fields. Alchemical free energy calculations based on molecular dynamics simulations provide a rigorous way to calculate these free energies for a particular force field, given sufficient sampling. Here, we report results of alchemical hydration free energy calculations for the set of small molecules comprising the 2011 Statistical Assessment of Modeling of Proteins and Ligands challenge. Our calculations are largely based on the Generalized Amber Force Field with several different charge models, and we achieved RMS errors in the 1.4–2.2 kcal/mol range depending on charge model, marginally higher than what we typically observed in previous studies (Mobley et al. in J Phys Chem B 111(9):2242–2254, 2007, J Chem Theory Comput 5(2):350–358, 2009, J Phys Chem B 115:1329–1332, 2011; Nicholls et al. in J Med Chem 51:769–779, 2008; Klimovich and Mobley in J Comput Aided Mol Design 24(4):307–316, 2010). The test set consists of ethane, biphenyl, and a dibenzyl dioxin, as well as a series of chlorinated derivatives of each. We found that, for this set, using high-quality partial charges from MP2/cc-PVTZ SCRF RESP fits provided marginally improved agreement with experiment over using AM1-BCC partial charges as we have more typically done, in keeping with our recent findings (Mobley et al. in J Phys Chem B 115:1329–1332, 2011). Switching to OPLS Lennard–Jones parameters with AM1-BCC charges also improves agreement with experiment. We also find a number of chemical trends within each molecular series which we can explain, but there are also some surprises, including some that are captured by the calculations and some that are not. © Springer Science+Business Media B.V. 2012 |
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