[1] Newcastle Univ, Sch Nat & Environm Sci, Newcastle Upon Tyne NE1 7RU, Tyne & Wear, England
[2] Boothroyd Sci Consulting Ltd, London WC2H 9JQ, England
[3] Univ Calif Irvine, Dept Pharmaceut Sci, Irvine, CA 92697 USA
[4] Univ Calif Irvine, Dept Chem, Irvine, CA 92697 USA
来源:
DIGITAL DISCOVERY
|
2023年
/
2卷
/
04期
基金:
英国工程与自然科学研究理事会;
英国医学研究理事会;
美国国家卫生研究院;
关键词:
OPEN FORCE-FIELD;
RATIONAL DESIGN;
DIPOLE-MOMENT;
FREE-ENERGIES;
EFFICIENT;
PARAMETERS;
ACCURATE;
MODELS;
D O I:
10.1039/d3dd00070b
中图分类号:
O6 [化学];
学科分类号:
0703 ;
摘要:
The Lennard-Jones potential is the most widely-used function for the description of non-bonded interactions in transferable force fields for the condensed phase. This is not because it has an optimal functional form, but rather it is a legacy resulting from when computational expense was a major consideration and this potential was particularly convenient numerically. At present, it persists because the effort that would be required to re-write molecular modelling software and train new force fields has, until now, been prohibitive. Here, we present Smirnoff-plugins as a flexible framework to extend the Open Force Field software stack to allow custom force field functional forms. We deploy Smirnoff-plugins with the automated Open Force Field infrastructure to train a transferable, small molecule force field based on the recently-proposed double exponential functional form, on over 1000 experimental condensed phase properties. Extensive testing of the resulting force field shows improvements in transfer free energies, with acceptable conformational energetics, run times and convergence properties compared to state-of-the-art Lennard-Jones based force fields. The Open Force Field software stack is employed to automatically train a transferable, small molecule force field, based on the double exponential functional form, on over 1000 experimental condensed phase physical properties.
机构:
Boothroyd Sci Consulting Ltd, London WC2H 9JQ, EnglandBoothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Boothroyd, Simon
Behara, Pavan Kumar
论文数: 0引用数: 0
h-index: 0
机构:
Univ Calif Irvine, Dept Pharmaceut Sci, Irvine, CA 92697 USABoothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Behara, Pavan Kumar
Madin, Owen C.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado Boulder, Chem & Biol Engn Dept, Boulder, CO 80309 USABoothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Madin, Owen C.
Hahn, David F.
论文数: 0引用数: 0
h-index: 0
机构:
Janssen Res & Dev, Computat Chem, B-2340 Beerse, BelgiumBoothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Hahn, David F.
Jang, Hyesu
论文数: 0引用数: 0
h-index: 0
机构:
Univ Calif Davis, Chem Dept, Davis, CA 95616 USA
OpenEye Sci Software, Santa Fe, NM 87508 USABoothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Jang, Hyesu
Gapsys, Vytautas
论文数: 0引用数: 0
h-index: 0
机构:
Janssen Res & Dev, Computat Chem, B-2340 Beerse, Belgium
Max Planck Inst Multidisciplinary Sci, Dept Theoret & Computat Biophys, Computat Biomol Dynam Grp, D-37077 Gottingen, GermanyBoothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Gapsys, Vytautas
Wagner, Jeffrey R.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Calif Irvine, Dept Pharmaceut Sci, Irvine, CA 92697 USA
Open Mol Software Fdn, Open Force Field Initiat, Davis, CA 95616 USABoothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Wagner, Jeffrey R.
Horton, Joshua T.
论文数: 0引用数: 0
h-index: 0
机构:
Newcastle Univ, Sch Nat & Environm Sci, Newcastle Upon Tyne NE1 7RU, EnglandBoothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Horton, Joshua T.
Dotson, David L.
论文数: 0引用数: 0
h-index: 0
机构:
Open Mol Software Fdn, Open Force Field Initiat, Davis, CA 95616 USA
Datryllic LLC, Phoenix, AZ 85003 USABoothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Dotson, David L.
Thompson, Matthew W.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado Boulder, Chem & Biol Engn Dept, Boulder, CO 80309 USA
Open Mol Software Fdn, Open Force Field Initiat, Davis, CA 95616 USABoothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Thompson, Matthew W.
Maat, Jessica
论文数: 0引用数: 0
h-index: 0
机构:Boothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Maat, Jessica
Gokey, Trevor
论文数: 0引用数: 0
h-index: 0
机构:Boothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Gokey, Trevor
Wang, Lee-Ping
论文数: 0引用数: 0
h-index: 0
机构:
Univ Calif Davis, Chem Dept, Davis, CA 95616 USABoothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Wang, Lee-Ping
Cole, Daniel J.
论文数: 0引用数: 0
h-index: 0
机构:
Newcastle Univ, Sch Nat & Environm Sci, Newcastle Upon Tyne NE1 7RU, EnglandBoothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Cole, Daniel J.
Gilson, Michael K.
论文数: 0引用数: 0
h-index: 0
机构:Boothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Gilson, Michael K.
Chodera, John D.
论文数: 0引用数: 0
h-index: 0
机构:Boothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Chodera, John D.
Bayly, Christopher I.
论文数: 0引用数: 0
h-index: 0
机构:
OpenEye Sci Software, Santa Fe, NM 87508 USABoothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Bayly, Christopher I.
Shirts, Michael R.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado Boulder, Chem & Biol Engn Dept, Boulder, CO 80309 USABoothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Shirts, Michael R.
Mobley, David L.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Calif Irvine, Dept Pharmaceut Sci, Irvine, CA 92697 USABoothroyd Sci Consulting Ltd, London WC2H 9JQ, England
机构:
Univ Calif Davis, Dept Chem, Davis, CA 95616 USAMem Sloan Kettering Canc Ctr, Computat & Syst Biol Program, Sloan Kettering Inst, New York, NY 10065 USA
Wang, Lee-Ping
Mobley, David L.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Calif Davis, Dept Chem, Davis, CA 95616 USA
Univ Calif Irvine, Dept Pharmaceut Sci, Irvine, CA 92617 USAMem Sloan Kettering Canc Ctr, Computat & Syst Biol Program, Sloan Kettering Inst, New York, NY 10065 USA
Mobley, David L.
Chodera, John D.
论文数: 0引用数: 0
h-index: 0
机构:
Mem Sloan Kettering Canc Ctr, Computat & Syst Biol Program, Sloan Kettering Inst, New York, NY 10065 USAMem Sloan Kettering Canc Ctr, Computat & Syst Biol Program, Sloan Kettering Inst, New York, NY 10065 USA
Chodera, John D.
Shirts, Michael R.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Dept Chem & Biol Engn, Boulder, CO 80309 USAMem Sloan Kettering Canc Ctr, Computat & Syst Biol Program, Sloan Kettering Inst, New York, NY 10065 USA
机构:
Genentech Inc, San Francisco, CA 94080 USAJanssen R&D, Computat Chem, Toledo 45007, Spain
Swope, William C.
in't Veld, Pieter J.
论文数: 0引用数: 0
h-index: 0
机构:
BASF SE, Mol Modeling & Drug Discovery, D-67056 Ludwigshafen, GermanyJanssen R&D, Computat Chem, Toledo 45007, Spain
in't Veld, Pieter J.
Wagner, Jeffrey
论文数: 0引用数: 0
h-index: 0
机构:
Open Mol Software Fdn, Open Force Field Initiat, Davis, CA 95616 USA
Univ Calif Irvine, Chem Dept, Irvine, CA 92617 USAJanssen R&D, Computat Chem, Toledo 45007, Spain
机构:
DE Shaw Res, New York, NY 10036 USADE Shaw Res, New York, NY 10036 USA
Donchev, Alexander G.
Taube, Andrew G.
论文数: 0引用数: 0
h-index: 0
机构:
DE Shaw Res, New York, NY 10036 USADE Shaw Res, New York, NY 10036 USA
Taube, Andrew G.
Decolvenaere, Elizabeth
论文数: 0引用数: 0
h-index: 0
机构:
DE Shaw Res, New York, NY 10036 USADE Shaw Res, New York, NY 10036 USA
Decolvenaere, Elizabeth
Hargus, Cory
论文数: 0引用数: 0
h-index: 0
机构:
DE Shaw Res, New York, NY 10036 USADE Shaw Res, New York, NY 10036 USA
Hargus, Cory
McGibbon, Robert T.
论文数: 0引用数: 0
h-index: 0
机构:
DE Shaw Res, New York, NY 10036 USADE Shaw Res, New York, NY 10036 USA
McGibbon, Robert T.
Law, Ka-Hei
论文数: 0引用数: 0
h-index: 0
机构:
DE Shaw Res, New York, NY 10036 USADE Shaw Res, New York, NY 10036 USA
Law, Ka-Hei
Gregersen, Brent A.
论文数: 0引用数: 0
h-index: 0
机构:
DE Shaw Res, New York, NY 10036 USADE Shaw Res, New York, NY 10036 USA
Gregersen, Brent A.
Li, Je-Luen
论文数: 0引用数: 0
h-index: 0
机构:
DE Shaw Res, New York, NY 10036 USADE Shaw Res, New York, NY 10036 USA
Li, Je-Luen
Palmo, Kim
论文数: 0引用数: 0
h-index: 0
机构:
DE Shaw Res, New York, NY 10036 USADE Shaw Res, New York, NY 10036 USA
Palmo, Kim
Siva, Karthik
论文数: 0引用数: 0
h-index: 0
机构:
DE Shaw Res, New York, NY 10036 USADE Shaw Res, New York, NY 10036 USA
Siva, Karthik
Bergdorf, Michael
论文数: 0引用数: 0
h-index: 0
机构:
DE Shaw Res, New York, NY 10036 USADE Shaw Res, New York, NY 10036 USA
Bergdorf, Michael
Klepeis, John L.
论文数: 0引用数: 0
h-index: 0
机构:
DE Shaw Res, New York, NY 10036 USADE Shaw Res, New York, NY 10036 USA
Klepeis, John L.
Shaw, David E.
论文数: 0引用数: 0
h-index: 0
机构:
DE Shaw Res, New York, NY 10036 USA
Columbia Univ, Dept Biochem & Mol Biophys, 630 W 168th St, New York, NY 10032 USADE Shaw Res, New York, NY 10036 USA
机构:
Boothroyd Sci Consulting Ltd, London WC2H 9JQ, EnglandBoothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Boothroyd, Simon
Behara, Pavan Kumar
论文数: 0引用数: 0
h-index: 0
机构:
Univ Calif Irvine, Dept Pharmaceut Sci, Irvine, CA 92697 USABoothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Behara, Pavan Kumar
Madin, Owen C.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado Boulder, Chem & Biol Engn Dept, Boulder, CO 80309 USABoothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Madin, Owen C.
Hahn, David F.
论文数: 0引用数: 0
h-index: 0
机构:
Janssen Res & Dev, Computat Chem, B-2340 Beerse, BelgiumBoothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Hahn, David F.
Jang, Hyesu
论文数: 0引用数: 0
h-index: 0
机构:
Univ Calif Davis, Chem Dept, Davis, CA 95616 USA
OpenEye Sci Software, Santa Fe, NM 87508 USABoothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Jang, Hyesu
Gapsys, Vytautas
论文数: 0引用数: 0
h-index: 0
机构:
Janssen Res & Dev, Computat Chem, B-2340 Beerse, Belgium
Max Planck Inst Multidisciplinary Sci, Dept Theoret & Computat Biophys, Computat Biomol Dynam Grp, D-37077 Gottingen, GermanyBoothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Gapsys, Vytautas
Wagner, Jeffrey R.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Calif Irvine, Dept Pharmaceut Sci, Irvine, CA 92697 USA
Open Mol Software Fdn, Open Force Field Initiat, Davis, CA 95616 USABoothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Wagner, Jeffrey R.
Horton, Joshua T.
论文数: 0引用数: 0
h-index: 0
机构:
Newcastle Univ, Sch Nat & Environm Sci, Newcastle Upon Tyne NE1 7RU, EnglandBoothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Horton, Joshua T.
Dotson, David L.
论文数: 0引用数: 0
h-index: 0
机构:
Open Mol Software Fdn, Open Force Field Initiat, Davis, CA 95616 USA
Datryllic LLC, Phoenix, AZ 85003 USABoothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Dotson, David L.
Thompson, Matthew W.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado Boulder, Chem & Biol Engn Dept, Boulder, CO 80309 USA
Open Mol Software Fdn, Open Force Field Initiat, Davis, CA 95616 USABoothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Thompson, Matthew W.
Maat, Jessica
论文数: 0引用数: 0
h-index: 0
机构:Boothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Maat, Jessica
Gokey, Trevor
论文数: 0引用数: 0
h-index: 0
机构:Boothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Gokey, Trevor
Wang, Lee-Ping
论文数: 0引用数: 0
h-index: 0
机构:
Univ Calif Davis, Chem Dept, Davis, CA 95616 USABoothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Wang, Lee-Ping
Cole, Daniel J.
论文数: 0引用数: 0
h-index: 0
机构:
Newcastle Univ, Sch Nat & Environm Sci, Newcastle Upon Tyne NE1 7RU, EnglandBoothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Cole, Daniel J.
Gilson, Michael K.
论文数: 0引用数: 0
h-index: 0
机构:Boothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Gilson, Michael K.
Chodera, John D.
论文数: 0引用数: 0
h-index: 0
机构:Boothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Chodera, John D.
Bayly, Christopher I.
论文数: 0引用数: 0
h-index: 0
机构:
OpenEye Sci Software, Santa Fe, NM 87508 USABoothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Bayly, Christopher I.
Shirts, Michael R.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado Boulder, Chem & Biol Engn Dept, Boulder, CO 80309 USABoothroyd Sci Consulting Ltd, London WC2H 9JQ, England
Shirts, Michael R.
Mobley, David L.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Calif Irvine, Dept Pharmaceut Sci, Irvine, CA 92697 USABoothroyd Sci Consulting Ltd, London WC2H 9JQ, England
机构:
Univ Calif Davis, Dept Chem, Davis, CA 95616 USAMem Sloan Kettering Canc Ctr, Computat & Syst Biol Program, Sloan Kettering Inst, New York, NY 10065 USA
Wang, Lee-Ping
Mobley, David L.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Calif Davis, Dept Chem, Davis, CA 95616 USA
Univ Calif Irvine, Dept Pharmaceut Sci, Irvine, CA 92617 USAMem Sloan Kettering Canc Ctr, Computat & Syst Biol Program, Sloan Kettering Inst, New York, NY 10065 USA
Mobley, David L.
Chodera, John D.
论文数: 0引用数: 0
h-index: 0
机构:
Mem Sloan Kettering Canc Ctr, Computat & Syst Biol Program, Sloan Kettering Inst, New York, NY 10065 USAMem Sloan Kettering Canc Ctr, Computat & Syst Biol Program, Sloan Kettering Inst, New York, NY 10065 USA
Chodera, John D.
Shirts, Michael R.
论文数: 0引用数: 0
h-index: 0
机构:
Univ Colorado, Dept Chem & Biol Engn, Boulder, CO 80309 USAMem Sloan Kettering Canc Ctr, Computat & Syst Biol Program, Sloan Kettering Inst, New York, NY 10065 USA
机构:
Genentech Inc, San Francisco, CA 94080 USAJanssen R&D, Computat Chem, Toledo 45007, Spain
Swope, William C.
in't Veld, Pieter J.
论文数: 0引用数: 0
h-index: 0
机构:
BASF SE, Mol Modeling & Drug Discovery, D-67056 Ludwigshafen, GermanyJanssen R&D, Computat Chem, Toledo 45007, Spain
in't Veld, Pieter J.
Wagner, Jeffrey
论文数: 0引用数: 0
h-index: 0
机构:
Open Mol Software Fdn, Open Force Field Initiat, Davis, CA 95616 USA
Univ Calif Irvine, Chem Dept, Irvine, CA 92617 USAJanssen R&D, Computat Chem, Toledo 45007, Spain
机构:
DE Shaw Res, New York, NY 10036 USADE Shaw Res, New York, NY 10036 USA
Donchev, Alexander G.
Taube, Andrew G.
论文数: 0引用数: 0
h-index: 0
机构:
DE Shaw Res, New York, NY 10036 USADE Shaw Res, New York, NY 10036 USA
Taube, Andrew G.
Decolvenaere, Elizabeth
论文数: 0引用数: 0
h-index: 0
机构:
DE Shaw Res, New York, NY 10036 USADE Shaw Res, New York, NY 10036 USA
Decolvenaere, Elizabeth
Hargus, Cory
论文数: 0引用数: 0
h-index: 0
机构:
DE Shaw Res, New York, NY 10036 USADE Shaw Res, New York, NY 10036 USA
Hargus, Cory
McGibbon, Robert T.
论文数: 0引用数: 0
h-index: 0
机构:
DE Shaw Res, New York, NY 10036 USADE Shaw Res, New York, NY 10036 USA
McGibbon, Robert T.
Law, Ka-Hei
论文数: 0引用数: 0
h-index: 0
机构:
DE Shaw Res, New York, NY 10036 USADE Shaw Res, New York, NY 10036 USA
Law, Ka-Hei
Gregersen, Brent A.
论文数: 0引用数: 0
h-index: 0
机构:
DE Shaw Res, New York, NY 10036 USADE Shaw Res, New York, NY 10036 USA
Gregersen, Brent A.
Li, Je-Luen
论文数: 0引用数: 0
h-index: 0
机构:
DE Shaw Res, New York, NY 10036 USADE Shaw Res, New York, NY 10036 USA
Li, Je-Luen
Palmo, Kim
论文数: 0引用数: 0
h-index: 0
机构:
DE Shaw Res, New York, NY 10036 USADE Shaw Res, New York, NY 10036 USA
Palmo, Kim
Siva, Karthik
论文数: 0引用数: 0
h-index: 0
机构:
DE Shaw Res, New York, NY 10036 USADE Shaw Res, New York, NY 10036 USA
Siva, Karthik
Bergdorf, Michael
论文数: 0引用数: 0
h-index: 0
机构:
DE Shaw Res, New York, NY 10036 USADE Shaw Res, New York, NY 10036 USA
Bergdorf, Michael
Klepeis, John L.
论文数: 0引用数: 0
h-index: 0
机构:
DE Shaw Res, New York, NY 10036 USADE Shaw Res, New York, NY 10036 USA
Klepeis, John L.
Shaw, David E.
论文数: 0引用数: 0
h-index: 0
机构:
DE Shaw Res, New York, NY 10036 USA
Columbia Univ, Dept Biochem & Mol Biophys, 630 W 168th St, New York, NY 10032 USADE Shaw Res, New York, NY 10036 USA