Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field

被引:12
作者
D'Amore, Lorenzo [1 ]
Hahn, David F. [2 ]
Dotson, David L. [3 ]
Horton, Joshua T. [4 ]
Anwar, Jamshed [5 ]
Craig, Ian [6 ]
Fox, Thomas [7 ]
Gobbi, Alberto [8 ]
Lakkaraju, Sirish Kaushik [9 ]
Lucas, Xavier [10 ,11 ]
Meier, Katharina [12 ]
Mobley, David L. [13 ]
Narayanan, Arjun [14 ]
Schindler, Christina E. M. [15 ]
Swope, William C. [8 ]
in't Veld, Pieter J. [6 ]
Wagner, Jeffrey [16 ,17 ]
Xue, Bai [18 ]
Tresadern, Gary [2 ]
机构
[1] Janssen R&D, Computat Chem, Toledo 45007, Spain
[2] Janssen R&D, Computat Chem, B-2340 Beerse, Belgium
[3] Open Mol Software Fdn, Open Force Field Initiat, Davis, CA 95616 USA
[4] Newcastle Univ, Sch Nat & Environm Sci, NE1 7RU, Newcastle Upon Tyne, England
[5] Univ Lancaster, Dept Chem, Lancaster LA1 4YW, England
[6] BASF SE, Mol Modeling & Drug Discovery, D-67056 Ludwigshafen, Germany
[7] Boehringer Ingelheim Pharm GmbH & Co KG, Med Chem, D-88397 Biberach, Germany
[8] Genentech Inc, San Francisco, CA 94080 USA
[9] Bristol Myers Squibb, Small Mol Drug Discovery, Princeton, NJ 08540 USA
[10] F Hoffmann La Roche Ltd, Roche Innovat Ctr Basel, Roche Pharm Res & Early Dev, Therapeut Modal, S-4070 Basel, Switzerland
[11] Monte Rosa Therapeut AG, Klybeckstrasse 191,WKL-136-3, CH-4057 Basel, Switzerland
[12] Bayer AG, Computat Life Sci Technol Funct, Crop Sci, R&D, D-40789 Monheim, Germany
[13] Univ Calif Irvine, Dept Pharmaceut Sci & Chem, Irvine, CA 92617 USA
[14] Vertex Pharmaceut, Data & Computat Sci, Boston, MA 02210 USA
[15] Merck KGaA, Computat Chem & Biol, D-64293 Darmstadt, Germany
[16] Open Mol Software Fdn, Open Force Field Initiat, Davis, CA 95616 USA
[17] Univ Calif Irvine, Chem Dept, Irvine, CA 92617 USA
[18] XtalPi Inc, Floor 3,Int Biomed Innovat Pk 2, Shenzhen 518040, Guangdong, Peoples R China
关键词
NUCLEIC-ACIDS; CONFORMATIONAL ENERGIES; EFFICIENT GENERATION; AM1-BCC MODEL; DYNAMICS; OPTIMIZATION; SIMULATION; PREDICTION; PEPTIDES; ACCURACY;
D O I
10.1021/acs.jcim.2c01185
中图分类号
R914 [药物化学];
学科分类号
100701 ;
摘要
Force fields form the basis for classical molecular simulations, and their accuracy is crucial for the quality of; for instance, protein-ligand binding simulations in drug discovery. The huge diversity of small-molecule chemistry makes it a challenge to build and parameterize a suitable force field. The Open Force Field Initiative is a combined industry and academic consortium developing a state-of-the-art small-molecule force field. In this report, industry members of the consortium worked together to objectively evaluate the performance of the force fields (referred to here as OpenFF) produced by the initiative on a combined public and proprietary dataset of 19,653 relevant molecules selected from their internal research and compound collections. This evaluation was important because it was completely blind; at most partners, none of the molecules or data were used in force field development or testing prior to this work. We compare the Open Force Field "Sage" version 2.0.0 and "Parsley" version 1.3.0 with GAFF-2.11-AM1BCC, OPLS4, and SMIRNOFF99Frosst. We analyzed force-field-optimized geometries and conformer energies compared to reference quantum mechanical data. We show that OPLS4 performs best, and the latest Open Force Field release shows a dear improvement compared to its predecessors. The performance of established force fields such as GAFF-2.11 was generally worse. While OpenFF researchers were involved in building the benchmarking infrastructure used in this work, benchmarking was done entirely in-house within industrial organizations and the resulting assessment is reported here. This work assesses the force field performance using separate benchmarking steps, external datasets, and involving external research groups. This effort may also be unique in terms of the number of different industrial partners involved, with 10 different companies participating in the benchmark efforts.
引用
收藏
页码:6094 / 6104
页数:11
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