225 related articles for article (PubMed ID: 34551262)
1. Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field.
Qiu Y; Smith DGA; Boothroyd S; Jang H; Hahn DF; Wagner J; Bannan CC; Gokey T; Lim VT; Stern CD; Rizzi A; Tjanaka B; Tresadern G; Lucas X; Shirts MR; Gilson MK; Chodera JD; Bayly CI; Mobley DL; Wang LP
J Chem Theory Comput; 2021 Oct; 17(10):6262-6280. PubMed ID: 34551262
[TBL] [Abstract][Full Text] [Related]
2. Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field.
Boothroyd S; Behara PK; Madin OC; Hahn DF; Jang H; Gapsys V; Wagner JR; Horton JT; Dotson DL; Thompson MW; Maat J; Gokey T; Wang LP; Cole DJ; Gilson MK; Chodera JD; Bayly CI; Shirts MR; Mobley DL
J Chem Theory Comput; 2023 Jun; 19(11):3251-3275. PubMed ID: 37167319
[TBL] [Abstract][Full Text] [Related]
3. Escaping Atom Types in Force Fields Using Direct Chemical Perception.
Mobley DL; Bannan CC; Rizzi A; Bayly CI; Chodera JD; Lim VT; Lim NM; Beauchamp KA; Slochower DR; Shirts MR; Gilson MK; Eastman PK
J Chem Theory Comput; 2018 Nov; 14(11):6076-6092. PubMed ID: 30351006
[TBL] [Abstract][Full Text] [Related]
4. Collaborative Assessment of Molecular Geometries and Energies from the Open Force Field.
D'Amore L; Hahn DF; Dotson DL; Horton JT; Anwar J; Craig I; Fox T; Gobbi A; Lakkaraju SK; Lucas X; Meier K; Mobley DL; Narayanan A; Schindler CEM; Swope WC; In 't Veld PJ; Wagner J; Xue B; Tresadern G
J Chem Inf Model; 2022 Dec; 62(23):6094-6104. PubMed ID: 36433835
[TBL] [Abstract][Full Text] [Related]
5. Benchmark assessment of molecular geometries and energies from small molecule force fields.
Lim VT; Hahn DF; Tresadern G; Bayly CI; Mobley DL
F1000Res; 2020; 9():. PubMed ID: 33604023
[No Abstract] [Full Text] [Related]
6. End-to-end differentiable construction of molecular mechanics force fields.
Wang Y; Fass J; Kaminow B; Herr JE; Rufa D; Zhang I; Pulido I; Henry M; Bruce Macdonald HE; Takaba K; Chodera JD
Chem Sci; 2022 Oct; 13(41):12016-12033. PubMed ID: 36349096
[TBL] [Abstract][Full Text] [Related]
7. Open Force Field Evaluator: An Automated, Efficient, and Scalable Framework for the Estimation of Physical Properties from Molecular Simulation.
Boothroyd S; Wang LP; Mobley DL; Chodera JD; Shirts MR
J Chem Theory Comput; 2022 Jun; 18(6):3566-3576. PubMed ID: 35507313
[TBL] [Abstract][Full Text] [Related]
8. Open Force Field BespokeFit: Automating Bespoke Torsion Parametrization at Scale.
Horton JT; Boothroyd S; Wagner J; Mitchell JA; Gokey T; Dotson DL; Behara PK; Ramaswamy VK; Mackey M; Chodera JD; Anwar J; Mobley DL; Cole DJ
J Chem Inf Model; 2022 Nov; 62(22):5622-5633. PubMed ID: 36351167
[TBL] [Abstract][Full Text] [Related]
9. Modification and optimization of the united-residue (UNRES) potential energy function for canonical simulations. I. Temperature dependence of the effective energy function and tests of the optimization method with single training proteins.
Liwo A; Khalili M; Czaplewski C; Kalinowski S; Ołdziej S; Wachucik K; Scheraga HA
J Phys Chem B; 2007 Jan; 111(1):260-85. PubMed ID: 17201450
[TBL] [Abstract][Full Text] [Related]
10. A transferable double exponential potential for condensed phase simulations of small molecules.
Horton JT; Boothroyd S; Behara PK; Mobley DL; Cole DJ
Digit Discov; 2023 Aug; 2(4):1178-1187. PubMed ID: 38013814
[TBL] [Abstract][Full Text] [Related]
11. Current State of Open Source Force Fields in Protein-Ligand Binding Affinity Predictions.
Hahn DF; Gapsys V; de Groot BL; Mobley DL; Tresadern G
J Chem Inf Model; 2024 Jul; 64(13):5063-5076. PubMed ID: 38895959
[TBL] [Abstract][Full Text] [Related]
12. Derivation of class II force fields. VIII. Derivation of a general quantum mechanical force field for organic compounds.
Ewig CS; Berry R; Dinur U; Hill JR; Hwang MJ; Li H; Liang C; Maple J; Peng Z; Stockfisch TP; Thacher TS; Yan L; Ni X; Hagler AT
J Comput Chem; 2001 Nov; 22(15):1782-1800. PubMed ID: 12116411
[TBL] [Abstract][Full Text] [Related]
13. Benchmarking Force Field and the ANI Neural Network Potentials for the Torsional Potential Energy Surface of Biaryl Drug Fragments.
Lahey SJ; Thien Phuc TN; Rowley CN
J Chem Inf Model; 2020 Dec; 60(12):6258-6268. PubMed ID: 33263401
[TBL] [Abstract][Full Text] [Related]
14. Tree Parzen estimator for global geometry optimization: A benchmark and database of experimental gas-phase structures of organic molecules.
Andreadi N; Zankov D; Karpov K; Mitrofanov A
J Comput Chem; 2022 Aug; 43(21):1434-1441. PubMed ID: 35678223
[TBL] [Abstract][Full Text] [Related]
15. Paramfit: automated optimization of force field parameters for molecular dynamics simulations.
Betz RM; Walker RC
J Comput Chem; 2015 Jan; 36(2):79-87. PubMed ID: 25413259
[TBL] [Abstract][Full Text] [Related]
16. Global Optimization of the Lennard-Jones Parameters for the Drude Polarizable Force Field.
Rupakheti CR; MacKerell AD; Roux B
J Chem Theory Comput; 2021 Nov; 17(11):7085-7095. PubMed ID: 34609863
[TBL] [Abstract][Full Text] [Related]
17. QUBEKit: Automating the Derivation of Force Field Parameters from Quantum Mechanics.
Horton JT; Allen AEA; Dodda LS; Cole DJ
J Chem Inf Model; 2019 Apr; 59(4):1366-1381. PubMed ID: 30742438
[TBL] [Abstract][Full Text] [Related]
18. Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics.
Hagler AT
J Comput Aided Mol Des; 2019 Feb; 33(2):205-264. PubMed ID: 30506159
[TBL] [Abstract][Full Text] [Related]
19. Automated conformational energy fitting for force-field development.
Guvench O; MacKerell AD
J Mol Model; 2008 Aug; 14(8):667-79. PubMed ID: 18458967
[TBL] [Abstract][Full Text] [Related]
20. Macromolecular crowding: chemistry and physics meet biology (Ascona, Switzerland, 10-14 June 2012).
Foffi G; Pastore A; Piazza F; Temussi PA
Phys Biol; 2013 Aug; 10(4):040301. PubMed ID: 23912807
[TBL] [Abstract][Full Text] [Related]
[Next] [New Search]