FESetup: Automating Setup for Alchemical Free Energy Simulations

Journal of Chemical Information and Modeling

Volumn 55, Issue 12, 2015, Pages 2485-2490

  Loeffler, Hannes H ^a   Michel, Julien ^b   Woods, Christopher ^c  

^a DARESBURY LABORATORY   (United Kingdom)

^b UNIVERSITY OF EDINBURGH   (United Kingdom)

^c Tankard's Close   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMBER; MOLECULAR DYNAMICS;

ALCHEMICAL FREE ENERGY SIMULATIONS; AMBER FORCE-FIELD; EASE-OF-USE; GROMACS; MOLECULAR SIMULATIONS; OPEN DEVELOPMENT; POSTPROCESSING METHODS; WORK-FLOWS;

FREE ENERGY;

LIGAND;

CHEMICAL MODEL; COMPUTER SIMULATION; MOLECULAR DYNAMICS; THERMODYNAMICS;

COMPUTER SIMULATION; LIGANDS; MODELS, CHEMICAL; MOLECULAR DYNAMICS SIMULATION; THERMODYNAMICS;

EID: 84952815475     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/acs.jcim.5b00368     Document Type: Article

References (40)

1. Michel, J. Current and emerging opportunities for molecular simulations in structure-based drug design Phys. Chem. Chem. Phys. 2014, 16, 4465-4477 10.1039/C3CP54164A
2. Homeyer, N.; Gohlke, H. FEW: A workflow tool for free energy calculations of ligand binding J. Comput. Chem. 2013, 34, 965-973 10.1002/jcc.23218
3. Jorgensen, W. L. Efficient Drug Lead Discovery and Optimization Acc. Chem. Res. 2009, 42, 724-733 10.1021/ar800236t
4. Case, D. A.; Cheatham, T. E., III; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M., Jr.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. The Amber biomolecular simulation programs J. Comput. Chem. 2005, 26, 1668-1688 10.1002/jcc.20290
5. Srinivasan, J.; Cheatham, T. E.; Cieplak, P.; Kollman, P. A.; Case, D. A. Continuum Solvent Studies of the Stability of DNA, RNA, and Phosphoramidate-DNA Helices J. Am. Chem. Soc. 1998, 120, 9401-9409 10.1021/ja981844+
6. Gutiérrez-de-Terán, H.; Åqvist, J. Linear Interaction Energy: Method and Applications in Drug Design. In Computational Drug Discovery and Design; Baron, R., Ed.; Springer: New York, 2012; pp 305-323.
7. Christ, C. D.; Fox, T. Accuracy Assessment and Automation of Free Energy Calculations for Drug Design J. Chem. Inf. Model. 2014, 54, 108-120 10.1021/ci4004199
8. Gapsys, V.; Michielssens, S.; Seeliger, D.; de Groot, B. L. pmx: Automated protein structure and topology generation for alchemical perturbations J. Comput. Chem. 2015, 36, 348-354 10.1002/jcc.23804
9. Van Der Spoel, D.; Lindahl, E.; Hess, B.; Groenhof, G.; Mark, A. E.; Berendsen, H. J. C. GROMACS: Fast, flexible, and free J. Comput. Chem. 2005, 26, 1701-1718 10.1002/jcc.20291
10. Lundborg, M.; Lindahl, E. Automatic GROMACS Topology Generation and Comparisons of Force Fields for Solvation Free Energy Calculations J. Phys. Chem. B 2015, 119, 810-823 10.1021/jp505332p
11. Liu, S.; Wu, Y.; Lin, T.; Abel, R.; Redmann, J. P.; Summa, C. M.; Jaber, V. R.; Lim, N. M.; Mobley, D. L. Lead optimization mapper: automating free energy calculations for lead optimization J. Comput.-Aided Mol. Des. 2013, 27, 755-770 10.1007/s10822-013-9678-y
12. Sadiq, S. K.; Wright, D.; Watson, S. J.; Zasada, S. J.; Stoica, I.; Coveney, P. V. Automated Molecular Simulation Based Binding Affinity Calculator for Ligand-Bound HIV-1 Proteases J. Chem. Inf. Model. 2008, 48, 1909-1919 10.1021/ci8000937
13. Woods, C. J.; Michel, J. M. Sire: An advanced, multiscale, molecular simulation framework. http://siremol.org/ (accessed September 4, 2015).
14. Phillips, J. C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R. D.; Kale, L.; Schulten, K. Scalable molecular dynamics with NAMD J. Comput. Chem. 2005, 26, 1781-1802 10.1002/jcc.20289
15. Hansen, N.; van Gunsteren, W. F. Practical Aspects of Free-Energy Calculations: A Review J. Chem. Theory Comput. 2014, 10, 2632-2647 10.1021/ct500161f
16. Mobley, D.; Guthrie, J. FreeSolv: a database of experimental and calculated hydration free energies, with input files J. Comput.-Aided Mol. Des. 2014, 28, 711-720 10.1007/s10822-014-9747-x
17. Boresch, S.; Karplus, M. The Role of Bonded Terms in Free Energy Simulations: 1. Theoretical Analysis J. Phys. Chem. A 1999, 103, 103-118 10.1021/jp981628n
18. Michel, J.; Essex, J. Prediction of protein - ligand binding affinity by free energy simulations: assumptions, pitfalls and expectations J. Comput.-Aided Mol. Des. 2010, 24, 639-658 10.1007/s10822-010-9363-3
19. Gumbart, J. C.; Roux, B.; Chipot, C. Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy? J. Chem. Theory Comput. 2013, 9, 794-802 10.1021/ct3008099
20. Dalke, A.; Hastings, J. FMCS: a novel algorithm for the multiple MCS problem J. Cheminf. 2013, 5, O6 10.1186/1758-2946-5-S1-O6
21. Raymond, J. W.; Willett, P. Maximum common subgraph isomorphism algorithms for the matching of chemical structures J. Comput.-Aided Mol. Des. 2002, 16, 521-533 10.1023/A:1021271615909
22. Liu, S.; Wang, L.; Mobley, D. L. Is Ring Breaking Feasible in Relative Binding Free Energy Calculations? J. Chem. Inf. Model. 2015, 55, 727-735 10.1021/acs.jcim.5b00057
23. OBoyle, N.; Banck, M.; James, C.; Morley, C.; Vandermeersch, T.; Hutchison, G. Open Babel: An open chemical toolbox J. Cheminf. 2011, 3, 33-46 10.1186/1758-2946-3-33
24. Landrum, G. RDKit: Open-source cheminformatics. http://www.rdkit.org (accessed September 4, 2015).
25. Wang, J.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. Development and testing of a general amber force field J. Comput. Chem. 2004, 25, 1157-1174 10.1002/jcc.20035
26. Mishra, S. K; Calabro, G.; Loeffler, H. H.; Michel, J.; Koča, J. Evaluation of selected classical force fields for alchemical binding free energy calculations of protein-carbohydrate complexes J. Chem. Theory Comput. 2015, 11, 3333-3345 10.1021/acs.jctc.5b00159
27. Kirschner, K. N.; Yongye, A. B.; Tschampel, S. M.; González-Outeiriño, J.; Daniels, C. R.; Foley, B. L.; Woods, R. J. GLYCAM06: A generalizable biomolecular force field. Carbohydrates J. Comput. Chem. 2008, 29, 622-655 10.1002/jcc.20820
28. Jakalian, A.; Bush, B. L.; Jack, D. B.; Bayly, C. I. Fast, efficient generation of high-quality atomic charges. AM1-BCC model: I. Method J. Comput. Chem. 2000, 21, 132-146 10.1002/(SICI)1096-987X(20000130)21:2<132::AID-JCC5>3.0.CO;2-P
29. Sayle, R. So you think you understand tautomerism? J. Comput.-Aided Mol. Des. 2010, 24, 485-496 10.1007/s10822-010-9329-5
30. Todorov, I. T.; Smith, W.; Trachenko, K.; Dove, M. T. DLPOLY 3: new dimensions in molecular dynamics simulations via massive parallelism J. Mater. Chem. 2006, 16, 1911-1918 10.1039/b517931a
31. Søndergaard, C. R.; Olsson, M. H. M.; Rostkowski, M.; Jensen, J. H. Improved Treatment of Ligands and Coupling Effects in Empirical Calculation and Rationalization of pKa Values J. Chem. Theory Comput. 2011, 7, 2284-2295 10.1021/ct200133y
32. Olsson, M. H. M.; Søndergaard, C. R.; Rostkowski, M.; Jensen, J. H. PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKa Predictions J. Chem. Theory Comput. 2011, 7, 525-537 10.1021/ct100578z
33. Kaus, J. W.; Pierce, L. T.; Walker, R. C.; McCammon, J. A. Improving the Efficiency of Free Energy Calculations in the Amber Molecular Dynamics Package J. Chem. Theory Comput. 2013, 9, 4131-4139 10.1021/ct400340s
34. Michel, J.; Henchman, R. H.; Gerogiokas, G.; Southey, M. W. Y.; Mazanetz, M. P.; Law, R. J. Evaluation of Host - Guest Binding Thermodynamics of Model Cavities with Grid Cell Theory J. Chem. Theory Comput. 2014, 10, 4055-4068 10.1021/ct500368p
35. Gerogiokas, G.; Calabro, G.; Henchman, R. H.; Southey, M. W. Y.; Law, R. J.; Michel, J. Prediction of Small Molecule Hydration Thermodynamics with Grid Cell Theory J. Chem. Theory Comput. 2014, 10, 35-48 10.1021/ct400783h
36. Gerogiokas, G.; Southey, M. W. Y.; Mazanetz, M. P.; Hefeitz, A.; Bodkin, M.; Law, R. J.; Michel, J. Evaluation of water displacement energetics in protein binding sites with grid cell theory Phys. Chem. Chem. Phys. 2015, 17, 16213-16213 10.1039/C5CP90084K
37. Brooks, B. R.; Brooks, C. L.; Mackerell, A. D.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. CHARMM: The biomolecular simulation program J. Comput. Chem. 2009, 30, 1545-1614 10.1002/jcc.21287
38. Bayly, C. I.; Cieplak, P.; Cornell, W.; Kollman, P. A. A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: the RESP model J. Phys. Chem. 1993, 97, 10269-10280 10.1021/j100142a004
39. Mobley, D. L.; Klimovich, P. V. Perspective: Alchemical free energy calculations for drug discovery J. Chem. Phys. 2012, 137, 230901 10.1063/1.4769292
40. Michel, J.; Verdonk, M. L.; Essex, J. W. Protein-ligand complexes: computation of the relative binding free energy of different scaffolds and binding modes J. Chem. Theory Comput. 2007, 3, 1645-1655 10.1021/ct700081t