Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM)

Journal of Computer-Aided Molecular Design

Volumn 26, Issue 5, 2012, Pages 505-516

  Gallicchio, Emilio ^a   Levy, Ronald M ^a  

^a RUTGERS UNIVERSITY   (United States)

Author keywords

AGBNP; BEDAM; Binding free energy; Host guest; Replica exchange; SAMPL3

Indexed keywords

ANESTHETICS; FORECASTING; FREE ENERGY; LIGANDS; MOLECULAR DYNAMICS; STEREOCHEMISTRY;

AGBNP; ANALYSIS METHOD; BINDING ENERGY DISTRIBUTION ANALYSE METHOD; BINDING FREE ENERGY; ENERGY DISTRIBUTION ANALYSIS; ENERGY ESTIMATES; HOST:GUEST; QUANTITATIVE AGREEMENT; REPLICA EXCHANGE; SAMPL3;

BINDING ENERGY;

ALGORITHM; BINDING AFFINITY; BINDING ENERGY DISTRIBUTION ANALYSIS METHOD; CHEMICAL STRUCTURE; COMPUTER AIDED DESIGN; COMPUTER PROGRAM; CONFERENCE PAPER; CORRELATION COEFFICIENT; ENANTIOMER; ENERGY; ENTROPY; MOLECULAR DYNAMICS; MOLECULAR RECOGNITION; PREDICTION; PRIORITY JOURNAL; PROTON TRANSPORT; STATISTICAL ANALYSIS; STEREOISOMERISM; THERMODYNAMICS;

EID: 84863089147     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-012-9552-3     Document Type: Conference Paper

References (38)

1. Gilson MK, Given JA, Bush BL, McCammon JA (1997) The statistical- thermodynamic basis for computation of binding affinities: a critical review. Biophys J 72:1047-1069 (Pubitemid 27113632)
2. Gallicchio E, Levy RM (2011) Recent theoretical and computational advances for modeling protein-ligand binding affinities. In: Advances in protein chemistry and structural biology, vol 85. Academic Press, London, pp 27-80
3. Gilson MK, Zhou H-X (2007) Calculation of protein-ligand binding affinities. Ann Rev Biophys Biomol Struct 36:21-42 (Pubitemid 46998108)
4. Shirts MR, Mobley DL, Chodera JD (2007) Alchemical free energy calculations: ready for prime time? Ann Rep Comput Chem 3:41-59
5. Mobley DL, Dill KA (2009) Binding of small-molecule ligands to proteins: "what you see" is not always "what you get". Structure 17(4):489-498
6. Deng Y, Roux B (2009) Computations of standard binding free energies with molecular dynamics simulations. J Phys Chem B 113(8):2234-2246
7. Chodera JD, Mobley DL, Shirts MR, Dixon RW, Branson K, Pande VS (2011) Alchemical free energy methods for drug discovery: progress and challenges. Curr Opin Struct Biol 21:150-160
8. Jorgensen WL (2004) The many roles of computation in drug discovery. Science 303(5665):1813-1818 (Pubitemid 38374866)
9. Shirts MR, Mobley DL, Brown SP (2010) Free energy calculations in structure-based drug design. In: Structure based drug discovery. Cambridge University Press, Cambridge
10. Chipot C, Pohorille A (eds) (2007) Free energy calculations. Theory and applications in chemistry and biology. Springer Series in Chemical Physics. Springer, Berlin
11. Head MS, Given JA, Gilson MK (1997) Mining minima: direct computation of conformational free energy. J Phys Chem A 101(8):1609-1618 (Pubitemid 127619859)
12. Chang CA, Chen W, Gilson MK (2007) Ligand configurational entropy and protein binding. Proc Natl Acad Sci USA 104(5): 1534-1539 (Pubitemid 46214625)
13. Moghaddam S, Yang C, Rekharsky M, Ko YH, Kim K, Inoue Y, Gilson MK (2011) New ultrahigh affinity host-guest complexes of cucurbit7. uril with bicyclo[2.2.2]octane and adamantane guests: thermodynamic analysis and evaluation of M2 affinity calculations. J Am Chem Soc 133(10):3570-3581
14. Gallicchio E, Lapelosa M, Levy RM (2010) Binding energy distribution analysis method (BEDAM) for estimation of proteinligand binding affinities. J Chem Theory Comput 6(9):2961-2977
15. Lapelosa M, Gallicchio E, Levy RM (2012) Conformational transitions and convergence of absolute binding free energy calculations. J Chem Theory Comput 8:47-60
16. Gallicchio E, Levy RM (2004) AGBNP: an analytic implicit solvent model suitable for molecular dynamics simulations and high-resolution modeling. J Comput Chem 25:479-499
17. Gallicchio E, Paris K, Levy RM (2009) The AGBNP2 implicit solvation model. J Chem Theory Comput 5(9):2544-2564
18. Wyman IW, Macartney DH (2010) Host-guest complexations of local anaesthetics by cucurbit7. uril in aqueous solution. Org Biomol Chem 8(1):247-252
19. Ma D, Zavalij PY, Isaacs L (2010) Acyclic cucurbit[n]uril congeners are high affinity hosts. J Org Chem 75(14):4786-4795
20. Muddana HS, Varnado CD, Bielawski CW, Urbach AR, Isaacs L, Geballe MT, Gilson M (2012) Blind prediction of host-guest binding affinities: a new SAMPL3 challenge. J Comp Aided Mol Design (in press)
21. Gallicchio E, Levy RM (2011) Advances in all atom sampling methods for modeling protein-ligand binding affinities. Curr Opin Struct Biol 21(2):161-166
22. Gallicchio E, Andrec M, Felts AK, Levy RM (2005) Temperature weighted histogram analysis method, replica exchange, and transition paths. J Phys Chem B 109:6722-6731 (Pubitemid 40538440)
23. Shirts MR, Chodera JD (2008) Statistically optimal analysis of samples from multiple equilibrium states. J Chem Phys 129(12): 124105
24. Moult J, Fidelis K, Kryshtafovych A, Rost B, Tramontano A (2009) Critical assessment of methods of protein structure prediction - round viii. Proteins 77(Suppl 9):1-4
25. Guthrie JP (2009) A blind challenge for computational solvation free energies: introduction and overview. J Phys Chem B 113(14):4501-4507
26. Nielsen JE, Gunner MR, Bertrand García-Moreno E (2011) The pka cooperative: A collaborative effort to advance structurebased calculations of pka values and electrostatic effects in proteins. Proteins 79(12):3249-3259
27. Wodak SJ (2007) From the mediterranean coast to the shores of lake ontario: Capri's premiere on the american continent. Proteins 69(4):697-698 (Pubitemid 350210128)
28. Boyce SE, Mobley DL, Rocklin GJ, Graves AP, Dill KA, Shoichet BK (2009) Predicting ligand binding affinity with alchemical free energy methods in a polar model binding site. J Mol Biol 394(4):747-763
29. Hagen M, Kim B, Liu P, Berne BJ (2006) Serial replica exchange. J Phys Chem B 111:1416-1423 (Pubitemid 46339069)
30. Roitberg AE, Okur A, Simmerling C (2007) Coupling of replica exchange simulations to a non-boltzmann structure reservoir. J Phys Chem B 111(10):2415-2418 (Pubitemid 46548721)
31. Okumura H, Gallicchio E, Levy RM (2010) Conformational populations of ligand-sized molecules by replica exchange molecular dynamics and temperature reweighting. J Comput Chem 31: 1357-1367
32. Gallicchio E, Levy RM, Parashar M (2008) Asynchronous replica exchange for molecular simulations. J Comput Chem 29(5): 788-794 (Pubitemid 351364853)
33. Jorgensen WL, Maxwell DS, Tirado-Rives J (1996) Developement and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 118:11225-11236 (Pubitemid 26399746)
34. Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL (2001) Evaluation and reparameterization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem B 105:6474-6487 (Pubitemid 35339015)
35. Nguyen C, Gilson MK, Young T (2011) Structure and thermodynamics of molecular hydration via grid inhomogeneous solvation theory. arXiv:1108.4876v1 [q-bio.BM]
36. Banks JL, Beard JS, Cao Y, Cho AE, Damm W, Farid R, Felts AK, Halgren TA, Mainz DT, Maple JR, Murphy R, Philipp DM, Repasky MP, Zhang LY, Berne BJ, Friesner RA, Gallicchio E, Levy RM (2005) Integrated modeling program, applied chemical theory (IMPACT). J Comp Chem 26:1752-1780 (Pubitemid 43076184)
37. Pohorille A, Jarzynski C, Chipot C (2010) Good practices in freeenergy calculations. J Phys Chem B 114(32):10235-10253
38. Zheng W, Andrec M, Gallicchio E, Levy RM (2008) Simple continuous and discrete models for simulating replica exchange simulations of protein folding. J Phys Chem B 112(19):6083-6093