\begin{thebibliography}{36}
\setlength{\itemsep}{1mm}
\providecommand{\natexlab}[1]{#1}

\bibitem[{Andricioaei et~al.(2001)Andricioaei, Straub, and
  Voter}]{smart-darting-mc}
Andricioaei, I., Straub, J.E., and Voter, A.F.
\newblock Smart Darting Monte Carlo.
\newblock \emph{J. Chem. Physics}, 114(16):6994--7000, 2001.

\bibitem[{Boyce et~al.(2009)Boyce, Mobley, Rocklin, Graves, Dill, and
  Shoichet}]{mobley:jmb:2009:lysozyme-m102q}
Boyce, S.E., Mobley, D.L., Rocklin, G., Graves, A.P., Dill, K.A., and Shoichet,
  B.K.
\newblock Predicting ligand binding affinity with alchemical free energy
  methods in a polar binding site.
\newblock \emph{J. Mol. Biol.}, to appear, 2009.

\bibitem[{Brown and Muchmore(2006)}]{brown.jcim.2006.high-throughput}
Brown, S.P. and Muchmore, S.W.
\newblock High-Throughput Calculation of Protein-Ligand Binding Affinities:
  Modification and Adaptation of the MM-PBSA Protocol to Enterprise Grid
  Computing.
\newblock \emph{J. Chem. Inf. Model}, 46:999--1005,
  2006.

\bibitem[{Dullweber et~al.(2001)Dullweber, Stubbs, Musil, St\"{u}rzebecher, and
  Klebe}]{klebe:jmb:2001:thrombin}
Dullweber, F., Stubbs, M.T., Musil, D., St\"{u}rzebecher, J., and Klebe, G.
\newblock Factorising ligand affinity: a combined thermodynamic and
  crystallographic study of trypsin and thrombin inhibition.
\newblock \emph{J. Mol. Biol.}, 313:593--614, 2001.

\bibitem[{Escobedo and Abreu(2006)}]{escobedo_use_2006}
Escobedo, F.A. and Abreu, C.R.A.
\newblock On the use of transition matrix methods with extended ensembles.
\newblock \emph{J. Chem. Phys.}, 124(10):104110--11, 2006.

\bibitem[{Escobedo and
  {Mart\'{i}nez-Veracoechea}(2007)}]{escobedo_optimized_2007}
Escobedo, F.A. and {Mart\'{i}nez-Veracoechea}, F.J.
\newblock Optimized expanded ensembles for simulations involving molecular
  insertions and deletions. I. Closed systems.
\newblock \emph{J. Chem. Phys.}, 127(17):174103, 2007.

\bibitem[{et~al.(2009)}]{merck:bio-med-chem-lett:2009:beta-secretase}
et~al., S.J.S.
\newblock Discovery of aminoheterocycles as a novel $\beta$-secretase inhibitor
  class: {pH} dependence on binding activity part 1.
\newblock \emph{Bioorg. Med. Chem. Lett.}, 19:2977--2980, 2009.

\bibitem[{Friedrichs et~al.(2009)Friedrichs, Eastman, Vaidyanathan, Houston,
  Legrand, Beberg, Ensign, Bruns, and
  Pande}]{friedrichs:j-comput-chem:2009:openmm}
Friedrichs, M.S., Eastman, P., Vaidyanathan, V., Houston, M., Legrand, S.,
  Beberg, A.L., Ensign, D.L., Bruns, C.M., and Pande, V.S.
\newblock Accelerating molecular dynamics simulation on graphics processing
  units.
\newblock \emph{J. Comput. Chem.}, 30:864--872, 2009.

\bibitem[{Gallicchio et~al.(2009)Gallicchio, Paris, and Levy}]{agbnp2}
Gallicchio, E., Paris, K., and Levy, R.M.
\newblock The {AGBNP2} implicit solvation model.
\newblock \emph{J. Chem. Theory Comput.}, 5:2544--2564, 2009.

\bibitem[{Gan and Roux(2008)}]{gan_binding_2008}
Gan, W. and Roux, B.
\newblock Binding specificity of {SH2} domains: Insight from free energy
  simulations.
\newblock \emph{Proteins}, 2008.

\bibitem[{Genheden and Ryde(2009)}]{genheden-ryde:j-comput-chem:2009:mm-gbsa}
Genheden, S. and Ryde, U.
\newblock How to obtain statistically converged {MM/GBSA} results.
\newblock \emph{J. Comput. Chem.}, in press, 2009.

\bibitem[{Jayachandran et~al.(2006)Jayachandran, Shirts, Park, and
  Pande}]{jayachandran_parallelized-over-parts_2006}
Jayachandran, G., Shirts, M.R., Park, S., and Pande, V.S.
\newblock Parallelized-over-parts computation of absolute binding free energy
  with docking and molecular dynamics.
\newblock \emph{J. Chem. Phys.}, 125:084901, 2006.

\bibitem[{Kollman et~al.(2000)Kollman, Massova, Reyes, Kuhn, Huo, Chong, Lee,
  Lee, Duan, Wang, Donini, Cieplak, Srinivasan, Case, and Cheatham}]{kollman.accchemres.2000.calculating}
Kollman, P.A., Massova, I., Reyes, C., Kuhn, B., Huo, S., Chong, L., Lee, M.,
  Lee, T., Duan, Y., Wang, W., Donini, O., Cieplak, P., Srinivasan, J., Case,
  D.A., and Cheatham, T.~E.,
\newblock Calculating structures and free energies of complex molecules:
  combining molecular mechanics and continuum models.
\newblock \emph{Acc. Chem. Res.}, 33:889--97, 2000.

\bibitem[{Labute(2008)}]{GBVI}
Labute, P.
\newblock The {generalized Born/volume integral} implicit solvent model:
  Estimation of the free energy of hydration using {London} dispersion instead
  of atomic surface area.
\newblock \emph{J. Comput. Chem.}, 29:1693--1698, 2008.

\bibitem[{Lee and Olsen(2006)}]{lee_calculation_2006}
Lee, M.S. and Olsen, M.A.
\newblock Calculation of Absolute {Protein-Ligand} Binding Affinity Using Path
  and Endpoint Approaches.
\newblock \emph{Biophys. J.}, 90:864―877, 2006.

\bibitem[{Lyubartsev et~al.(1992)Lyubartsev, Martsinovski, Shevkunov, and
  {Vorontsov-Velyaminov}}]{lyubartsev_new_1992}
Lyubartsev, A.P., Martsinovski, A.A., Shevkunov, S.V., and
  {Vorontsov-Velyaminov}, P.N.
\newblock New approach to Monte Carlo calculation of the free energy: Method of
  expanded ensembles.
\newblock \emph{J. Chem. Phys.}, 96:1776―1783, 1992.

\bibitem[{Michel et~al.(2006)Michel, Verdonk, and
  Essex}]{michel_protein-ligand_2006}
Michel, J., Verdonk, M.L., and Essex, J.W.
\newblock Protein-ligand binding free energy predictions by implicit solvent
  simulation: A tool for lead optimization?
\newblock \emph{J. Med. Chem.}, 49:7427―7439, 2006.

\bibitem[{Mobley et~al.(2006)Mobley, Chodera, and Dill}]{mobley_use_2006}
Mobley, D.L., Chodera, J.D., and Dill, K.A.
\newblock On the use of orientational restraints and symmetry corrections in
  alchemical free energy calculations.
\newblock \emph{J. Chem. Phys.}, 125:084902, 2006.

\bibitem[{Mobley et~al.(2007{\natexlab{a}})Mobley, Chodera, and
  Dill}]{mobley_confine-and-release_2007}
Mobley, D.L., Chodera, J.D., and Dill, K.A.
\newblock Confine-and-release method: Obtaining correct binding free energies
  in the presence of protein conformational change.
\newblock \emph{J. Chem. Theo. Comput.}, 3(4):1231―1235,
  2007{\natexlab{a}}.

\bibitem[{Mobley and Dill(2009)}]{mobley-dill:structure:2009:review}
Mobley, D.L. and Dill, K.A.
\newblock Binding of small-molecule ligands to proteins: ``What you see'' is
  not always ``what you get''.
\newblock \emph{Structure}, 17:489--498, 2009.

\bibitem[{Mobley et~al.(2008{\natexlab{a}})Mobley, Dill, and
  Chodera}]{mobley_treating_2008}
Mobley, D.L., Dill, K.A., and Chodera, J.D.
\newblock Treating Entropy and Conformational Changes in Implicit Solvent
  Simulations of Small Molecules.
\newblock \emph{J. Phys. Chem. B}, 112(3):938―946,
  2008{\natexlab{a}}.

\bibitem[{Mobley et~al.(2007{\natexlab{b}})Mobley, Graves, Chodera,
  {McReynolds}, Shoichet, and Dill}]{mobley_predicting_2007}
Mobley, D.L., Graves, A.P., Chodera, J.D., {McReynolds}, A.C., Shoichet, B.K.,
  and Dill, K.A.
\newblock Predicting absolute ligand binding free energies to a simple model
  site.
\newblock \emph{J. Mol. Bio.}, 371(4):1118―1134,
  2007{\natexlab{b}}.

\bibitem[{Mobley et~al.(2007{\natexlab{c}})Mobley, Graves, Chodera,
  {McReynolds}, Shoichet, and Dill}]{mobley_predicting_2007-1}
Mobley, D.L., Graves, A.P., Chodera, J.D., {McReynolds}, A.C., Shoichet, B.K.,
  and Dill, K.A.
\newblock Predicting Absolute Ligand Binding Free Energies to a Simple Model
  Site.
\newblock \emph{J. Mol. Bio.}, 371(4):1118--1134,
  2007{\natexlab{c}}.

\bibitem[{Mobley et~al.(2008{\natexlab{b}})Mobley, {II}, Fennell, and
  Dill}]{mobley_charge_2008}
Mobley, D.L., {II}, A.E.B., Fennell, C.J., and Dill, K.A.
\newblock Charge Asymmetries in Hydration of Polar Solutes.
\newblock \emph{J. Phys. Chem. B}, 2008{\natexlab{b}}.

\bibitem[{Mongan et~al.(2004)Mongan, Case, and
  {McCammon}}]{mongan_constant_2004}
Mongan, J., Case, D.A., and {McCammon}, J.A.
\newblock Constant {pH} molecular dynamics in the generalized Born implicit
  solvent.
\newblock \emph{J. Comput. Chem}, 25:2038―2048, 2004.

\bibitem[{Mongan et~al.(2006)Mongan, Simmerling, {McCammon}, Case, and
  Onufriev}]{mongan_gb_2006}
Mongan, J., Simmerling, C., {McCammon}, J.A., Case, D.A., and Onufriev, A.
\newblock A generalized {Born} with a simple, robust molecular volume
  correction.
\newblock \emph{J. Chem. Theor. Comput.}, 3:156--169, 2006.

\bibitem[{Newman et~al.(2009)Newman, Fazio, Caradoc-Davies, Branson, and
  Peat}]{sampl2}
Newman, J., Fazio, V.J., Caradoc-Davies, T.T., Branson, K., and Peat, T.S.
\newblock Practical aspects of the {SAMPL} challenge: Providing an extensive
  experimental data set for the modeling community.
\newblock \emph{J. Biomol. Screen.}, in press, 2009.

\bibitem[{Onufriev et~al.(2000)Onufriev, Bashford, and
  Case}]{onufriev_modification_2000}
Onufriev, A., Bashford, D., and Case, D.A.
\newblock Modification of the Generalized Born Model Suitable for
  Macromolecules.
\newblock \emph{J. Phys. Chem. B}, 104:3712―3720, 2000.

\bibitem[{Onufriev et~al.(2004)Onufriev, Bashford, and
  Case}]{onufriev_exploring_2004}
Onufriev, A., Bashford, D., and Case, D.A.
\newblock Exploring protein native states and large-scale conformational
  changes with a modified generalized Born model.
\newblock \emph{Proteins}, 55:383―394,
  2004.

\bibitem[{Park(2008)}]{park_comparison_2008}
Park, S.
\newblock Comparison of the serial and parallel algorithms of generalized
  ensemble simulations: An analytical approach.
\newblock \emph{Phys. Rev. E}, 77(1):016709, 2008.

\bibitem[{Shirts and Chodera(2008)}]{shirts_statistically_2008}
Shirts, M.R. and Chodera, J.D.
\newblock Statistically optimal analysis of samples from multiple equilibrium
  states.
\newblock \emph{J. Chem. Phys.}, 129:129105, 2008.

\bibitem[{Shirts et~al.(2009)Shirts, Mobley, and Brown}]{shirts-mobley-brown}
Shirts, M.R., Mobley, D.L., and Brown, S.P.
\newblock Free energy calculations in structure-based drug design.
\newblock In \emph{Drug Design: Structure- and Ligand-Based Approaches}.
  Cambridge University Press, 2009.

\bibitem[{Shirts et~al.(2007)Shirts, Mobley, and
  Chodera}]{shirts_alchemical_2007}
Shirts, M.R., Mobley, D.L., and Chodera, J.D.
\newblock Alchemical Free Energy Calculations: Ready for Prime Time?
\newblock \emph{Annu. Rep. Comput. Chem.}, 3:41―59, 2007.

\bibitem[{Shirts and Pande(2005)}]{shirts_solvation_2005}
Shirts, M.R. and Pande, V.S.
\newblock Solvation free energies of amino acid side chains for common
  molecular mechanics water models.
\newblock \emph{J. Chem. Phys.}, 122:134508, 2005.

\bibitem[{Shirts et~al.(2003)Shirts, Pitera, Swope, and
  Pande}]{shirts_extremely_2003}
Shirts, M.R., Pitera, J.W., Swope, W.C., and Pande, V.S.
\newblock Extremely precise free energy calculations of amino acid side chain
  analogs: Comparison of common molecular mechanics force fields for proteins.
\newblock \emph{J. Chem. Phys.}, 119(11):5740―5761, 2003.

\bibitem[{Srinivasan et~al.(1999)Srinivasan, Trevathan, Beroza, and
  Case}]{case:theor-chem-acc:1999:gb-salt-screening}
Srinivasan, J., Trevathan, M.W., Beroza, P., and Case, D.A.
\newblock Application of a pairwise generalized {Born} model to proteins and
  nucleic acids: inclusion of salt effects.
\newblock \emph{Theor. Chem. Acc.}, 101:426--434, 1999.

\end{thebibliography}
