Laage D, Elsaesser T, Hynes JT (2017) Water dynamics in the hydration shells of biomolecules. Chem Rev 117:10694–10725

CAS  PubMed  PubMed Central  Article  Google Scholar 

Maurer M, De Beer SBA, Oostenbrink C (2016) Calculation of relative binding free energy in the water-filled active site of oligopeptide-binding protein A. Molecules 21:499

PubMed  PubMed Central  Article  Google Scholar 

Michel J, Tirado-Rives J, Jorgensen WL (2009) Energetics of displacing water molecules from protein binding sites: consequences for ligand optimization. J Am Chem Soc 131:15403–15411

CAS  PubMed  PubMed Central  Article  Google Scholar 

Cournia Z, Allen B, Sherman W (2017) Relative binding free energy calculations in drug discovery: recent advances and practical considerations. J Chem Inf Model 57:2911–2937

CAS  PubMed  Article  Google Scholar 

Ge Y, Baumann H, Mobley D (2022) Absolute binding free energy calculations for buried water molecules. ChemRxiv

Adams D (1974) Chemical potential of hard-sphere fluids by monte carlo methods. Mol Phys 28:1241–1252

CAS  Article  Google Scholar 

Adams D (1975) Grand canonical ensemble Monte Carlo for a Lennard-Jones fluid. Mol Phys 29:307–311

CAS  Article  Google Scholar 

Mezei M (1980) A cavity-biased ( T, V, \(\mu\) ) Monte Carlo method for the computer simulation of fluids. Mol Phys 40:901–906

CAS  Article  Google Scholar 

Mezei M (1987) Grand-canonical ensemble monte carlo study of dense liquid: Lennard-Jones. Soft Spheres Water Mol Phys 61:565–582

CAS  Article  Google Scholar 

Ross GA, Bodnarchuk MS, Essex JW (2015) Water sites, networks, and free energies with grand canonical Monte Carlo. J Am Chem Soc 137:14930–14943

CAS  PubMed  Article  Google Scholar 

Ross GA, Bruce Macdonald HE, Cave-Ayland C, Cabedo Martinez AI, Essex JW (2017) Replica-exchange and standard state binding free energies with grand canonical Monte Carlo. J Chem Theory Comput 13:6373–6381

CAS  PubMed  PubMed Central  Article  Google Scholar 

Bruce Macdonald HE, Cave-Ayland C, Ross GA, Essex JW (2018) Ligand binding free energies with adaptive water networks: two-dimensional grand canonical alchemical perturbations. J Chem Theory Comput 14:6586–6597

CAS  PubMed  PubMed Central  Article  Google Scholar 

Bodnarchuk MS, Packer MJ, Haywood A (2020) Utilizing grand canonical Monte Carlo methods in drug discovery. ACS Med Chem Lett 11:77–82

CAS  PubMed  Article  Google Scholar 

Ross GA, Russell E, Deng Y, Lu C, Harder ED, Abel R, Wang L (2020) Enhancing water sampling in free energy calculations with grand canonical Monte Carlo. J Chem Theory Comput 16:6061–6076

CAS  PubMed  Article  Google Scholar 

Ge Y, Wych DC, Samways ML, Wall ME, Essex JW, Mobley DL (2022) Enhancing sampling of water rehydration on ligand binding: a comparison of techniques. J Chem Theory Comput 18:1359–1381

PubMed  Article  Google Scholar 

Bergazin TD, Ben-Shalom IY, Lim NM, Gill SC, Gilson MK, Mobley DL (2021) Enhancing water sampling of buried binding sites using nonequilibrium candidate Monte Carlo. J Comput Aided Mol Des 35:167–177

CAS  PubMed  Article  Google Scholar 

Melling O, Samways M, Ge Y, Mobley D, Essex J (2022) Enhanced grand canonical sampling of occluded water sites using nonequilibrium candidate Monte Carlo. ChemRxiv

Ben-Shalom IY, Lin Z, Radak BK, Lin C, Sherman W, Gilson MK (2020) Accounting for the central role of interfacial water in protein-ligand binding free energy calculations. J Chem Theory Comput 16:7883–7894

CAS  PubMed  PubMed Central  Article  Google Scholar 

Barillari C, Taylor J, Viner R, Essex JW (2007) Classification of water molecules in protein binding sites. J Am Chem Soc 129:2577–2587

CAS  PubMed  Article  Google Scholar 

Wall ME (2009) Micro and nano technologies in bioanalysis. Methods in molecular Biolog\(^\). In: Lee JW, Foote RS (eds) Methods and protocols. Humana Press, Totowa, pp 269–279

Google Scholar 

Grosse-Kunstleve RW, Sauter NK, Moriarty NW, Adams PD (2002) The computational crystallography toolbox: crystallographic algorithms in a reusable software framework. J Appl Crystallogr 35:126–136

CAS  Article  Google Scholar 

McGibbon RT, Beauchamp KA, Harrigan MP, Klein C, Swails JM, Hernández CX, Schwantes CR, Wang L-P, Lane TJ, Pande VS (2015) MDTraj: a modern open library for the analysis of molecular dynamics trajectories. Biophys J 109:1528–1532

CAS  PubMed  PubMed Central  Article  Google Scholar 

Emsley P, Cowtan K (2004) Coot : model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60:2126–2132

PubMed  Article  Google Scholar 

Emsley P, Lohkamp B, Scott WG, Cowtan K (2010) Features and development of coot. Acta Crystallogr D Biol Crystallogr 66:486–501

CAS  PubMed  PubMed Central  Article  Google Scholar 

Samways ML, Bruce Macdonald HE, Essex JW (2020) Grand: a python module for grand canonical water sampling in OpenMM. J Chem Inf Model 60:4436–4441

CAS  PubMed  Article  Google Scholar 

Eastman P, Swails J, Chodera JD, McGibbon RT, Zhao Y, Beauchamp KA, Wang L-P, Simmonett AC, Harrigan MP, Stern CD, Wiewiora RP, Brooks BR, Pande VS (2017) OpenMM 7: rapid development of high performance algorithms for molecular dynamics. PLoS Comput Biol 13:e1005659

PubMed  PubMed Central  Article  Google Scholar 

Maier JA, Martinez C, Kasavajhala K, Wickstrom L, Hauser KE, Simmerling C (2015) ff14SB: improving the accuracy of protein side chain and backbone parameters from ff99SB. J Chem Theory Comput 11:3696–3713

CAS  PubMed  PubMed Central  Article  Google Scholar 

Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926–935

CAS  Article  Google Scholar 

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 (2021) Development and benchmarking of open force field v1.0.0–the parsley small-molecule force field. J Chem Theory Comput 17:6262–6280

CAS  PubMed  Article  Google Scholar 

Wagner J, Thompson M, Dotson D hyejang,; Rodríguez-Guerra, J. openforcefield/openforcefields: version 1.2.1 “Parsley” update. https://doi.org/10.5281/zenodo.4021623

Leimkuhler B, Matthews C (2012) Rational construction of stochastic numerical methods for molecular sampling. Appl Math Res eXpress 2012:abs010

Google Scholar 

Darden T, York D, Pedersen L (1993) Particle mesh Ewald: an N -( N ) method for Ewald sums in large systems. J Chem Phys 98:10089–10092

CAS  Article  Google Scholar 

Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) A smooth particle mesh Ewald method. J Chem Phys 103:8577–8593

CAS  Article  Google Scholar 

Søndergaard CR, Olsson MHM, Rostkowski M, Jensen JH (2011) Improved treatment of ligands and coupling effects in empirical calculation and rationalization of p K \(}\) values. J Chem Theory Comput 7:2284–2295

PubMed  Article  Google Scholar 

Olsson MHM, Søndergaard CR, Rostkowski M, Jensen JH (2011) PROPKA3: consistent treatment of internal and surface residues in empirical p K \(}\) predictions. J Chem Theory Comput 7:525–537

CAS  PubMed  Article  Google Scholar 

Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA (2004) PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Nucleic Acids Res 32:W665–W667

CAS  PubMed  PubMed Central  Article  Google Scholar 

Liu DC, Nocedal J (1989) On the limited memory BFGS method for large scale optimization. Math Program 45:503–528

Article  Google Scholar 

Fields BA, Bartsch HH, Bartunik HD, Cordes F, Guss JM, Freeman HC (1994) Accuracy and precision in protein crystal structure analysis: two independent refinements of the structure of poplar plastocyanin at 173 K. Acta Crystallogr D Biol Crystallogr 50:709–730

CAS  PubMed  Article  Google Scholar 

Ohlendorf DH (1994) Accuracy of refined protein structures. II. Comparison of four independently refined models of human interleukin 1beta. Acta Crystallogr D Biol Crystallogr 50:808–812

CAS  PubMed  Article  Google Scholar 

Samways ML, Taylor RD, Bruce Macdonald HE, Essex JW (2021) Water molecules at protein-drug interfaces: computational prediction and analysis methods. Chem Soc Rev 50:9104–9120

CAS  PubMed  Article  Google Scholar