Zeng J, Huang Z (2019) From levinthal’s paradox to the effects of cell environmental perturbation on protein folding. Curr Med Chem 26:7537–7554

Article  CAS  PubMed  Google Scholar 

Chen J, Zeng Q, Wang W, Hu Q, Bao H (2022) Q61 mutant-mediated dynamics changes of the GTP-KRAS complex probed by Gaussian accelerated molecular dynamics and free energy landscapes. RSC Adv 12:1742–1757

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sotriffer, C. A.; Sanschagrin, P.; Matter, H.; Klebe, G., SFCscore: scoring functions for affinity prediction of protein–ligand complexes. Proteins: Structure, Function, and Bioinformatics 2008, 73, 395–419.

Pecina A, Eyrilmez SM, Köprülüoğlu C, Miriyala VM, Lepšík M, Fanfrlík J, Řezáč J, Hobza P (2020) SQM/COSMO scoring function: reliable quantum-mechanical tool for sampling and ranking in structure-based drug design. ChemPlusChem 85:2362–2371

Article  CAS  PubMed  Google Scholar 

Wang, X., Conformational Fluctuations in GTP-Bound K-Ras: A Metadynamics Perspective with Harmonic Linear Discriminant Analysis. J. Chem. Inf. Model. 2021.

Goel H, Yu W, MacKerell AD (2022) hERG blockade prediction by combining site identification by ligand competitive saturation and physicochemical properties. Chemistry 4:630–646

Article  CAS  Google Scholar 

Nicolaï A, Petiot N, Grassein P, Delarue P, Neiers F, Senet P (2022) Free-energy landscape analysis of protein-ligand binding: the case of human glutathione transferase A1. Appl Sci 12:8196

Article  Google Scholar 

Giordano D, Biancaniello C, Argenio MA, Facchiano A (2022) Drug design by pharmacophore and virtual screening approach. Pharmaceuticals 15:646

Article  CAS  PubMed  PubMed Central  Google Scholar 

Homeyer N, Gohlke H (2012) Free energy calculations by the molecular mechanics poisson−boltzmann surface area method. Mol Inf 31:114–122

Article  CAS  Google Scholar 

Lindstrom A, Edvinsson L, Johansson A, Andersson CD, Andersson IE, Raubacher F, Linusson A (2011) Postprocessing of docked protein− ligand complexes using implicit solvation models. J Chem Inf Model 51:267–282

Article  CAS  PubMed  Google Scholar 

Yang T, Wu JC, Yan C, Wang Y, Luo R, Gonzales MB, Dalby KN, Ren P (2011) Virtual screening using molecular simulations. Proteins 79:1940–1951

Article  CAS  PubMed  PubMed Central  Google Scholar 

Khalak, Y.; Tresadern, G.; de Groot, B. L.; Gapsys, V., Non-equilibrium approach for binding free energies in cyclodextrins in SAMPL7: force fields and software. J. Comput.-Aided Mol. Des. 2021, 35, 49–61.

Sun Z, Wang X, Zhang JZH (2017) BAR-based optimum adaptive sampling regime for variance minimization in alchemical transformation. Phys Chem Chem Phys 19:15005–15020

Article  CAS  PubMed  Google Scholar 

Sun, Z.; Wang, M.; He, Q.; Liu, Z., Molecular modelling of ionic liquids: force-field validation and thermodynamic perspective from large-scale fast-growth solvation free energy calculations. Adv. Theory Simul. 2022, 2200274.

Sun Z, Gong Z, Zheng L, Payam K, Huai Z, Liu Z (2022) Molecular modelling of ionic liquids: general guidelines on fixed-charge force fields for balanced descriptions. Journal of Ionic Liquids 2:100043

Article  Google Scholar 

Sun Z, Kayal A, Gong Z, Zheng L, He Q (2022) Molecular modelling of ionic liquids: physical properties of species with extremely long aliphatic chains from a near-optimal regime. J Mol Liq 367:120492

Article  CAS  Google Scholar 

Ferrari AM, Degliesposti G, Sgobba M, Rastelli G (2007) Validation of an automated procedure for the prediction of relative free energies of binding on a set of aldose reductase inhibitors. Biorg Med Chem 15:7865–7877

Article  CAS  Google Scholar 

Rapp C, Kalyanaraman C, Schiffmiller A, Schoenbrun EL, Jacobson MP (2011) A molecular mechanics approach to modeling protein-ligand interactions: relative binding affinities in congeneric series. J Chem Inf Model 51:2082–2089

Article  CAS  PubMed  PubMed Central  Google Scholar 

Miller BR, Mcgee TD, Swails JM, Homeyer N, Gohlke H, Roitberg AE (2012) MMPBSA.py: an efficient program for end-state free energy calculations. J Chem Theory Comput 8:3314–3321

Article  CAS  PubMed  Google Scholar 

Wan S, Knapp B, Wright DW, Deane CM, Coveney PV (2015) Rapid, precise, and reproducible prediction of peptide–MHC binding affinities from molecular dynamics that correlate well with experiment. J Chem Theory Comput 11:3346–3356

Article  CAS  PubMed  Google Scholar 

Panday SK, Alexov E (2022) Protein-protein binding free energy predictions with the MM/PBSA approach complemented with the gaussian-based method for entropy estimation. ACS Omega 7:11057–11067

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tian S, Zeng J, Liu X, Chen J, Zhang JZ, Zhu T (2019) Understanding the selectivity of inhibitors toward PI4KIIIα and PI4KIIIβ based molecular modeling. Phys Chem Chem Phys 21:22103–22112

Article  CAS  PubMed  Google Scholar 

Su PC, Tsai CC, Mehboob S, Hevener KE, Johnson ME (2015) Comparison of radii sets, entropy, QM methods, and sampling on MM-PBSA, MM-GBSA, and QM/MM-GBSA ligand binding energies of F. tularensis enoyl-ACP reductase (F abI). J Comput Chem 36:1859–1873

Article  CAS  PubMed  PubMed Central  Google Scholar 

Sangpheak W, Khuntawee W, Wolschann P, Pongsawasdi P, Rungrotmongkol T (2014) Enhanced stability of a naringenin/2, 6-dimethyl β-cyclodextrin inclusion complex: Molecular dynamics and free energy calculations based on MM-and QM-PBSA/GBSA. J Mol Graph Model 50:10–15

Article  CAS  PubMed  Google Scholar 

Tsitsanou KE, Hayes JM, Keramioti M, Mamais M, Oikonomakos NG, Kato A, Leonidas DD, Zographos SE (2013) Sourcing the affinity of flavonoids for the glycogen phosphorylase inhibitor site via crystallography, kinetics and QM/MM-PBSA binding studies: comparison of chrysin and flavopiridol. Food Chem Toxicol 61:14–27

Article  CAS  PubMed  Google Scholar 

Huai Z, Yang H, Li X, Sun Z (2021) SAMPL7 TrimerTrip host-guest binding affinities from extensive alchemical and end-point free energy calculations. J Comput Aided Mol Des 35:117–129

Article  CAS  PubMed  Google Scholar 

Van Zundert G, Rodrigues J, Trellet M, Schmitz C, Kastritis P, Karaca E, Melquiond A, van Dijk M, De Vries S, Bonvin A (2016) The HADDOCK2. 2 web server user-friendly integrative modeling of biomolecular complexes. J Mol Biol 428:720–725

Article  PubMed  Google Scholar 

Krammer A, Kirchhoff PD, Jiang X, Venkatachalam C, Waldman M (2005) LigScore: a novel scoring function for predicting binding affinities. J Mol Graph Model 23:395–407

Article  CAS  PubMed  Google Scholar 

Wang X, Chong B, Sun Z, Ruan H, Yang Y, Song P, Liu Z (2022) More is simpler: Decomposition of ligand-binding affinity for proteins being disordered. Protein Sci 31:e4375

Article  CAS  PubMed  Google Scholar 

Ahmadian N, Mehrnejad F, Amininasab M (2020) Molecular insight into the interaction between camptothecin and acyclic cucurbit[4]urils as efficient nanocontainers in comparison with cucurbit[7]uril: molecular docking and molecular dynamics simulation. J Chem Inf Model 60:1791–1803

Article  CAS  PubMed  Google Scholar 

Mitkina T, Naumov DY, Gerasko O, Dolgushin F, Vicent C, Llusar R, Sokolov M, Fedin V (2004) Inclusion of nickel (II) and copper (II) complexes with aliphatic polyamines in cucurbit [8] uril. Russ Chem Bull 53:2519–2524

Article  CAS  Google Scholar 

Samsonenko, D.; Virovets, A.; Lipkowski, J.; Geras' ko, O.; Fedin, V., Distortion of the cucurbituril molecule by an included 4‐methylpyridinum cation. J. Struct. Chem. 2002, 43, 664–668.

Sun Z, He Q, Li X, Zhu Z (2020) SAMPL6 host–guest binding affinities and binding poses from spherical-coordinates-biased simulations. J Comput Aided Mol Des 34:589–600

Article  CAS  PubMed  Google Scholar 

Litim A, Belhocine Y, Benlecheb T, Ghoniem MG, Kabouche Z, Ali FAM, Abdulkhair BY, Seydou M, Rahali S (2021) DFT-D4 insight into the inclusion of amphetamine and methamphetamine in cucurbit[7]uril: energetic, structural and biosensing properties. Molecules 26:7479

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hsiao Y-W, Söderhjelm P (2014) Prediction of SAMPL4 host–guest binding affinities using funnel metadynamics. J Comput Aided Mol Des 28:443–454

Article  CAS  PubMed  Google Scholar 

Jansook P, Ogawa N, Loftsson T (2018) Cyclodextrins: structure, physicochemical properties and pharmaceutical applications. Int J Pharm 535:272–284

Article  CAS  PubMed  Google Scholar 

Gebhardt J, Kleist C, Jakobtorweihen S, Hansen N (2018) Validation and comparison of force fields for native cyclodextrins in aqueous solution. J Phys Chem B 122:1608–1626

Article  CAS  PubMed  Google Scholar 

Peerannawar SR, Gejji SP (2013) Theoretical investigations on vibrational spectra of pillar [5] arene-bis (pyridinium) complexes. Spectrochim Acta Part A Mol Biomol Spectrosc 104:368–376

Article  CAS  Google Scholar 

Li S-H, Zhang H-Y, Xu X, Liu Y (2015) Mechanically selflocked chiral gemini-catenanes. Nat Commun 6:1–7

Google Scholar 

Qin S, Xiong S, Han Y, Hu XY, Wang L (2015) Controllable fabrication of various supramolecular nanostructures based on nonamphiphilic azobenzene derivatives and pillar [6] arene. Chin J Chem 33:107–111

Article  CAS  Google Scholar 

Liu L, Cao D, Jin Y, Tao H, Kou Y, Meier H (2011) Efficient synthesis of copillar [5] arenes and their host–guest properties with dibromoalkanes. Org Biomol Chem 9:7007–7010

Article