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1.

Prediction of cyclin-dependent kinase 2 inhibitor potency using the fragment molecular orbital method.

Mazanetz MP, Ichihara O, Law RJ, Whittaker M.

J Cheminform. 2011 Jan 10;3(1):2. doi: 10.1186/1758-2946-3-2.

2.

Estimates of ligand-binding affinities supported by quantum mechanical methods.

Söderhjelm P, Kongsted J, Genheden S, Ryde U.

Interdiscip Sci. 2010 Mar;2(1):21-37. doi: 10.1007/s12539-010-0083-0. Epub 2010 Jan 28.

PMID:
20640794
4.

Empirical calculation of the relative free energies of peptide binding to the molecular chaperone DnaK.

Kasper P, Christen P, Gehring H.

Proteins. 2000 Aug 1;40(2):185-92.

PMID:
10842335
5.

Molecular recognition mechanism of FK506 binding protein: an all-electron fragment molecular orbital study.

Nakanishi I, Fedorov DG, Kitaura K.

Proteins. 2007 Jul 1;68(1):145-58.

PMID:
17387719
6.

Develop and test a solvent accessible surface area-based model in conformational entropy calculations.

Wang J, Hou T.

J Chem Inf Model. 2012 May 25;52(5):1199-212. doi: 10.1021/ci300064d. Epub 2012 Apr 24.

7.

Converging free energy estimates: MM-PB(GB)SA studies on the protein-protein complex Ras-Raf.

Gohlke H, Case DA.

J Comput Chem. 2004 Jan 30;25(2):238-50.

PMID:
14648622
8.

Validation of an automated procedure for the prediction of relative free energies of binding on a set of aldose reductase inhibitors.

Ferrari AM, Degliesposti G, Sgobba M, Rastelli G.

Bioorg Med Chem. 2007 Dec 15;15(24):7865-77. Epub 2007 Aug 22.

PMID:
17870536
10.

Ab initio fragment molecular orbital study of ligand binding to human progesterone receptor ligand-binding domain.

Harada T, Yamagishi K, Nakano T, Kitaura K, Tokiwa H.

Naunyn Schmiedebergs Arch Pharmacol. 2008 Jun;377(4-6):607-15. doi: 10.1007/s00210-008-0268-9. Epub 2008 Mar 11.

PMID:
18330543
11.

PHOENIX: a scoring function for affinity prediction derived using high-resolution crystal structures and calorimetry measurements.

Tang YT, Marshall GR.

J Chem Inf Model. 2011 Feb 28;51(2):214-28. doi: 10.1021/ci100257s. Epub 2011 Jan 7.

12.

Accurate predictions of nonpolar solvation free energies require explicit consideration of binding-site hydration.

Genheden S, Mikulskis P, Hu L, Kongsted J, Söderhjelm P, Ryde U.

J Am Chem Soc. 2011 Aug 24;133(33):13081-92. doi: 10.1021/ja202972m. Epub 2011 Jul 29.

PMID:
21728337
13.

Ab initio fragment molecular orbital (FMO) method applied to analysis of the ligand-protein interaction in a pheromone-binding protein.

Nemoto T, Fedorov DG, Uebayasi M, Kanazawa K, Kitaura K, Komeiji Y.

Comput Biol Chem. 2005 Dec;29(6):434-9. Epub 2005 Nov 10.

PMID:
16290169
14.

Effect of conformational flexibility and solvation on receptor-ligand binding free energies.

Vajda S, Weng Z, Rosenfeld R, DeLisi C.

Biochemistry. 1994 Nov 29;33(47):13977-88.

PMID:
7947806
16.

A QM/MM study of the binding of RAPTA ligands to cathepsin B.

Ciancetta A, Genheden S, Ryde U.

J Comput Aided Mol Des. 2011 Aug;25(8):729-42. doi: 10.1007/s10822-011-9448-7. Epub 2011 Jun 24.

PMID:
21701919
17.

Structure based prediction of binding affinity of human immunodeficiency virus-1 protease inhibitors.

Kulkarni SS, Kulkarni VM.

J Chem Inf Comput Sci. 1999 Nov-Dec;39(6):1128-40.

PMID:
10614027
18.

Binding interaction analysis of the active site and its inhibitors for neuraminidase (N1 subtype) of human influenza virus by the integration of molecular docking, FMO calculation and 3D-QSAR CoMFA modeling.

Zhang Q, Yang J, Liang K, Feng L, Li S, Wan J, Xu X, Yang G, Liu D, Yang S.

J Chem Inf Model. 2008 Sep;48(9):1802-12. doi: 10.1021/ci800041k. Epub 2008 Aug 16.

PMID:
18707092
19.
20.

The thermodynamics of protein-ligand interaction and solvation: insights for ligand design.

Olsson TS, Williams MA, Pitt WR, Ladbury JE.

J Mol Biol. 2008 Dec 26;384(4):1002-17. doi: 10.1016/j.jmb.2008.09.073. Epub 2008 Oct 9.

PMID:
18930735
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