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14761204,10813821,10395487,10024025,14997538,15521089,18266357,15331051,14696186,12579585,10491851,8346190,20413725,16300378,11101351,12825929,9526559,15556074,17433745,14640689,17349808,17238257,10377222,16134935,16245298,11953755,18511229,9751507,19101506,16898767,14736241,20074635,16838311,15080660,16426079,19583238,12723952,17999665,19286405,6548545,17870536,16972282,11944962,10397250,16884312,14770416,17112243,18452341,15219790,10036142,16728493,11918843,17249692,17258427,17335007,16307743,17266199,12954056,15236964,15556769,12479373,12495555,16293430,14635724,15018930,16995728,11741316,8672466,18398905,10072684,9439992,18937440,19161236,16481019,10099132,15698547,16473560,18646811,9632359,11187742,19643976,18692112,15001543,17559906,17280694,12825935,1868844,12471606,11017776,12866048,9927308,20151411,10921772,7932757,9893973,12456792,16940337,10377031,14761193,9599231,1944245,22898043,15081833,14735568,7066903,20662079,6528522,3965923,14565775,9822539,21495739,14667218,16889744,12615096,19705486,12598185,21303099,21420388,15281621,12074393,12203463,11775002,10533810,12077849,9857095,12889983,20145812,11559523,9406602,12672240,4002655,14517972,6685018,11258977,32019136,10964929,22079771,24098659,20524650,11913374,10585722,14667222,9398531,20707409,9141130,20099932,12069588,11086226,23467020,11866690,9030571,9619507,19423117,21650197,7191732,12650065,10791702,21710634,14680380,1758885,2233692,12964193,9292936,23712771,20227312,12016866,11197334,14612550,22183545,22482773,7716166,7113055,14758981,9048584,16234174,9125170,20427100,7427959,19421988,26639429,8951225,10338024,12833480,26180998,7565806,8054467,21999568,20965757,21334935,8632423,12870908,11431146,12733937,21194224,10746941,10447948,15844448,23312071,11162928,10555957,20589634,12925993,21192670,10377225,31092862,12413831,20839299,10451553,12759331,25099693,21612285,20511291,12579577,21554075,12613043,17601655,14664857,12699377,20942836,12077850,19857971,20937559,9275094,10803607,21117661,12116383,30149188,12071661,16439113,9875295,11518614,10630711,14667221,12579579,9029508,7570711,12772312,12630884,24160181,9071738,15157104,12833263,20180264,14696074,23955176,20839830,10727269,1871786,11204627,12736688,12833537,24063761,8962920,14584960,12502357,11099639,21321128,12569455,11380259,11948588,11786020,14640544,19762243,23020867,20608691,23694906,19843074,10406482,12699383,21374633,11871136,17400923,26551865,19941322,10028702,7286201,29557271,3955129,21038436,23137989,19891004,18026938,15123288,6267445,24689804,23725291,27589781,14741014,3630007,7731955,20387803,2925625,10369411,12506394,7824520,32652920,15767587,25349983,10552911,10942316,21942536,2213825,28805144,20175582,9492339,15789567,1931126,21315613,17173372,7150748,8391709,12682912,19938833,179639,15743715,28889350,23726343,21595427,1445887,10930140,22847637,9770207,14692768,22113809,12518232,19535082,11076692,15694777,8650702,20199097,11296624,9022746,30986440,21227405,11922773,26575935,7058286,12669775,20949512,18626116,16398133,11353539,21075131,30218199,8743443,27156127,10994514,11790143,19373827,14712934,9241826,14517908,23420697,28328298,25587872,3905370,2769689,18172994,11107321,14741036,15253041,11226833,12767230,32999147,760355,17259589,12014971,26598992,10691688,8399136,21783746,9570087,19693787,2275977,23268595,25180905,25030373,18313305,20947335,19894688,10896109,19863142,11384241,12658702,25060147,19598265,10559464,22890857,26588766,18921983,10072891,6834826,16099765,9439733,23035525,16844742,21714553,7411555,10026940,2432356,18691152,28882502,20877819,2601332,11689070,16351736,11457149,11020294,20025931,22877232,11758802,25761118,12656634,25921217,11818562,11708930,6506576,19894723,18317942,11325590,9139802,21985436,21133348,21085738,12866082,25076043,12606005,32899216,27507430,18785725,30553876,30924335,27221711,30018014,12123109,24615679,19063592,20231885,28854402,24507131,3600604,12139447,33799482,16513342,21384831,8049135,15127823,20526495,8593856,11306352,26615694,28549265,14564443,8547251,3390222,25061691,18320337,23532250,25681551,26757914,23157418,23975271,8593873,12069620,3020601,11027358,16279785,30935971,11087673,21466196,26450350,9533868,24434499,30811808,17690926,24548648,3708019,33402049,11906282,15669333,12197663,11803545,10645481,28842010,20958252,22183544,16234175,24256082,21132839,10400338,22183551,31437548,6510599,27504698,7526397,9353176,1895295,23938954,11003145,25123650,28527150,28776988,25014157,31532675,7509256,18678925,25748991,9600906,3748009,22061644,7342720,20466011,9721254,26400829,12616628,18989626,25098505,17676936,9254912,17092915,26626851,30744198,25003283,29772410,8205232,4004954,12546558,9795281,22089882,12077320,17514577,15290790,7769464,12672236,9379435,12615097,27770746,21689932,20599778,25119978,8664164,24564918,27367662,18834163,12653517,12002784,8354873,30731268,12236347,30143207,19689279,27832947,22453607,26636209,16833982,11358696,18959400,15282407,11241219,18591792,21469160,20931118,26188794,28564537,33112150,25266275,32484689,317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894602,22276614,13723200,27924312,9025766,13735660,31188006,21825505,27492236,13623720,21024867,13556605,9917308,33431030,13596799,2633192,20282423,13415566,13117345,25254318,20250007,13689984,13691222,13161993,15432031,14737355,26414214,24063742,13408838,19281364,14372151,28514424,28514419[uid]

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Prediction of ligand binding affinity and orientation of xenoestrogens to the estrogen receptor by molecular dynamics simulations and the linear interaction energy method.

van Lipzig MM, ter Laak AM, Jongejan A, Vermeulen NP, Wamelink M, Geerke D, Meerman JH. van Lipzig MM, et al. J Med Chem. 2004 Feb 12;47(4):1018-30. doi: 10.1021/jm0309607. J Med Chem. 2004. PMID: 14761204

Examining methods for calculations of binding free energies: LRA, LIE, PDLD-LRA, and PDLD/S-LRA calculations of ligands binding to an HIV protease.

Sham YY, Chu ZT, Tao H, Warshel A. Sham YY, et al. Proteins. 2000 Jun 1;39(4):393-407. Proteins. 2000. PMID: 10813821

Estrogen receptor subtype-selective ligands: asymmetric synthesis and biological evaluation of cis- and trans-5,11-dialkyl- 5,6,11, 12-tetrahydrochrysenes.

Meyers MJ, Sun J, Carlson KE, Katzenellenbogen BS, Katzenellenbogen JA. Meyers MJ, et al. J Med Chem. 1999 Jul 1;42(13):2456-68. doi: 10.1021/jm990101b. J Med Chem. 1999. PMID: 10395487

What determines the van der Waals coefficient beta in the LIE (linear interaction energy) method to estimate binding free energies using molecular dynamics simulations?

Wang W, Wang J, Kollman PA. Wang W, et al. Proteins. 1999 Feb 15;34(3):395-402. Proteins. 1999. PMID: 10024025

Free energy simulations and MM-PBSA analyses on the affinity and specificity of steroid binding to antiestradiol antibody.

Laitinen T, Kankare JA, Peräkylä M. Laitinen T, et al. Proteins. 2004 Apr 1;55(1):34-43. doi: 10.1002/prot.10399. Proteins. 2004. PMID: 14997538

Ab initio quantum mechanical study of the binding energies of human estrogen receptor alpha with its ligands: an application of fragment molecular orbital method.

Fukuzawa K, Kitaura K, Uebayasi M, Nakata K, Kaminuma T, Nakano T. Fukuzawa K, et al. J Comput Chem. 2005 Jan 15;26(1):1-10. doi: 10.1002/jcc.20130. J Comput Chem. 2005. PMID: 15521089

Insights into ligand selectivity in estrogen receptor isoforms: molecular dynamics simulations and binding free energy calculations.

Zeng J, Li W, Zhao Y, Liu G, Tang Y, Jiang H. Zeng J, et al. J Phys Chem B. 2008 Mar 6;112(9):2719-26. doi: 10.1021/jp710029r. Epub 2008 Feb 12. J Phys Chem B. 2008. PMID: 18266357

Use of binding energy in comparative molecular field analysis of isoform selective estrogen receptor ligands.

Wolohan P, Reichert DE. Wolohan P, et al. J Mol Graph Model. 2004 Sep;23(1):23-38. doi: 10.1016/j.jmgm.2004.03.002. J Mol Graph Model. 2004. PMID: 15331051

Free energies of binding of polychlorinated biphenyls to the estrogen receptor from a single simulation.

Oostenbrink C, van Gunsteren WF. Oostenbrink C, et al. Proteins. 2004 Feb 1;54(2):237-46. doi: 10.1002/prot.10558. Proteins. 2004. PMID: 14696186

Simulation of the different biological activities of diethylstilbestrol (DES) on estrogen receptor alpha and estrogen-related receptor gamma.

Nam K, Marshall P, Wolf RM, Cornell W. Nam K, et al. Biopolymers. 2003 Jan;68(1):130-8. doi: 10.1002/bip.10307. Biopolymers. 2003. PMID: 12579585

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