mrgunner
commented
8 years ago when you say ligand removed - is this removed with optimization or just removed and everything kept the same. I would like to get structures that provide a good picture of the apo to see if the ∆structure induces ∆protonation independent of the ligand (if/when possible)
For loops modeled - is this for places where the crystal structure has breaks?
FYI right now we will rebuild all protons and remove all waters. So they are harmless but won’t be used by us now. For loops far from the inhibitor. We will use them but I would be very surprised if they had any impact on the MCCE results (so nice but not essential)
On May 4, 2016, at 12:55 PM, Steven Albanese notifications@github.com wrote:
Checking in PDBs for all of the FDA-approved ligands with their approved targets, if available. There are four PDBs each: (1) unchanged from rcsb (2) fixed- has hydrogens and loops modeled in (3) apo- has the ligand removed, but retains crystal waters (4) apo no waters- has no ligand or crystal waters
Just a note: some inhibitors (like Sorafenib) have a large number of targets, so I'm still working on putting together a comprehensive list that makes sense for those! Let me know if you're interested in having ALL of the targets for a given ligand, I can put those together easily as well using the automated PDB query
You can view, comment on, or merge this pull request online at:
https://github.com/choderalab/mcce-charges/pull/22 https://github.com/choderalab/mcce-charges/pull/22 Commit Summary
adding the PDBs for use File Changes
A pdbs/Afatinib-EGFR/4G5J.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-0 (2707) A pdbs/Afatinib-EGFR/4G5J_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-1 (5346) A pdbs/Afatinib-EGFR/4G5J_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-2 (5244) A pdbs/Afatinib-EGFR/4G5J_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-3 (5165) A pdbs/Afatinib-EGFR/4G5P.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-4 (4944) A pdbs/Afatinib-EGFR/4G5P_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-5 (5245) A pdbs/Afatinib-EGFR/4G5P_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-6 (5211) A pdbs/Afatinib-EGFR/4G5P_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-7 (5168) A pdbs/Alectinib-ALK/3AOX.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-8 (2699) A pdbs/Alectinib-ALK/3AOX_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-9 (5716) A pdbs/Alectinib-ALK/3AOX_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-10 (5664) A pdbs/Alectinib-ALK/3AOX_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-11 (4955) A pdbs/Axitinib-VEGFR1/4AG8.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-12 (2768) A pdbs/Axitinib-VEGFR1/4AG8_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-13 (5780) A pdbs/Axitinib-VEGFR1/4AG8_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-14 (5752) A pdbs/Axitinib-VEGFR1/4AG8_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-15 (4773) A pdbs/Axitinib-VEGFR1/4AGC.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-16 (2654) A pdbs/Axitinib-VEGFR1/4AGC_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-17 (5394) A pdbs/Axitinib-VEGFR1/4AGC_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-18 (5366) A pdbs/Axitinib-VEGFR1/4AGC_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-19 (4912) A pdbs/Bosutinib-BCR-ABL/3UE4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-20 (4669) A pdbs/Bosutinib-BCR-ABL/3UE4_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-21 (4665) A pdbs/Bosutinib-BCR-ABL/3UE4_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-22 (4628) A pdbs/Bosutinib-BCR-ABL/3UE4_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-23 (4360) A pdbs/Ceritinib-ALK/4MKC.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-24 (2665) A pdbs/Ceritinib-ALK/4MKC_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-25 (5419) A pdbs/Ceritinib-ALK/4MKC_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-26 (5369) A pdbs/Ceritinib-ALK/4MKC_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-27 (4843) A pdbs/Cobimetinib-MEK/4AN2.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-28 (2376) A pdbs/Cobimetinib-MEK/4AN2_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-29 (4631) A pdbs/Cobimetinib-MEK/4AN2_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-30 (4569) A pdbs/Cobimetinib-MEK/4AN2_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-31 (4454) A pdbs/Cobimetinib-MEK/4LMN.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-32 (2423) A pdbs/Cobimetinib-MEK/4LMN_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-33 (5104) A pdbs/Cobimetinib-MEK/4LMN_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-34 (5037) A pdbs/Cobimetinib-MEK/4LMN_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-35 (5037) A pdbs/Crizotinib-ALK/2XP2.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-36 (2494) A pdbs/Crizotinib-ALK/2XP2_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-37 (5379) A pdbs/Crizotinib-ALK/2XP2_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-38 (5349) A pdbs/Crizotinib-ALK/2XP2_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-39 (4847) A pdbs/Crizotinib-ALK/2YFX.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-40 (2602) A pdbs/Crizotinib-ALK/2YFX_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-41 (5587) A pdbs/Crizotinib-ALK/2YFX_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-42 (5557) A pdbs/Crizotinib-ALK/2YFX_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-43 (4845) A pdbs/Crizotinib-ALK/4ANQ.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-44 (2587) A pdbs/Crizotinib-ALK/4ANQ_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-45 (5515) A pdbs/Crizotinib-ALK/4ANQ_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-46 (5485) A pdbs/Crizotinib-ALK/4ANQ_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-47 (4857) A pdbs/Crizotinib-ALK/4ANS.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-48 (2588) A pdbs/Crizotinib-ALK/4ANS_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-49 (5516) A pdbs/Crizotinib-ALK/4ANS_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-50 (5486) A pdbs/Crizotinib-ALK/4ANS_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-51 (4855) A pdbs/Crizotinib-MET/2WGJ.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-52 (2554) A pdbs/Crizotinib-MET/2WGJ_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-53 (5289) A pdbs/Crizotinib-MET/2WGJ_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-54 (5259) A pdbs/Crizotinib-MET/2WGJ_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-55 (4718) A pdbs/Dabrafenib-BRAF/4XV2.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-56 (4173) A pdbs/Dabrafenib-BRAF/4XV2_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-57 (4495) A pdbs/Dabrafenib-BRAF/4XV2_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-58 (4459) A pdbs/Dabrafenib-BRAF/4XV2_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-59 (4374) A pdbs/Dabrafenib-BRAF/5CSW.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-60 (4225) A pdbs/Dabrafenib-BRAF/5CSW_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-61 (4458) A pdbs/Dabrafenib-BRAF/5CSW_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-62 (4422) A pdbs/Dabrafenib-BRAF/5CSW_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-63 (4394) A pdbs/Dabrafenib-BRAF/5HIE.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-64 (8544) A pdbs/Dabrafenib-BRAF/5HIE_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-65 (4289) A pdbs/Dabrafenib-BRAF/5HIE_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-66 (4253) A pdbs/Dabrafenib-BRAF/5HIE_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-67 (4192) A pdbs/Dasatinib-BCR-ABL/2GQG.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-68 (4995) A pdbs/Dasatinib-BCR-ABL/2GQG_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-69 (4931) A pdbs/Dasatinib-BCR-ABL/2GQG_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-70 (4897) A pdbs/Dasatinib-BCR-ABL/2GQG_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-71 (4461) A pdbs/Dasatinib-BCR-ABL/4XEY.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-72 (5253) A pdbs/Dasatinib-BCR-ABL/4XEY_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-73 (4440) A pdbs/Dasatinib-BCR-ABL/4XEY_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-74 (4406) A pdbs/Dasatinib-BCR-ABL/4XEY_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-75 (4406) A pdbs/Erlotinib-EGFR/1M17.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-76 (2580) A pdbs/Erlotinib-EGFR/1M17_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-77 (5307) A pdbs/Erlotinib-EGFR/1M17_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-78 (5278) A pdbs/Erlotinib-EGFR/1M17_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-79 (5217) A pdbs/Erlotinib-EGFR/4HJO.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-80 (2298) A pdbs/Erlotinib-EGFR/4HJO_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-81 (4728) A pdbs/Erlotinib-EGFR/4HJO_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-82 (4699) A pdbs/Erlotinib-EGFR/4HJO_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-83 (4596) A pdbs/Gefitinib-EGFR/2ITO.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-84 (2520) A pdbs/Gefitinib-EGFR/2ITO_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-85 (5355) A pdbs/Gefitinib-EGFR/2ITO_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-86 (5324) A pdbs/Gefitinib-EGFR/2ITO_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-87 (5221) A pdbs/Gefitinib-EGFR/2ITY.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-88 (2482) A pdbs/Gefitinib-EGFR/2ITY_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-89 (5299) A pdbs/Gefitinib-EGFR/2ITY_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-90 (5268) A pdbs/Gefitinib-EGFR/2ITY_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-91 (5210) A pdbs/Gefitinib-EGFR/2ITZ.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-92 (2548) A pdbs/Gefitinib-EGFR/2ITZ_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-93 (5460) A pdbs/Gefitinib-EGFR/2ITZ_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-94 (5428) A pdbs/Gefitinib-EGFR/2ITZ_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-95 (5232) A pdbs/Gefitinib-EGFR/3UG2.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-96 (2484) A pdbs/Gefitinib-EGFR/3UG2_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-97 (5412) A pdbs/Gefitinib-EGFR/3UG2_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-98 (5369) A pdbs/Gefitinib-EGFR/3UG2_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-99 (5203) A pdbs/Gefitinib-EGFR/4I22.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-100 (2621) A pdbs/Gefitinib-EGFR/4I22_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-101 (5543) A pdbs/Gefitinib-EGFR/4I22_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-102 (5502) A pdbs/Gefitinib-EGFR/4I22_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-103 (5099) A pdbs/Gefitinib-EGFR/4WKQ.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-104 (2539) A pdbs/Gefitinib-EGFR/4WKQ_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-105 (5669) A pdbs/Gefitinib-EGFR/4WKQ_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-106 (5625) A pdbs/Gefitinib-EGFR/4WKQ_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-107 (5261) A pdbs/Idelalisib-PI3K/4XE0.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-108 (6857) A pdbs/Idelalisib-PI3K/4XE0_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-109 (15498) A pdbs/Idelalisib-PI3K/4XE0_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-110 (15467) A pdbs/Idelalisib-PI3K/4XE0_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-111 (14794) A pdbs/Imatinib-BCR-ABL/2HYY.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-112 (8865) A pdbs/Imatinib-BCR-ABL/2HYY_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-113 (4462) A pdbs/Imatinib-BCR-ABL/2HYY_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-114 (4424) A pdbs/Imatinib-BCR-ABL/2HYY_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-115 (4270) A pdbs/Imatinib-BCR-ABL/3PYY.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-116 (4793) A pdbs/Imatinib-BCR-ABL/3PYY_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-117 (4782) A pdbs/Imatinib-BCR-ABL/3PYY_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-118 (4709) A pdbs/Imatinib-BCR-ABL/3PYY_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-119 (4351) A pdbs/Lapatinib-EGFR/1XKK.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-120 (2431) A pdbs/Lapatinib-EGFR/1XKK_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-121 (5408) A pdbs/Lapatinib-EGFR/1XKK_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-122 (5358) A pdbs/Lapatinib-EGFR/1XKK_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-123 (5126) A pdbs/Lenvatinib-VEGFR1/3WZD.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-124 (2624) A pdbs/Lenvatinib-VEGFR1/3WZD_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-125 (5200) A pdbs/Lenvatinib-VEGFR1/3WZD_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-126 (5111) A pdbs/Lenvatinib-VEGFR1/3WZD_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-127 (4471) A pdbs/Nilotinib-BCR-ABL/3CS9.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-128 (8855) A pdbs/Nilotinib-BCR-ABL/3CS9_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-129 (4668) A pdbs/Nilotinib-BCR-ABL/3CS9_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-130 (4628) A pdbs/Nilotinib-BCR-ABL/3CS9_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-131 (4330) A pdbs/Osimertinib-EGFR/4ZAU.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-132 (2260) A pdbs/Osimertinib-EGFR/4ZAU_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-133 (5212) A pdbs/Osimertinib-EGFR/4ZAU_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-134 (5175) A pdbs/Osimertinib-EGFR/4ZAU_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-135 (5162) A pdbs/Palbociclib-CDK6/2EUF.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-136 (4132) A pdbs/Palbociclib-CDK6/2EUF_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-137 (8936) A pdbs/Palbociclib-CDK6/2EUF_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-138 (8893) A pdbs/Palbociclib-CDK6/2EUF_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-139 (8889) A pdbs/Pazopanib-VEGFR1/3CJG.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-140 (2470) A pdbs/Pazopanib-VEGFR1/3CJG_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-141 (4935) A pdbs/Pazopanib-VEGFR1/3CJG_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-142 (4894) A pdbs/Pazopanib-VEGFR1/3CJG_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-143 (4545) A pdbs/Regorafenib-VEGFR1/2QU5.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-144 (2412) A pdbs/Regorafenib-VEGFR1/2QU5_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-145 (4737) A pdbs/Regorafenib-VEGFR1/2QU5_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-146 (4705) A pdbs/Regorafenib-VEGFR1/2QU5_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-147 (4686) A pdbs/Sorafenib-VEGFR1/3WZE.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-148 (2603) A pdbs/Sorafenib-VEGFR1/3WZE_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-149 (5185) A pdbs/Sorafenib-VEGFR1/3WZE_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-150 (5141) A pdbs/Sorafenib-VEGFR1/3WZE_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-151 (4819) A pdbs/Sorafenib-VEGFR1/4ASD.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-152 (2875) A pdbs/Sorafenib-VEGFR1/4ASD_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-153 (5997) A pdbs/Sorafenib-VEGFR1/4ASD_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-154 (5965) A pdbs/Sorafenib-VEGFR1/4ASD_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-155 (4905) A pdbs/Sunitinib-VEGFR1/4AGD.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-156 (2580) A pdbs/Sunitinib-VEGFR1/4AGD_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-157 (5182) A pdbs/Sunitinib-VEGFR1/4AGD_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-158 (5153) A pdbs/Sunitinib-VEGFR1/4AGD_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-159 (4891) A pdbs/Tofacitinib-JAK3/3LXK.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-160 (2519) A pdbs/Tofacitinib-JAK3/3LXK_fixed_ph7.4.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-161 (5333) A pdbs/Tofacitinib-JAK3/3LXK_fixed_ph7.4_apo.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-162 (5310) A pdbs/Tofacitinib-JAK3/3LXK_fixed_ph7.4_apo_nowater.pdb https://github.com/choderalab/mcce-charges/pull/22/files#diff-163 (4532) Patch Links:
https://github.com/choderalab/mcce-charges/pull/22.patch https://github.com/choderalab/mcce-charges/pull/22.patch https://github.com/choderalab/mcce-charges/pull/22.diff https://github.com/choderalab/mcce-charges/pull/22.diff — You are receiving this because you are subscribed to this thread. Reply to this email directly or view it on GitHub https://github.com/choderalab/mcce-charges/pull/22
steven-albanese
Checking in PDBs for all of the FDA-approved ligands with their approved targets, if available. There are four PDBs each: (1) unchanged from rcsb (2) fixed- has hydrogens and loops modeled in (3) apo- has the ligand removed, but retains crystal waters (4) apo no waters- has no ligand or crystal waters
Just a note: some inhibitors (like Sorafenib) have a large number of targets, so I'm still working on putting together a comprehensive list that makes sense for those! Let me know if you're interested in having ALL of the targets for a given ligand, I can put those together easily as well using the automated PDB query