As of May 17th, 2017:

3.5 billion docking jobs have been submitted

2 billion results have been received

As of February 1st, 2017:

2.56 billion docking jobs have been submitted

Virtual screening of 427 different target sites versus 6 million compounds

As of November 18th, 2016:

We have received 100% of the results for Experiments 1A, 1B (NS5 class), 2A, 2B, and 2C (NS3 helicase class).

We have received 46% of the results for Experiment 3A (NS1 class).

1A = 132 million docking jobs

1B = 42 million

2A = 354 million

2B = 360 million

2C = 54 million

3A = we have received 160 million out of 348 million.

In total, we have submitted ~ 1.6 billion docking jobs, and we have already received ~ 1.1 billion results.

As of June 19th, 2016:

The results from the first 3 experiments involve 84 different target sites (74 unique targets, mostly from Dengue Virus, HCV, Yellow Fever Virus, Japanese Encephalitis Virus and Zika Virus). Thus, as of June 19th, 2016, we have received 254 million different docking results (in approximately 2 months).

Experiment 1A = Virtual Screening against the NS5 class (first binding site)

The non-structural protein 5 (NS5) of flaviviruses is the most conserved amongst the viral proteins. The N-terminal domain of NS5 possesses the methyltransferase and guanylyltransferase activities necessary for forming mature RNA cap structures.

The best NS5 homology model for ZIKV was built using the full-length Japanese encephalitis virus NS5 as a template (PDB ID: 4K6M).
The first binding site for NS5 is related to the ligand 2′-deoxy-2′-fluoro-2′-methyluridine 5′-(trihydrogen diphosphate) position (PDB ID: 4WTG).

Thus, as of July 19th, 2016, we have received 99.75% of the results for Experiment 1A, corresponding to 125,688,000 docking jobs.

Libraries
Batch Range LibraryNickname
1 – 21 Drugs_and_Leads_FromPrestwick_MicroSourceSpectrum_FDA_and_NIHclinicalCollection
22 – 4956 Enamine_Full_Library
4957 – 8127 Vitas-M Labs_Full_Library
8128 – 10269 ChemBridge_Full_Library
10270 – 11340 Asinex_Full_Library
11341 – 12012 NCI_Full_Library
12013 – 19026 Otava_Full_Library (note: only 1,000 ligands/batch)

Batches for all other libraries have ~10,000 ligands/batch

Targets

Targets employed to virtual screening:

NS5 Hepatitis C virus complexed with Sofosbuvir and RNA
NS5 Homology Model of Zika virus minimized
RNA polymerase Hepatitis C virus,  Chain A
RNA polymerase, Hepatitis C virus, Chain B
 RNA polymerase, Hepatitis C virus,complexed with RNA and Mn, Chain A
RNA polymerase, Hepatitis C virus, complexed with RNA and Mn, Chain B
 RNA polymerase, West Nile virus
NS5B Hepatitis C virus complex with 1,5 benzodiazepine inhibitor 6, Chain A, Configuration B
NS5B Hepatitis C virus complex with 1,5 benzodiazepine inhibitor 6, Chain A
NS5B Hepatitis C virus complex with 1,5 benzodiazepine inhibitor 6, Chain B
NS5B Hepatitis C virus complex with 1,5 benzodiazepine inhibitor 6, Chain C
RNA polymerase, Hepatitis C virus,  without RNA
 RNA polymerase,Hepatitis C virus, with RNA
NS5 Japanese encephalitis virus, complexed with S-ADENOSYL-L-HOMOCYSTEINE, Chain A
NS5 Japanese encephalitis virus, complexed with S-ADENOSYL-L-HOMOCYSTEINE, Chain B
NS5 Dengue virus, complexed with S-ADENOSYL-L-HOMOCYSTEINE
NS5 Dengue virus, complexed with S-ADENOSYL-L-HOMOCYSTEINE
NS5 Dengue virus, complexed with S-ADENOSYL-L-HOMOCYSTEINE and GTP
NS5 Hepatitis C virus complexed with Sofosbuvir and without RNA
NS5 Homology Model of Zika virus align to template 4k6m
NS5 Homology Model of Zika virus align to template 4v0r

These images below show a “positive control” experiment.  This experiment demonstrates that we can accurately predict/reproduce the specific way that a known inhibitor binds to this important drug target, NS5 class.

Positive control for NS5 class of target: Alpha test

 crystallographic binding mode: ball-and-stick, dark purple carbon atoms;

predicted binding mode: green carbons atoms

Positive control for NS5 class of target: Beta test

Positive control for NS5 class of target: Beta test

 crystallographic binding mode: purple carbon atoms,

predicted binding mode: cyan carbon atoms

Experiment 1B = Virtual Screening against the NS5 class (refined NS5 and second binding site)

The protein structure NS5, obtained by homology modeling, was refined using the server KobaMIN. This refinement provided us a better structure, decreasing the number steric overlaps, bad bonds/angles, Ramachandran outliers, twisted peptides…

The second binding site of NS5 is related to the ligand S-Adenosyl Methionine (SAM) position in the binding site.

Thus, as of July 19th, 2016, we have received 87% of the results for Experiment 1B, corresponding to ~ 42 million docking jobs.

Libraries
Batch Range Library Nickname
19027 – 19034 Drugs_and_Leads_FromPrestwick_MicroSourceSpectrum_FDA_and_NIHclinicalCollection
19035 – 20914 Enamine_Full_Library
20915 – 22122 Vitas-M Labs_Full_Library
22123 – 22938 ChemBridge_Full_Library
22939 – 23346 Asinex_Full_Library
23347 – 23602 NCI_Full_Library
23603 – 23874 Otava_Full_Library (note: now has 10,000 ligands/batch)

 

Targets

Targets employed to virtual screening:

NS5 Model Refined
NS5 Japanese encephalitis virus, complexed with S-ADENOSYL-L-HOMOCYSTEINE, Chain A, binding site 2
NS5 Japanese encephalitis virus, complexed with S-ADENOSYL-L-HOMOCYSTEINE, Chain B, binding site 2
NS5 Dengue virus, complexed with S-ADENOSYL-L-HOMOCYSTEINE, binding site 2
NS5 Dengue virus, complexed with S-ADENOSYL-L-HOMOCYSTEINE, binding site 2
NS5 Dengue virus, complexed with S-ADENOSYL-L-HOMOCYSTEINE and GTP, binding site 2
NS5 Homology Model of Zika virus align to template 4k6m, binding site 2
NS5 Homology Model of Zika virus align to template 4v0r, binding site 2

Experiment 2A = Virtual Screening against the NS3 helicase class (first binding site).

The NS3 helicase domain exhibits intrinsic nucleoside triphosphatase activity (upon stimulation by RNA), which then provides the chemical energy to unwind viral RNA replication intermediates to facilitate replication of the viral genome together with RNA-dependent RNA polymerase (NS5). Given its essential role in genome replication, ZIKV NS3 helicase could be an attractive target for drug development against ZIKV.

The NS3 helicase crystallographic structure was solved in May 12th 2016 (PDB ID: 5JMT)

The NS3 helicase  structure revealed a conserved triphosphate pocket critical for nonspecific hydrolysis of nucleoside triphosphates across multiple flavivirus species. A positive-charged tunnel has been identified in the viral helicase, which is potentially responsible for accommodating the RNA.

The first binding site of NS3 is related to the nucleic acid binding site.

Thus, as of July 19th, 2016, we have received 26% of the results for Experiment 2A, corresponding to ~ 86 million docking jobs.

Libraries
Batch Range LibraryNickname
23875 – 23929 Drugs_and_Leads_FromPrestwick_MicroSourceSpectrum_FDA_and_NIHclinicalCollection
23930 – 36854 Enamine_Full_Library
36855 – 45159 Vitas-M Labs_Full_Library
45160 – 50769 ChemBridge_Full_Library
50770 – 53574 Asinex_Full_Library
53575 – 55334 NCI_Full_Library
55335 – 57204 Otava_Full_Library (note: now has 10,000 ligands/batch)
Targets

Targets employed to virtual screening:

5jmt ZIKV NS3helicase A
5jmt ZIKV NS3helicase B
1yks YFV NS3hlcs
2jlu DV4 NS3hlcs ssRNA chA
2jlu DV4 NS3hlcs ssRNA chB
2jlv_DV4_NS3hlcs_ssRNA_chA_A
2jlv_DV4_NS3hlcs_ssRNA_chA_B
2jlv_DV4_NS3_ssRNAdelMn_chA_A
2jlv_DV4_NS3_ssRNAdelMn_chA_B
2jlv_DV4_NS3_ssRNAdelMn_chB_A
2jlv_DV4_NS3_ssRNAdelMn_chB_B
2jlw_Deng4_NS3_ssRNA2_chA
2jlw_Deng4_NS3_ssRNA2_chB
2jlx_DV4_NS3hlcs_RNAdelMnChA
2jlx_DV4_NS3hlcs_RNAdelMnChB
2jlx_DV4_NS3hlcs_ssRNA_chA
2jlx_DV4_NS3hlcs_ssRNA_chB
2jly_DV4_NS3hlcs_ssRNA_chA_A
2jly_DV4_NS3hlcs_ssRNA_chA_B
2jly_DV4_NS3hlcs_ssRNAdelMn_chA_A
2jly_DV4_NS3hlcs_ssRNAdelMn_chA_B
2jly_DV4_NS3hlcs_ssRNAdelMn_chB
2jlz_DV4_NS3hlcs_ssRNA_chA
2jlz_DV4_NS3_ssRNAdelMn_chA
2whx_DV_NS3hlcsDelMn_PRwasBnd
2whx_DV_NS3hlcs_PRwasPepBnd
2z83_JEV_NS3hlcs
1a1v_HCV_NS3hlcs_ssDNA
3kqh_HCV_NS3hlcs_ssDNA_chA
3kqh_HCV_NS3hlcs_ssDNA_chB
3kqk_HCV_NS3hlcs_chA
3kqk_HCV_NS3hlcs_chB
3kql_HCV_NS3hlcs_chnA
3kql_HCV_NS3hlcs_chnB
3kql_HCV_NS3hlcsDelMg_chA
3kql_HCV_NS3hlcsDelMgChB
3kqn_HCV_NS3hlcs_ssDNA_DelMn
3kqn_HCV_NS3hlcs_ssDNA
3o8b_HCV_NS3hlcs_PR_chA
3o8b_HCV_NS3hlcs_PR_chB
3o8c_HCV_NS3_Hlcs_PR_chB
3o8c_HCV_NS3_ssRNA_wPR_chA
4wxp_HCV_NS3helcs_A
1nkt_Mtb_SecA_chnA
1nkt_Mtb_SecA_chnB
1nkt_Mtb_SecA_DelMg_chnA
1nkt_Mtb_SecA_DelMg_chnB
4uaq_Mtb_SecA2
3mla_Anthrax_BaNadDApochB
3mla_Anthrax_BaNadD_chA_A
3mla_Anthrax_BaNadD_chA_B
4es6_PAeru_HemD_A
4es6_PAeru_HemD_B
4nl4_Klebp_PriA_A
4nl4_Klebp_PriA_B
Results

Results available for the scientific community

Results of Virtual Screening of ZIKV NS3 helicase  (PDB ID: 5jmt) with the databases: Prestwick + MicroSource Spectrum + FDA approved + NIH clinical collection set

ZIKA_000023875_x5jmt_ZIKV_NS3helicase_A_results.tgz

The ZIKV NS3 helicase structure is available below.

x5jmt_ZIKV_NS3helicase_A.pdbqt

ZIKV NS3 helicase with three candidate inhibitors selected by VS, shown as solvent-accessible surfaces, with different shades of green. The identification of these candidates and the video were made by Dr. Alexander L. Perryman.

Experiment 2B = Virtual Screening against the NS3 helicase class (second binding site)

The second binding site of NS3 is related to the ATP binding site.

Libraries
Batch Range LibraryNickname
57205 – 57259 Drugs_and_Leads_FromPrestwick_MicroSourceSpectrum_FDA_and_NIHclinicalCollection
57260 – 70184 Enamine_Full_Library
70185 – 78489 Vitas-M Labs_Full_Library
78490 – 84099 ChemBridge_Full_Library
84100 – 86904 Asinex_Full_Library
86905 – 88664 NCI_Full_Library
88665 – 90534 Otava_Full_Library (note: now has 10,000 ligands/batch)
Targets

Targets employed to virtual screening:

5jmt_ZIKV_NS3helicase_A_s2
5jmt_ZIKV_NS3helicase_B_s2
2jlu_DV4_NS3hlcs_ssRNA_chA_s2
2jlu_DV4_NS3hlcs_ssRNA_chB_s2
2jlv_DV4_NS3hlcs_ssRNA_chA_A_s2
2jlv_DV4_NS3hlcs_ssRNA_chA_B_s2
2jlv_DV4_NS3_ssRNAdelMn_chA_A_s2
2jlv_DV4_NS3_ssRNAdelMn_chA_B_s2
2jlv_DV4_NS3_ssRNAdelMn_chB_A_s2
2jlv_DV4_NS3_ssRNAdelMn_chB_B_s2
2jlw_Deng4_NS3_ssRNA2_chA_s2
2jlw_Deng4_NS3_ssRNA2_chB_s2
2jlx_DV4_NS3hlcs_RNAdelMnChA_s2
2jlx_DV4_NS3hlcs_RNAdelMnChB_s2
2jlx_DV4_NS3hlcs_ssRNA_chA_s2
2jlx_DV4_NS3hlcs_ssRNA_chB_s2
2jly_DV4_NS3hlcs_ssRNA_chA_A_s2
2jly_DV4_NS3hlcs_ssRNA_chA_B_s2
2jly_DV4_NS3hlcs_ssRNAdelMn_chA_A_s2
2jly_DV4_NS3hlcs_ssRNAdelMn_chA_B_s2
2jly_DV4_NS3hlcs_ssRNAdelMn_chB_s2
2jlz_DV4_NS3hlcs_ssRNA_chA_s2
2jlz_DV4_NS3_ssRNAdelMn_chA_s2
2whx_DV_NS3hlcsDelMn_PRwasBnd_s2
2whx_DV_NS3hlcs_PRwasPepBnd_s2
1yks_YFV_NS3hlcs_s2
2z83_JEV_NS3hlcs_s2
1a1v_HCV_NS3hlcs_ssDNA_s2
4wxp_HCV_NS3helcs_A_s2
3kqh_HCV_NS3hlcs_ssDNA_chA_s2
3kqh_HCV_NS3hlcs_ssDNA_chB_s2
3kqk_HCV_NS3hlcs_chA_s2
3kqk_HCV_NS3hlcs_chB_s2
3kql_HCV_NS3hlcs_chnA_s2
3kql_HCV_NS3hlcs_chnB_s2
3kql_HCV_NS3hlcsDelMg_chA_s2
3kql_HCV_NS3hlcsDelMgChB_s2
3kqn_HCV_NS3hlcs_ssDNA_DelMn_s2
3kqn_HCV_NS3hlcs_ssDNA_s2
3o8b_HCV_NS3hlcs_PR_chA_s2
3o8b_HCV_NS3hlcs_PR_chB_s2
3o8c_HCV_NS3_Hlcs_PR_chB_s2
3o8c_HCV_NS3_ssRNA_wPR_chA_s2
1nkt_Mtb_SecA_chnA_s2
1nkt_Mtb_SecA_chnB_s2
1nkt_Mtb_SecA_DelMg_chnA_s2
1nkt_Mtb_SecA_DelMg_chnB_s2
4uaq_Mtb_SecA2_s2
4es6_PAeru_HemD_A_s2
4es6_PAeru_HemD_B_s2
4nl4_Klebp_PriA_A_s2
4nl4_Klebp_PriA_B_s2
3mla_Anthrax_BaNadDApochB_s2
3mla_Anthrax_BaNadD_chA_A_s2
3mla_Anthrax_BaNadD_chA_B_s2

Experiment 2C = Virtual Screening against the NS3 helicase class (first and second binding site)

New NS3 helicase crystallographic structures were solved (PDB ID: 5GJB, 5GJC, 5JRZ). The dockings were performed for both binding sites.

Libraries
Batch Range LibraryNickname
90535 – 90543 Drugs_and_Leads_FromPrestwick_MicroSourceSpectrum_FDA_and_NIHclinicalCollection
90544 – 92658 Enamine_Full_Library
92659 – 94017 Vitas-M Labs_Full_Library
94018 – 94935 ChemBridge_Full_Library
94936 – 95394 Asinex_Full_Library
95395 – 95682 NCI_Full_Library
95683 – 95988 Otava_Full_Library (note: now has 10,000 ligands/batch)
Targets

Targets employed to virtual screening:

x5gjb_ZIKV_NS3helicase_w_ssRNA.pdbqt
x5gjc_ZIKV_NS3helicase_wMn.pdbqt
x5jrz_NS3_ZIKV_FrPolynesia_A.pdbqt
x5jrz_NS3_ZIKV_FrPolynesia_B.pdbqt
x5gjc_ZIKV_NS3helicase_DelMn_s2.pdbqt
x5gjc_ZIKV_NS3helicase_wMn_s2.pdbqt
x5jrz_NS3_ZIKV_FrPolynesia_A_s2.pdbqt
x5jrz_NS3_ZIKV_FrPolynesia_B_s2.pdbqt
x5gjb_ZIKV_NS3helicase_w_ssRNA_s2.pdbqt

Experiment 3A = Virtual Screening against the NS1 class (first to fifth binding site)

Glycoprotein NS1, present in all flaviviruses, appears to be essential for virus viability. This protein contains two conserved N-glycosylation sites and 12 invariant cysteine residues. The dockings  were performed for five binding sites.

Libraries
Batch Range LibraryNickname
95989 – 96046 Drugs_and_Leads_FromPrestwick_MicroSourceSpectrum_FDA_and_NIHclinicalCollection
96047 – 109676 Enamine_Full_Library
109677 – 118434 Vitas-M Labs_Full_Library
118435 – 124350 ChemBridge_Full_Library
124351 – 127308 Asinex_Full_Library
127309 – 129164 NCI_Full_Library
129165 – 131136 Otava_Full_Library (note: now has 10,000 ligands/batch)
Targets

Targets employed to virtual screening:

x5k6k_NS1_ZIKV_cA_plr1.pdbqt
x5k6k_NS1_ZIKV_cA_plr2.pdbqt
x5k6k_NS1_ZIKV_cA_NclcA5.pdbqt
x5k6k_NS1_ZIKV_cA_phL4.pdbqt
x5k6k_NS1_ZIKV_cA_phB3.pdbqt
x5k6k_NS1_ZIKV_cB_plr1.pdbqt
x5k6k_NS1_ZIKV_cB_plr2.pdbqt
x5k6k_NS1_ZIKV_cB_NclcA5.pdbqt
x5k6k_NS1_ZIKV_cB_phL4.pdbqt
x5k6k_NS1_ZIKV_cB_phB3.pdbqt
x5iy3_NS1_ZIKV_plr1.pdbqt
x5iy3_NS1_ZIKV_plr2.pdbqt
x5iy3_NS1_ZIKV_phL4.pdbqt
x5iy3_NS1_ZIKV_phB3.pdbqt
x4o6b_NS1_Dengue_plr1.pdbqt
x4o6d_NS1_WNV_Holo_plr1.pdbqt
x4o6d_NS1_WNV_wWATs_plr1.pdbqt
x4oie_NS1_WNV_Holo_plr1.pdbqt
x4oie_NS1_WNV_wWATs_plr1.pdbqt
x4oig_NS1_Dengue_AB_plr1.pdbqt
x4oig_NS1_Dengue_DE_plr1.pdbqt
x4oii_NS1_WNV_plr1.pdbqt
x4tpl_NS1_WNV_plr1.pdbqt
x4o6b_NS1_Dengue_plr2.pdbqt
x4o6d_NS1_WNV_Holo_plr2.pdbqt
x4o6d_NS1_WNV_wWATs_plr2.pdbqt
x4oie_NS1_WNV_Holo_plr2.pdbqt
x4oie_NS1_WNV_wWATs_plr2.pdbqt
x4oig_NS1_Dengue_AB_plr2.pdbqt
x4oig_NS1_Dengue_DE_plr2.pdbqt
x4oii_NS1_WNV_plr2.pdbqt
x4tpl_NS1_WNV_plr2.pdbqt
x4o6b_NS1_Dengue_NclcA5.pdbqt
x4o6d_NS1_WNV_Holo_NclcA5.pdbqt
x4o6d_NS1_WNV_wWATs_NclcA5.pdbqt
x4tpl_NS1_WNV_NclcA5.pdbqt
x4o6b_NS1_Dengue_phL4.pdbqt
x4o6d_NS1_WNV_Holo_phL4.pdbqt
x4o6d_NS1_WNV_wWATs_phL4.pdbqt
x4oie_NS1_WNV_Holo_phL4.pdbqt
x4oie_NS1_WNV_wWATs_phL4.pdbqt
x4oig_NS1_Dengue_AB_phL4.pdbqt
x4oig_NS1_Dengue_DE_phL4.pdbqt
x4oii_NS1_WNV_phL4.pdbqt
x4tpl_NS1_WNV_phL4.pdbqt
x4o6b_NS1_Dengue_phB3.pdbqt
x4o6d_NS1_WNV_Holo_phB3.pdbqt
x4o6d_NS1_WNV_wWATs_phB3.pdbqt
x4oie_NS1_WNV_Holo_phB3.pdbqt
x4oie_NS1_WNV_wWATs_phB3.pdbqt
x4oig_NS1_Dengue_AB_phB3.pdbqt
x4oig_NS1_Dengue_DE_phB3.pdbqt
x4oii_NS1_WNV_phB3.pdbqt
x4tpl_NS1_WNV_phB3.pdbqt
x3lv2_DTBS_BioA_Mtb_A.pdbqt
x3lv2_DTBS_BioA_Mtb_A_s2.pdbqt
x3lv2_DTBS_BioA_Mtb_B.pdbqt
x3lv2_DTBS_BioA_Mtb_B_s2.pdbqt

Experiment 2D = Virtual Screening against the NS3 class (new crystallographic proteins)

New NS3 helicase crystallographic structures were solved (PDB ID: 5K8L, 5K8I, 5K8U, 5K8T). The dockings were performed for both binding sites.

Experiment 4A = Virtual Screening against the NS2B-NS3 protease class

NS2B-NS3 protease is responsible for all cytoplasmic cleavages including at junctions between NS2A/NS2B, NS2B/NS3, NS3/NS4A and NS4B/NS5 proteins and within the capsid, NS2A and NS4A proteins. Similar to NS3-NS4A protease from hepatitis C virus, the flavivirus NS2B-NS3 protease is essential for the virus replicative cycle, and thus constitutes an ideal target for antiviral drug development. NS2B-NS3 protease also suppresses the immune response by cleaving stimulator of interferon genes (STING) in DENV, triggers apoptosis via activating caspases in WNV, and induces neurotropic pathogenesis by inhibiting activator protein 1 (AP-1) in JEV.

Libraries
Batch Range LibraryNickname
166891 – 166960 Drugs_and_Leads_FromPrestwick_MicroSourceSpectrum_FDA_and_NIHclinicalCollection
166961 – 183410 Enamine_Full_Library
183411 – 193980 Vitas-M Labs_Full_Library
193981 – 201120 ChemBridge_Full_Library
201121 – 204690 Asinex_Full_Library
204691 – 206930 NCI_Full_Library
206931 – 209310 Otava_Full_Library (note: now has 10,000 ligands/batch)
Targets

Targets employed to virtual screening:

x5gj4_NS2BNS3pr_ZIKV_A_AB.pdbqt
x5h4i_ZIKV_NS2bNS3pr_HadFrag.pdbqt
x5lc0_ZIKV_NS2BNS3pr_Bo_chnA.pdbqt
x5gj4_NS2BNS3pr_ZIKV_A_CD.pdbqt
x5gj4_NS2BNS3pr_ZIKV_A_EF.pdbqt
x5gj4_NS2BNS3pr_ZIKV_A_GH.pdbqt
x5gpi_ZIKV_NS2bNS3pr_A_AB.pdbqt
x5gpi_ZIKV_NS2bNS3pr_A_CD.pdbqt
x5gpi_ZIKV_NS2bNS3pr_A_EF.pdbqt
x5gpi_ZIKV_NS2bNS3pr_A_GH.pdbqt
x5t1v_NS2B_NS3pr_ZIKV_apo_chnA.pdbqt
x5gj4_NS2BNS3pr_ZIKV_A_AB_DelNS2b.pdbqt
x5h4i_ZIKV_NS2bNS3pr_DelNS2b.pdbqt
x5gj4_NS2BNS3pr_ZIKV_A_CD_DelNS2b.pdbqt
x5t1v_NS2bNS3_ZIKV_apoChnA_DelNS2b.pdbqt
x5gj4_NS2BNS3pr_ZIKV_A_EF_DelNS2b.pdbqt
x5gj4_NS2BNS3pr_ZIKV_A_GH_DelNS2b.pdbqt
x5gj4_NS2BNS3pr_ZIKV_B_AB.pdbqt
x5gj4_NS2BNS3pr_ZIKV_B_CD.pdbqt
x5gj4_NS2BNS3pr_ZIKV_B_EF.pdbqt
x5gj4_NS2BNS3pr_ZIKV_B_GH.pdbqt
x5gpi_ZIKV_NS2bNS3pr_B_AB.pdbqt
x5gpi_ZIKV_NS2bNS3pr_B_CD.pdbqt
x5gpi_ZIKV_NS2bNS3pr_B_EF.pdbqt
x5gpi_ZIKV_NS2bNS3pr_B_GH.pdbqt
x5gj4_NS2BNS3pr_ZIKV_B_AB_delNS2b.pdbqt
x5gj4_NS2BNS3pr_ZIKV_B_CD_delNS2b.pdbqt
x5gj4_NS2BNS3pr_ZIKV_B_EF_delNS2b.pdbqt
x5gj4_NS2BNS3pr_ZIKV_B_GH_delNS2b.pdbqt
x5gpi_ZIKV_NS2bNS3pr_A_AB_DelNS2m.pdbqt
x5gpi_ZIKV_NS2bNS3pr_A_CD_DelNS2m.pdbqt
x5gpi_ZIKV_NS2bNS3pr_A_EF_DelNS2m.pdbqt
x5gpi_ZIKV_NS2bNS3pr_A_GH_DelNS2m.pdbqt
x5lc0_ZIKV_NS2BNS3pr_Bo_chnB.pdbqt
x5lc0_ZIKV_NS2BNS3pr_Dimer.pdbqt
x5t1v_NS2B_NS3pr_ZIKV_apo_chnB.pdbqt
x5t1v_NS2bNS3_ZIKV_apoChnB_DelNS2b.pdbqt
x2fom_Deng_NS2bNS3pr_A.pdbqt
x2fom_Deng_NS2bNS3pr_dimer_B.pdbqt
x2fp7_Deng_NS2bNS3pr_wPepInhib.pdbqt
x2ijo_WNV_NS2bNS3pr_wBPTI.pdbqt
x2m9p_NMR10_DengNS3pr_wPepAnalog.pdbqt
x2m9p_NMR1_DengNS3pr_wPepAnalog.pdbqt
x2m9p_NMR2_DengNS3pr_wPepAnalog.pdbqt
x2m9p_NMR3_DengNS3pr_wPepAnalog.pdbqt
x2m9p_NMR4_DengNS3pr_wPepAnalog.pdbqt
x2m9p_NMR5_DengNS3pr_wPepAnalog.pdbqt
x2m9p_NMR6_DengNS3pr_wPepAnalog.pdbqt
x2m9p_NMR7_DengNS3pr_wPepAnalog.pdbqt
x2m9p_NMR8_DengNS3pr_wPepAnalog.pdbqt
x2m9p_NMR9_DengNS3pr_wPepAnalog.pdbqt
x2m9q_10NMR_DengNS3pr_wPepAnalog.pdbqt
x2m9q_1NMR_DengNS3pr_wPepAnalog.pdbqt
x2m9q_2NMR_DengNS3pr_wPepAnalog.pdbqt
x2m9q_3NMR_DengNS3pr_wPepAnalog.pdbqt
x2m9q_4NMR_DengNS3pr_wPepAnalog.pdbqt
x2m9q_5NMR_DengNS3pr_wPepAnalog.pdbqt
x2m9q_6NMR_DengNS3pr_wPepAnalog.pdbqt
x2m9q_7NMR_DengNS3pr_wPepAnalog.pdbqt
x2m9q_8NMR_DengNS3pr_wPepAnalog.pdbqt
x2m9q_9NMR_DengNS3pr_wPepAnalog.pdbqt
x2whx_Dengue_NS3NS2Bpr_DelNS2b.pdbqt
x2whx_Dengue_NS3NS2Bprotease.pdbqt
x3o8b_HCV_NS2BNS3protease_chA.pdbqt
x3o8b_HCV_NS2BNS3protease_chB.pdbqt
x3o8c_HCV_NS2BNS3protease_chA.pdbqt
x3o8c_HCV_NS2BNS3protease_chB.pdbqt
x1qy6_Saur_V8pr.pdbqt
x1wcz_Saur_V8pr.pdbqt
x2as9_Saur_SpI_pr_1.pdbqt

Experiment 4B = Virtual Screening against the NS2B-NS3 protease class

2nd set of VS versus the NS2B / NS3 protease class (which involved 91 new targets)
Libraries
Batch Range LibraryNickname
209311 – 209401 Drugs_and_Leads_FromPrestwick_MicroSourceSpectrum_FDA_and_NIHclinicalCollection
209402 – 230786 Enamine_Full_Library
230787 – 244527 Vitas-M Labs_Full_Library
244528 – 253809 ChemBridge_Full_Library
253810 – 258450 Asinex_Full_Library
258451 – 261362 NCI_Full_Library
261363 – 264456 Otava_Full_Library (note: now has 10,000 ligands/batch)
Targets

Targets employed to virtual screening:

x3u1j_Deng_NS2bNS3pr_Aprtnn_A.pdbqt
x4m9t_DengNS2bNS3pr_CtoA_PAllos_A.pdbqt
x4m9t_DengNS2bNS3pr_CtoA_PAllos_B.pdbqt
x4m9f_DengNS2bNS3pr_CmodtoA_A.pdbqt
x4m9f_DengNS2bNS3pr_CmodtoA_B.pdbqt
x4m9k_DengNS2bNS3pr_pH5.5_A.pdbqt
x4m9k_DengNS2bNS3pr_pH5.5_B.pdbqt
x4m9k_DengNS2bNS3pr_pH5.5_C.pdbqt
x4m9m_DengNS2bNS3pr_pH8.5_A.pdbqt
x4m9m_DengNS2bNS3pr_pH8.5_B.pdbqt
x4m9m_DengNS2bNS3pr_pH8.5_C.pdbqt
x2yol_WNV_NS2bNS3pr_hadInhib_A.pdbqt
x2yol_WNV_NS2bNS3pr_hadInhib_B.pdbqt
x3e90_WNV_NS2bNS3pr_Pep_AB_A.pdbqt
x3e90_WNV_NS2bNS3pr_Pep_AB_B.pdbqt
x3e90_WNV_NS2bNS3pr_Pep_CD_A.pdbqt
x3e90_WNV_NS2bNS3pr_Pep_CD_B.pdbqt
x2vbc_Deng_fullNS3prNhel.pdbqt
x2wv9_MVEV_NS3pr_chB.pdbqt
x4r8t_JEV_NS2bPR.pdbqt
x4wf8_HCV_NS3pr_Asnprvr_A.pdbqt
x4wf8_HCV_NS3pr_Asnprvr_B.pdbqt
x4wh8_1_HCV_NS3pr_CycAsnprvr.pdbqt
x4wh8_2_HCV_NS3pr_CycAsnprvr.pdbqt
x5epn_HCV_NS3pr_MK5172cyc.pdbqt
x5eqq_HCV_NS3pr_MK5172linear_A.pdbqt
x5eqq_HCV_NS3pr_MK5172linear_B.pdbqt
x4nwk_HCV_NS3pr_BMS339_A.pdbqt
x4nwk_HCV_NS3pr_BMS339_B.pdbqt
x4nwl_HCV_NS3pr_BMS032_A.pdbqt
x4nwl_HCV_NS3pr_BMS032_B.pdbqt
x3lon_HCV_NS3pr_Nrlprvr_A.pdbqt
x3lox_HCV_NS3pr_Boceprevir.pdbqt
x3p8n_HCV_NS3pr_BIinhib_chA.pdbqt
x3p8n_HCV_NS3pr_BIinhib_chB.pdbqt
x3su3_HCV_NS3pr_Vaniprevir_A.pdbqt
x3su3_HCV_NS3pr_Vaniprevir_B.pdbqt
x3su3_HCV_NS3pr_Vaniprevir_C.pdbqt
x3sv6_HCV_NS3pr_Telaprevir_A.pdbqt
x3sv6_HCV_NS3pr_Telaprevir_B.pdbqt
x3sv6_HCV_NS3pr_Telaprevir_C.pdbqt
x3sv6_HCV_NS3pr_Telaprevir_D.pdbqt
x3sv8_HCV_NS3prD168A_Tlprvr_A.pdbqt
x3sv9_HCV_NS3prA156T_Tlprvr_A.pdbqt
x3sv9_HCV_NS3prA156T_Tlprvr_B.pdbqt
x3sv9_HCV_NS3prA156T_Tlprvr_C.pdbqt
x3kee_HCV_NS3NS4aPR_TMC435_A_A.pdbqt
x3kee_HCV_NS3NS4aPR_TMC435_A_B.pdbqt
x3kee_HCV_NS3NS4aPR_TMC435_B_A.pdbqt
x3kee_HCV_NS3NS4aPR_TMC435_C_A.pdbqt
x3kee_HCV_NS3NS4aPR_TMC435_C_B.pdbqt
x3kee_HCV_NS3NS4aPR_TMC435_D_A.pdbqt
x3kee_HCV_NS3NS4aPR_TMC435_D_B.pdbqt
x3lon_HCV_NS3pr_apo_chC.pdbqt
x4a1v_HCV_NS3pr_OptPep_A.pdbqt
x4a1v_HCV_NS3pr_OptPep_B.pdbqt
x4a1x_HCV_NS3pr_PepCP546A_A_A.pdbqt
x4a1x_HCV_NS3pr_PepCP546A_A_B.pdbqt
x4a1x_HCV_NS3pr_PepCP546A_B_A.pdbqt
x4a1x_HCV_NS3pr_PepCP546A_B_B.pdbqt
x4i31_HCV_NS3pr_Macrocyc_A.pdbqt
x4i31_HCV_NS3pr_Macrocyc_B.pdbqt
x4jmy_HCV_NS3pr_DDIVPC_A.pdbqt
x4jmy_HCV_NS3pr_DDIVPC_B.pdbqt
x4ktc_HCV_NS3pr_Macrocyc1nm_A.pdbqt
x4ktc_HCV_NS3pr_Macrocyc1nm_C.pdbqt
x4u01_1_HCV_NS3pr_Macrocyc70.pdbqt
x4u01_2_HCV_NS3pr_Macrocyc70.pdbqt
x4u01_3_HCV_NS3pr_Macrocyc70.pdbqt
x4u01_4_HCV_NS3pr_Macrocyc70.pdbqt
x4u01_5_HCV_NS3pr_Macrocyc70.pdbqt
x4u01_6_HCV_NS3pr_Macrocyc70.pdbqt
x4u01_7_HCV_NS3pr_Macrocyc70.pdbqt
x4u01_8_HCV_NS3pr_Macrocyc70.pdbqt
x4u01_9_HCV_NS3pr_Macrocyc70.pdbqt
x3ufa_Saur_SplApr_PInhib_A.pdbqt
x3ufa_Saur_SplApr_PInhib_B.pdbqt
x4mvn_Saur_SplApr_Inhib_chA_A.pdbqt
x4mvn_Saur_SplApr_Inhib_chA_B.pdbqt
x4mvn_Saur_SplApr_Inhib_chB_A.pdbqt
x4mvn_Saur_SplApr_Inhib_chB_B.pdbqt
x4mvn_Saur_SplApr_Inhib_chC_A.pdbqt
x4mvn_Saur_SplApr_Inhib_chC_B.pdbqt
x4mvn_Saur_SplApr_Inhib_chD_A.pdbqt
x4mvn_Saur_SplApr_Inhib_chD_B.pdbqt
x2w7s_1_A_Saur_SplA_pr.pdbqt
x2w7s_1_B_Saur_SplA_pr.pdbqt
x2w7s_3_A_Saur_SplA_pr.pdbqt
x2w7s_3_B_Saur_SplA_pr.pdbqt
x2w7s_4_Saur_SplA_pr.pdbqt
x2o8l_Saur_V8pr.pdbqt

Experiment 4C = Virtual Screening against the NS2B-NS3 protease class

3rd set of VS versus the NS2B / NS3 protease class (ZINC15 Library: 30.2 million)
Libraries
Batch Range Library Nickname
264457 – 292511 BigLib (ZINC15 Library)
Targets

Targets employed to virtual screening:

x3u1j_Deng_NS2bNS3pr_Aprtnn_A.pdbqt
x4m9t_DengNS2bNS3pr_CtoA_PAllos_A.pdbqt
x4m9t_DengNS2bNS3pr_CtoA_PAllos_B.pdbqt
x4m9f_DengNS2bNS3pr_CmodtoA_A.pdbqt
x4m9f_DengNS2bNS3pr_CmodtoA_B.pdbqt
x4m9k_DengNS2bNS3pr_pH5.5_A.pdbqt
x4m9k_DengNS2bNS3pr_pH5.5_B.pdbqt
x4m9k_DengNS2bNS3pr_pH5.5_C.pdbqt
x4m9m_DengNS2bNS3pr_pH8.5_A.pdbqt
x4m9m_DengNS2bNS3pr_pH8.5_B.pdbqt
x4m9m_DengNS2bNS3pr_pH8.5_C.pdbqt
x2yol_WNV_NS2bNS3pr_hadInhib_A.pdbqt
x2yol_WNV_NS2bNS3pr_hadInhib_B.pdbqt
x3e90_WNV_NS2bNS3pr_Pep_AB_A.pdbqt
x3e90_WNV_NS2bNS3pr_Pep_AB_B.pdbqt
x3e90_WNV_NS2bNS3pr_Pep_CD_A.pdbqt
x3e90_WNV_NS2bNS3pr_Pep_CD_B.pdbqt
x2vbc_Deng_fullNS3prNhel.pdbqt
x2wv9_MVEV_NS3pr_chB.pdbqt
x4r8t_JEV_NS2bPR.pdbqt
x4wf8_HCV_NS3pr_Asnprvr_A.pdbqt
x4wf8_HCV_NS3pr_Asnprvr_B.pdbqt
x4wh8_1_HCV_NS3pr_CycAsnprvr.pdbqt
x4wh8_2_HCV_NS3pr_CycAsnprvr.pdbqt
x5epn_HCV_NS3pr_MK5172cyc.pdbqt
x5eqq_HCV_NS3pr_MK5172linear_A.pdbqt
x5eqq_HCV_NS3pr_MK5172linear_B.pdbqt
x4nwk_HCV_NS3pr_BMS339_A.pdbqt
x4nwk_HCV_NS3pr_BMS339_B.pdbqt
x4nwl_HCV_NS3pr_BMS032_A.pdbqt
x4nwl_HCV_NS3pr_BMS032_B.pdbqt
x3lon_HCV_NS3pr_Nrlprvr_A.pdbqt
x3lox_HCV_NS3pr_Boceprevir.pdbqt
x3p8n_HCV_NS3pr_BIinhib_chA.pdbqt
x3p8n_HCV_NS3pr_BIinhib_chB.pdbqt
x3su3_HCV_NS3pr_Vaniprevir_A.pdbqt
x3su3_HCV_NS3pr_Vaniprevir_B.pdbqt
x3su3_HCV_NS3pr_Vaniprevir_C.pdbqt
x3sv6_HCV_NS3pr_Telaprevir_A.pdbqt
x3sv6_HCV_NS3pr_Telaprevir_B.pdbqt
x3sv6_HCV_NS3pr_Telaprevir_C.pdbqt
x3sv6_HCV_NS3pr_Telaprevir_D.pdbqt
x3sv8_HCV_NS3prD168A_Tlprvr_A.pdbqt
x3sv9_HCV_NS3prA156T_Tlprvr_A.pdbqt
x3sv9_HCV_NS3prA156T_Tlprvr_B.pdbqt
x3sv9_HCV_NS3prA156T_Tlprvr_C.pdbqt
x3kee_HCV_NS3NS4aPR_TMC435_A_A.pdbqt
x3kee_HCV_NS3NS4aPR_TMC435_A_B.pdbqt
x3kee_HCV_NS3NS4aPR_TMC435_B_A.pdbqt
x3kee_HCV_NS3NS4aPR_TMC435_C_A.pdbqt
x3kee_HCV_NS3NS4aPR_TMC435_C_B.pdbqt
x3kee_HCV_NS3NS4aPR_TMC435_D_A.pdbqt
x3kee_HCV_NS3NS4aPR_TMC435_D_B.pdbqt
x3lon_HCV_NS3pr_apo_chC.pdbqt
x4a1v_HCV_NS3pr_OptPep_A.pdbqt
x4a1v_HCV_NS3pr_OptPep_B.pdbqt
x4a1x_HCV_NS3pr_PepCP546A_A_A.pdbqt
x4a1x_HCV_NS3pr_PepCP546A_A_B.pdbqt
x4a1x_HCV_NS3pr_PepCP546A_B_A.pdbqt
x4a1x_HCV_NS3pr_PepCP546A_B_B.pdbqt
x4i31_HCV_NS3pr_Macrocyc_A.pdbqt
x4i31_HCV_NS3pr_Macrocyc_B.pdbqt
x4jmy_HCV_NS3pr_DDIVPC_A.pdbqt
x4jmy_HCV_NS3pr_DDIVPC_B.pdbqt
x4ktc_HCV_NS3pr_Macrocyc1nm_A.pdbqt
x4ktc_HCV_NS3pr_Macrocyc1nm_C.pdbqt
x4u01_1_HCV_NS3pr_Macrocyc70.pdbqt
x4u01_2_HCV_NS3pr_Macrocyc70.pdbqt
x4u01_3_HCV_NS3pr_Macrocyc70.pdbqt
x4u01_4_HCV_NS3pr_Macrocyc70.pdbqt
x4u01_5_HCV_NS3pr_Macrocyc70.pdbqt
x4u01_6_HCV_NS3pr_Macrocyc70.pdbqt
x4u01_7_HCV_NS3pr_Macrocyc70.pdbqt
x4u01_8_HCV_NS3pr_Macrocyc70.pdbqt
x4u01_9_HCV_NS3pr_Macrocyc70.pdbqt
x3ufa_Saur_SplApr_PInhib_A.pdbqt
x3ufa_Saur_SplApr_PInhib_B.pdbqt
x4mvn_Saur_SplApr_Inhib_chA_A.pdbqt
x4mvn_Saur_SplApr_Inhib_chA_B.pdbqt
x4mvn_Saur_SplApr_Inhib_chB_A.pdbqt
x4mvn_Saur_SplApr_Inhib_chB_B.pdbqt
x4mvn_Saur_SplApr_Inhib_chC_A.pdbqt
x4mvn_Saur_SplApr_Inhib_chC_B.pdbqt
x4mvn_Saur_SplApr_Inhib_chD_A.pdbqt
x4mvn_Saur_SplApr_Inhib_chD_B.pdbqt
x2w7s_1_A_Saur_SplA_pr.pdbqt
x2w7s_1_B_Saur_SplA_pr.pdbqt
x2w7s_3_A_Saur_SplA_pr.pdbqt
x2w7s_3_B_Saur_SplA_pr.pdbqt
x2w7s_4_Saur_SplA_pr.pdbqt
x2o8l_Saur_V8pr.pdbqt