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OpenEye Scientific Software Inc oedocking 3.0.1
Oedocking 3.0.1, supplied by OpenEye Scientific Software Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/oedocking+3%2E0%2E1/oedocking+3+0+1/pm39369484-433-27-10
Average 90 stars, based on 1 article reviews
oedocking 3.0.1 - by Bioz Stars, 2026-09
90/100 stars

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Article Title: Identification of novel diarylpyrimidine derivatives as potent HIV-1 non-nucleoside reverse transcriptase inhibitors against wild-type and K103N mutant viruses.
Article Snippet: HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) play a crucial role in combination antiretroviral therapy (cART).. To further enhance their antiviral activity and anti-resistance properties, we developed a series of novel NNRTIs, by specifically targeting tolerant region I of the NNRTI binding pocket.. Among them, compound 9t-2 displayed excellent anti-HIV-1 potency against wild-type and prevalent mutant strains with EC50 values between 0.0019 and 0.012 μM.

Article Title: QSAR-Driven Design and Discovery of Novel Compounds With Antiplasmodial and Transmission Blocking Activities
Article Snippet: On Make Receptor tool, available on OEDocking 3.0.1 (OEDocking 3.2.0.2: OpenEye Scientific Software, Santa Fe, NM, United States 2 ), the receptor grid was generated with dimensions 22.34 Å × 19.65 Å × 25.24 Å and volume of 11,078 Å 3 .

Article Title: Discovery of diarylpyrimidine derivatives bearing piperazine sulfonyl as potent HIV-1 nonnucleoside reverse transcriptase inhibitors
Article Snippet: 18b1 and Etravirine conformers were generated by OMEGA module of OPENEYE Scientific Software Inc, and then they were docked into the binding site of each RT variant by OEDOCKING 3.0.1 with chemgauss4 scoring function.14-15 Conformers of either 18b1 or Etravirine with the highest chemgauss4 score docked to each of the four RT variants were used (as complex of the inhibitor and RT variant) in the subsequent molecular dynamics simulation.

Article Title: Discovery of phenylalanine derivatives as potent HIV-1 capsid inhibitors from click chemistry-based compound library
Article Snippet: 13p conformers were docked into the active site of the modeled 5HGL structure using OPENEYE Scientific Software Inc. module OEDOCKING 3.0.1 with chemgauss4 scoring function [42-45].

Article Title: Bioisosteric replacement strategy leads to novel DNA gyrase B inhibitors with improved potencies and properties.
Article Snippet: The identification of novel 4-hydroxy-2-quinolone-3-carboxamide antibacterials with improved properties is of great value for the control of antibiotic resistance.. In this study, a series of N-heteroaryl-substituted 4-hydroxy-2quinolone-3-carboxamides were developed using the bioisosteric replacement strategy.. As a result of our research, we discovered the two most potent GyrB inhibitors (WBX7 and WBX18), with IC50 values of 0.816 μM and 0.137 μM, respectively.

Article Title: New tools in nucleoside toolbox of tick-borne encephalitis virus reproduction inhibitors.
Article Snippet: Design and development of nucleoside analogs is an established strategy in the antiviral drug discovery field.. Nevertheless, for many viruses the coverage of structure-activity relationships (SAR) in the nucleoside chemical space is not sufficient.. Here we present the nucleoside SAR exploration for tick-borne encephalitis virus (TBEV), a member of Flavivirus genus.

Article Title: Discovery of Phenylalanine Derivatives as Potent HIV-1 Capsid Inhibitors from Click Chemistry-based Compound Library
Article Snippet: 13p conformers were docked into the active site of the modeled 5HGL structure using OPENEYE Scientific Software Inc. module OEDOCKING 3.0.1 with chemgauss4 scoring function [ 42 - 45 ].

Article Title: Design, synthesis, and mechanism study of dimerized phenylalanine derivatives as novel HIV-1 capsid inhibitors
Article Snippet: Q-c4 conformers were generated by OMEGA module of OPENEYE Scientific Software Inc, and then they were docked to the binding site of 5HGL by OEDOCKING 3.0.1 with chemgauss4 scoring function [ 9 , 63 - 67 ].

Variant Assay:

Article Title: Identification of novel diarylpyrimidine derivatives as potent HIV-1 non-nucleoside reverse transcriptase inhibitors against wild-type and K103N mutant viruses.
Article Snippet: HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) play a crucial role in combination antiretroviral therapy (cART).. To further enhance their antiviral activity and anti-resistance properties, we developed a series of novel NNRTIs, by specifically targeting tolerant region I of the NNRTI binding pocket.. Among them, compound 9t-2 displayed excellent anti-HIV-1 potency against wild-type and prevalent mutant strains with EC50 values between 0.0019 and 0.012 μM.

Article Title: QSAR-Driven Design and Discovery of Novel Compounds With Antiplasmodial and Transmission Blocking Activities
Article Snippet: On Make Receptor tool, available on OEDocking 3.0.1 (OEDocking 3.2.0.2: OpenEye Scientific Software, Santa Fe, NM, United States 2 ), the receptor grid was generated with dimensions 22.34 Å × 19.65 Å × 25.24 Å and volume of 11,078 Å 3 .

Article Title: Discovery of diarylpyrimidine derivatives bearing piperazine sulfonyl as potent HIV-1 nonnucleoside reverse transcriptase inhibitors
Article Snippet: 18b1 and Etravirine conformers were generated by OMEGA module of OPENEYE Scientific Software Inc, and then they were docked into the binding site of each RT variant by OEDOCKING 3.0.1 with chemgauss4 scoring function.14-15 Conformers of either 18b1 or Etravirine with the highest chemgauss4 score docked to each of the four RT variants were used (as complex of the inhibitor and RT variant) in the subsequent molecular dynamics simulation.

Article Title: Discovery of phenylalanine derivatives as potent HIV-1 capsid inhibitors from click chemistry-based compound library
Article Snippet: 13p conformers were docked into the active site of the modeled 5HGL structure using OPENEYE Scientific Software Inc. module OEDOCKING 3.0.1 with chemgauss4 scoring function [42-45].

Article Title: Bioisosteric replacement strategy leads to novel DNA gyrase B inhibitors with improved potencies and properties.
Article Snippet: The identification of novel 4-hydroxy-2-quinolone-3-carboxamide antibacterials with improved properties is of great value for the control of antibiotic resistance.. In this study, a series of N-heteroaryl-substituted 4-hydroxy-2quinolone-3-carboxamides were developed using the bioisosteric replacement strategy.. As a result of our research, we discovered the two most potent GyrB inhibitors (WBX7 and WBX18), with IC50 values of 0.816 μM and 0.137 μM, respectively.

Article Title: New tools in nucleoside toolbox of tick-borne encephalitis virus reproduction inhibitors.
Article Snippet: Design and development of nucleoside analogs is an established strategy in the antiviral drug discovery field.. Nevertheless, for many viruses the coverage of structure-activity relationships (SAR) in the nucleoside chemical space is not sufficient.. Here we present the nucleoside SAR exploration for tick-borne encephalitis virus (TBEV), a member of Flavivirus genus.

Article Title: Discovery of Phenylalanine Derivatives as Potent HIV-1 Capsid Inhibitors from Click Chemistry-based Compound Library
Article Snippet: 13p conformers were docked into the active site of the modeled 5HGL structure using OPENEYE Scientific Software Inc. module OEDOCKING 3.0.1 with chemgauss4 scoring function [ 42 - 45 ].

Article Title: Design, synthesis, and mechanism study of dimerized phenylalanine derivatives as novel HIV-1 capsid inhibitors
Article Snippet: Q-c4 conformers were generated by OMEGA module of OPENEYE Scientific Software Inc, and then they were docked to the binding site of 5HGL by OEDOCKING 3.0.1 with chemgauss4 scoring function [ 9 , 63 - 67 ].

Binding Assay:

Article Title: Identification of novel diarylpyrimidine derivatives as potent HIV-1 non-nucleoside reverse transcriptase inhibitors against wild-type and K103N mutant viruses.
Article Snippet: HIV-1 non-nucleoside reverse transcriptase inhibitors (NNRTIs) play a crucial role in combination antiretroviral therapy (cART).. To further enhance their antiviral activity and anti-resistance properties, we developed a series of novel NNRTIs, by specifically targeting tolerant region I of the NNRTI binding pocket.. Among them, compound 9t-2 displayed excellent anti-HIV-1 potency against wild-type and prevalent mutant strains with EC50 values between 0.0019 and 0.012 μM.

Article Title: QSAR-Driven Design and Discovery of Novel Compounds With Antiplasmodial and Transmission Blocking Activities
Article Snippet: On Make Receptor tool, available on OEDocking 3.0.1 (OEDocking 3.2.0.2: OpenEye Scientific Software, Santa Fe, NM, United States 2 ), the receptor grid was generated with dimensions 22.34 Å × 19.65 Å × 25.24 Å and volume of 11,078 Å 3 .

Article Title: Discovery of diarylpyrimidine derivatives bearing piperazine sulfonyl as potent HIV-1 nonnucleoside reverse transcriptase inhibitors
Article Snippet: 18b1 and Etravirine conformers were generated by OMEGA module of OPENEYE Scientific Software Inc, and then they were docked into the binding site of each RT variant by OEDOCKING 3.0.1 with chemgauss4 scoring function.14-15 Conformers of either 18b1 or Etravirine with the highest chemgauss4 score docked to each of the four RT variants were used (as complex of the inhibitor and RT variant) in the subsequent molecular dynamics simulation.

Article Title: Discovery of phenylalanine derivatives as potent HIV-1 capsid inhibitors from click chemistry-based compound library
Article Snippet: 13p conformers were docked into the active site of the modeled 5HGL structure using OPENEYE Scientific Software Inc. module OEDOCKING 3.0.1 with chemgauss4 scoring function [42-45].

Article Title: Bioisosteric replacement strategy leads to novel DNA gyrase B inhibitors with improved potencies and properties.
Article Snippet: The identification of novel 4-hydroxy-2-quinolone-3-carboxamide antibacterials with improved properties is of great value for the control of antibiotic resistance.. In this study, a series of N-heteroaryl-substituted 4-hydroxy-2quinolone-3-carboxamides were developed using the bioisosteric replacement strategy.. As a result of our research, we discovered the two most potent GyrB inhibitors (WBX7 and WBX18), with IC50 values of 0.816 μM and 0.137 μM, respectively.

Article Title: New tools in nucleoside toolbox of tick-borne encephalitis virus reproduction inhibitors.
Article Snippet: Design and development of nucleoside analogs is an established strategy in the antiviral drug discovery field.. Nevertheless, for many viruses the coverage of structure-activity relationships (SAR) in the nucleoside chemical space is not sufficient.. Here we present the nucleoside SAR exploration for tick-borne encephalitis virus (TBEV), a member of Flavivirus genus.

Article Title: Discovery of Phenylalanine Derivatives as Potent HIV-1 Capsid Inhibitors from Click Chemistry-based Compound Library
Article Snippet: 13p conformers were docked into the active site of the modeled 5HGL structure using OPENEYE Scientific Software Inc. module OEDOCKING 3.0.1 with chemgauss4 scoring function [ 42 - 45 ].

Article Title: Design, synthesis, and mechanism study of dimerized phenylalanine derivatives as novel HIV-1 capsid inhibitors
Article Snippet: Q-c4 conformers were generated by OMEGA module of OPENEYE Scientific Software Inc, and then they were docked to the binding site of 5HGL by OEDOCKING 3.0.1 with chemgauss4 scoring function [ 9 , 63 - 67 ].



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