oedocking toolkit version 4.0.01 (OpenEye Scientific Software Inc)
90
Structured Review
OpenEye Scientific Software Inc
oedocking toolkit version 4.0.01
Oedocking Toolkit Version 4.0.01, 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+toolkit/oedocking+module/pmc10900287-285-10-12
Average 90 stars, based on 1 article reviews
Oedocking Toolkit Version 4.0.01, 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+toolkit/oedocking+module/pmc10900287-285-10-12
Average 90 stars, based on 1 article reviews
oedocking toolkit version 4.0.01 - by Bioz Stars,
2026-09
90/100 stars
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other:Article Title: Expanded ensemble predictions of absolute binding free energies in the SAMPL9 host-guest challenge. Article Snippet: As part of the SAMPL9 community-wide blind host–guest challenge, we implemented an expanded ensemble workflow to predict absolute binding free energies for 13 small molecules against pillar[6]arene.. Notable features of our protocol include consideration of a variety of protonation and enantiomeric states for both host and guests, optimization of alchemical intermediates, and analysis of free energy estimates and their uncertainty using large numbers of simulation replicates performed using distributed computing.. Our predictions of absolute binding free energies resulted in a mean absolute error of 2.29 kcal mol 1 and an R of 0.54. Article Title: Deconstruction of Dual-Site Tankyrase Inhibitors Provides Insights into Binding Energetics and Suggests Critical Hotspots for Ligand Optimization Article Snippet: Docking of molecules 1 and S01-S13 into the prepared TNKS2 protein structure was performed using the Article Title: Input Pose is Key to Performance of Free Energy Perturbation: Benchmarking with Monoacylglycerol Lipase. Article Snippet: Free energy perturbation (FEP) methodologies have become commonplace methods for modeling potency in hit-to-lead and lead optimization stages of drug discovery.. The conformational states of the initial poses of compounds for FEP+ calculations are often set up by alignment to a cocrystal structure ligand, but it is not clear if this method provides the best result for all proteins or all ligands.. Not only are ligand conformational states potential variables in modeling compound potency in FEP but also the selection of crystallographic water molecules for inclusion in the FEP input structures can impact FEP models. Article Title: Thompson Sampling—An Efficient Method for Searching Ultralarge Synthesis on Demand Databases Article Snippet: Docking was performed using In Silico:Article Title: Cinnamaldehyde derivatives act as antimicrobial agents against Acinetobacter baumannii through the inhibition of cell division Article Snippet: .. Crystal structures of FtsZ in complex with di-fluoro-benzamide analogs ( ; ; ) were employed for in silico docking studies using the Inhibition:Article Title: Plants used in Ayurveda for Jwara or fever: A review of their antiviral studies. Article Snippet: .. Garcinia indica (Thouars) Choisy 1 HIV-1 HIV-1 RT-associated RNase H inhibition and RDDP inhibition assays, molecular docking study ( Article Title: Plants used in Ayurveda for Jwara or fever: A review of their antiviral studies Article Snippet: 8. , Eclipta prostrata (L.) L. , 1 , Fish nodavirus, grouper nervous necrosis virus (GNNV) , MTT, cytopathic inhibition assays, RT-PCR , Dasyscyphin C ( 18 ) from E. prostrata treated with nodavirus infected SIGE cells showed viral inhibition (IC 50 : 20 μg/mL) [ ] . .. 9. , Garcinia indica (Thouars) Choisy , 1 , HIV‐1 , HIV‐1 RT‐associated RNase H inhibition and RDDP inhibition assays, molecular docking study ( Generated:Article Title: Structural optimization and biological evaluation of 1-adamantylcarbonyl-4-phenylpiperazine derivatives as FXR agonists for NAFLD. Article Snippet: Farnesoid X receptor (FXR) is an attractive target for drug discovery against non-alcoholic fatty liver disease (NAFLD).. We previously reported an orally active, new-chemotype FXR agonist XJ034 by ensemble learningdriven drug discovery.. However, its FXR agonistic activity and the efficacy in vivo remain to be improved. |