We have located links that may give you full text access.
Protein-ligand pose and affinity prediction: Lessons from D3R Grand Challenge 3.
Journal of Computer-aided Molecular Design 2018 August 21
We report the performance of HADDOCK in the 2018 iteration of the Grand Challenge organised by the D3R consortium. Building on the findings of our participation in last year's challenge, we significantly improved our pose prediction protocol which resulted in a mean RMSD for the top scoring pose of 3.04 and 2.67 Å for the cross-docking and self-docking experiments respectively, which corresponds to an overall success rate of 63% and 71% when considering the top1 and top5 models respectively. This performance ranks HADDOCK as the 6th and 3rd best performing group (excluding multiple submissions from a same group) out of a total of 44 and 47 submissions respectively. Our ligand-based binding affinity predictor is the 3rd best predictor overall, behind only the two leading structure-based implementations, and the best ligand-based one with a Kendall's Tau correlation of 0.36 for the Cathepsin challenge. It also performed well in the classification part of the Kinase challenges, with Matthews Correlation Coefficients of 0.49 (ranked 1st), 0.39 (ranked 4th) and 0.21 (ranked 4th) for the JAK2, vEGFR2 and p38a targets respectively. Through our participation in last year's competition we came to the conclusion that template selection is of critical importance for the successful outcome of the docking. This year we have made improvements in two additional areas of importance: ligand conformer selection and initial positioning, which have been key to our excellent pose prediction performance this year.
Full text links
Related Resources
Trending Papers
Executive Summary: State-of-the-Art Review: Unintended Consequences: Risk of Opportunistic Infections Associated with Long-term Glucocorticoid Therapies in Adults.Clinical Infectious Diseases 2024 April 11
Autoimmune Hemolytic Anemias: Classifications, Pathophysiology, Diagnoses and Management.International Journal of Molecular Sciences 2024 April 13
Clinical practice guidelines on the management of status epilepticus in adults: A systematic review.Epilepsia 2024 April 13
Get seemless 1-tap access through your institution/university
For the best experience, use the Read mobile app
All material on this website is protected by copyright, Copyright © 1994-2024 by WebMD LLC.
This website also contains material copyrighted by 3rd parties.
By using this service, you agree to our terms of use and privacy policy.
Your Privacy Choices
You can now claim free CME credits for this literature searchClaim now
Get seemless 1-tap access through your institution/university
For the best experience, use the Read mobile app