ArticleJournal of computer-aided molecular design2014
SAMPL4 & DOCK3.7: lessons for automated docking procedures.
Article in Journal of computer-aided molecular design, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
What it found
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Who cites it
10 citing papers in PubMed.
- Computation of host-guest binding free energies with a new quantum mechanics based mining minima algorithm.The Journal of chemical physics · 2021Article
- The SAMPL6 SAMPLing challenge: assessing the reliability and efficiency of binding free energy calculations.Journal of computer-aided molecular design · 2020Article
- Structure-inspired design of β-arrestin-biased ligands for aminergic GPCRs.Nature chemical biology · 2018Article
- Bayesian Model Averaging for Ensemble-Based Estimates of Solvation-Free Energies.The journal of physical chemistry. B · 2017Article
- Towards a critical evaluation of an empirical and volume-based solvation function for ligand docking.PloS one · 2017Article
- Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations.Journal of computer-aided molecular design · 2016Article
- BEDAM binding free energy predictions for the SAMPL4 octa-acid host challenge.Journal of computer-aided molecular design · 2015Article
- Combining in silico and in cerebro approaches for virtual screening and pose prediction in SAMPL4.Journal of computer-aided molecular design · 2014Article
- The SAMPL4 host-guest blind prediction challenge: an overview.Journal of computer-aided molecular design · 2014Review
- Blind prediction of HIV integrase binding from the SAMPL4 challenge.Journal of computer-aided molecular design · 2014Review
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The SAMPL4 challenges were used to test current automated methods for solvation energy, virtual screening, pose and affinity prediction of the molecular docking pipeline DOCK 3.7. Additionally, first-order models of binding affinity were proposed as milestones for any method predicting binding affinity. Several important discoveries about the molecular docking software were made during the challenge: (1) Solvation energies of ligands were five-fold worse than any other method used in SAMPL4, including methods that were similarly fast, (2) HIV Integrase is a challenging target, but automated docking on the correct allosteric site performed well in terms of virtual screening and pose prediction (compared to other methods) but affinity prediction, as expected, was very poor, (3) Molecular docking grid sizes can be very important, serious errors were discovered with default settings that have been adjusted for all future work. Overall, lessons from SAMPL4 suggest many changes to molecular docking tools, not just DOCK 3.7, that could improve the state of the art. Future difficulties and projects will be discussed.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.