Dataset Information

Improving Blind Docking in DOCK6 through an Automated Preliminary Fragment Probing Strategy.

ABSTRACT: Probing protein surfaces to accurately predict the binding site and conformation of a small molecule is a challenge currently addressed through mainly two different approaches: blind docking and cavity detection-guided docking. Although cavity detection-guided blind docking has yielded high success rates, it is less practical when a large number of molecules must be screened against many detected binding sites. On the other hand, blind docking allows for simultaneous search of the whole protein surface, which however entails the loss of accuracy and speed. To bridge this gap, in this study, we developed and tested BLinDPyPr, an automated pipeline which uses FTMap and DOCK6 to perform a hybrid blind docking strategy. Through our algorithm, FTMap docked probe clusters are converted into DOCK6 spheres for determining binding regions. Because these spheres are solely derived from FTMap probes, their locations are contained in and specific to multiple potential binding pockets, which become the regions that are simultaneously probed and chosen by the search algorithm based on the properties of each candidate ligand. This method yields pose prediction results (45.2-54.3% success rates) comparable to those of site-specific docking with the classic DOCK6 workflow (49.7-54.3%) and is half as time-consuming as the conventional blind docking method with DOCK6.

SUBMITTER: Jofily P

PROVIDER: S-EPMC7956365 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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Improving Blind Docking in DOCK6 through an Automated Preliminary Fragment Probing Strategy.

Jofily Paula P Pascutti Pedro G PG Torres Pedro H M PHM

Molecules (Basel, Switzerland) 20210225 5

Probing protein surfaces to accurately predict the binding site and conformation of a small molecule is a challenge currently addressed through mainly two different approaches: blind docking and cavity detection-guided docking. Although cavity detection-guided blind docking has yielded high success rates, it is less practical when a large number of molecules must be screened against many detected binding sites. On the other hand, blind docking allows for simultaneous search of the whole protein ...[more]

PMID: 33668914

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Project description:BackgroundOnline peer support forums require oversight to ensure they remain safe and therapeutic. As online communities grow, they place a greater burden on their human moderators, which increases the likelihood that people at risk may be overlooked. This study evaluated the potential for machine learning to assist online peer support by directing moderators' attention where it is most needed.ObjectiveThis study aimed to evaluate the accuracy of an automated triage system and the extent to which it influences moderator behavior.MethodsA machine learning classifier was trained to prioritize forum messages as green, amber, red, or crisis depending on how urgently they require attention from a moderator. This was then launched as a set of widgets injected into a popular online peer support forum hosted by ReachOut.com, an Australian Web-based youth mental health service that aims to intervene early in the onset of mental health problems in young people. The accuracy of the system was evaluated using a holdout test set of manually prioritized messages. The impact on moderator behavior was measured as response ratio and response latency, that is, the proportion of messages that receive at least one reply from a moderator and how long it took for these replies to be made. These measures were compared across 3 periods: before launch, after an informal launch, and after a formal launch accompanied by training.ResultsThe algorithm achieved 84% f-measure in identifying content that required a moderator response. Between prelaunch and post-training periods, response ratios increased by 0.9, 4.4, and 10.5 percentage points for messages labelled as crisis, red, and green, respectively, but decreased by 5.0 percentage points for amber messages. Logistic regression indicated that the triage system was a significant contributor to response ratios for green, amber, and red messages, but not for crisis messages. Response latency was significantly reduced (P<.001), between the same periods, by factors of 80%, 80%, 77%, and 12% for crisis, red, amber, and green messages, respectively. Regression analysis indicated that the triage system made a significant and unique contribution to reducing the time taken to respond to green, amber, and red messages, but not to crisis messages, after accounting for moderator and community activity.ConclusionsThe triage system was generally accurate, and moderators were largely in agreement with how messages were prioritized. It had a modest effect on response ratios, primarily because moderators were already more likely to respond to high priority content before the introduction of triage. However, it significantly and substantially reduced the time taken for moderators to respond to prioritized content. Further evaluations are needed to assess the impact of mistakes made by the triage algorithm and how changes to moderator responsiveness impact the well-being of forum members.

Dataset Information

Improving Blind Docking in DOCK6 through an Automated Preliminary Fragment Probing Strategy.

Publications

Improving Blind Docking in DOCK6 through an Automated Preliminary Fragment Probing Strategy.

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