Dataset Information

VSpipe, an Integrated Resource for Virtual Screening and Hit Selection: Applications to Protein Tyrosine Phospahatase Inhibition.

ABSTRACT: The use of computational tools for virtual screening provides a cost-efficient approach to select starting points for drug development. We have developed VSpipe, a user-friendly semi-automated pipeline for structure-based virtual screening. VSpipe uses the existing tools AutoDock and OpenBabel together with software developed in-house, to create an end-to-end virtual screening workflow ranging from the preparation of receptor and ligands to the visualisation of results. VSpipe is efficient and flexible, allowing the users to make choices at different steps, and it is amenable to use in both local and cluster mode. We have validated VSpipe using the human protein tyrosine phosphatase PTP1B as a case study. Using a combination of blind and targeted docking VSpipe identified both new and known functional ligand binding sites. Assessment of different binding clusters using the ligand efficiency plots created by VSpipe, defined a drug-like chemical space for development of PTP1B inhibitors with potential applications to other PTPs. In this study, we show that VSpipe can be deployed to identify and compare different modes of inhibition thus guiding the selection of initial hits for drug discovery.

SUBMITTER: Alvarez-Carretero S

PROVIDER: S-EPMC6017540 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature

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Publications

VSpipe, an Integrated Resource for Virtual Screening and Hit Selection: Applications to Protein Tyrosine Phospahatase Inhibition.

Álvarez-Carretero Sandra S Pavlopoulou Niki N Adams James J Gilsenan Jane J Tabernero Lydia L

Molecules (Basel, Switzerland) 20180207 2

The use of computational tools for virtual screening provides a cost-efficient approach to select starting points for drug development. We have developed VSpipe, a user-friendly semi-automated pipeline for structure-based virtual screening. VSpipe uses the existing tools AutoDock and OpenBabel together with software developed in-house, to create an end-to-end virtual screening workflow ranging from the preparation of receptor and ligands to the visualisation of results. VSpipe is efficient and f ...[more]

PMID: 29414924

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Project description:BackgroundProactive integrated virtual healthcare resource (VHR) use can improve efficiency, maximize resource capacity for delivering optimal coordinated care and improve patient outcomes. Proactive integrated VHR use is vital for delivering high quality care. Our objectives were to identify proactive integrated VHR use among primary care teams, best practices and targeted implementation strategies to promote proactive integrated VHR use.MethodsThis is a mixed-method descriptive study. We employed a community-based participatory approach to collect data and the Consolidated Framework for Implementation Research to analyze and contextualize findings. A cross-sectional sample of primary care team members (n = 65) from a Department of Veterans Affairs medical center participated in focus groups, follow-up interviews (n = 16), and respond to self-report surveys. Operational subject matter experts (n = 15) participated in informant interviews.ResultsSurvey data described current use and factors that influenced singular VHR use and were convergent with qualitative findings. Focus group and interview data described no evidence of proactive integrated VHR use. Differences and similarities were identified between both utilization groups, such as facilitators and barriers, recommendations, patient education and preferred implementation strategies. All groups reported issues around VHR availability knowledge and access and functionality. Participants identified the need for best practices that are specific to care tasks and performance measures. Expert informant interviews identified a list of VHR tools that could be proactively integrated across the healthcare continuum.ConclusionsHealth systems are leveraging technologies to proactively integrate VHR to maximize information exchange, clinical decision support and patient engagement. VHR is critical during global pandemics, such as COVID-19, to maintain access to care coordination and delivery while abiding by public health recommendations. Though recent requirements for reducing contact create an intrinsic motivation, cultural change through education and best practices of proactive integrated use across the healthcare continuum is needed to create a culture of VHR super users.

Dataset Information

VSpipe, an Integrated Resource for Virtual Screening and Hit Selection: Applications to Protein Tyrosine Phospahatase Inhibition.

Publications

VSpipe, an Integrated Resource for Virtual Screening and Hit Selection: Applications to Protein Tyrosine Phospahatase Inhibition.

Similar Datasets

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