Dataset Information

POVME 3.0: Software for Mapping Binding Pocket Flexibility.

ABSTRACT: We present a substantial update to the open-source POVME binding pocket analysis software. New capabilities of POVME 3.0 include a flexible chemical coloring scheme for feature identification, postanalysis tools for comparing large ensembles of pockets (e.g., from molecular dynamics simulations), and the introduction of scripts and methods that facilitate binding pocket comparison and analysis. We envision the use of this software for visualization of binding pocket dynamics, selection of representative structures for ensemble docking, and incorporation of molecular dynamics results into ligand design efforts.

SUBMITTER: Wagner JR

PROVIDER: S-EPMC5751414 | biostudies-literature | 2017 Sep

REPOSITORIES: biostudies-literature

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POVME 3.0: Software for Mapping Binding Pocket Flexibility.

Wagner Jeffrey R JR Sørensen Jesper J Hensley Nathan N Wong Celia C Zhu Clare C Perison Taylor T Amaro Rommie E RE

Journal of chemical theory and computation 20170830 9

We present a substantial update to the open-source POVME binding pocket analysis software. New capabilities of POVME 3.0 include a flexible chemical coloring scheme for feature identification, postanalysis tools for comparing large ensembles of pockets (e.g., from molecular dynamics simulations), and the introduction of scripts and methods that facilitate binding pocket comparison and analysis. We envision the use of this software for visualization of binding pocket dynamics, selection of repres ...[more]

PMID: 28800393

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Project description:BackgroundCardiac optical mapping is an imaging technique that measures fluorescent signals across a cardiac preparation. Dual optical imaging of voltage-sensitive and calcium-sensitive probes allows for simultaneous recordings of cardiac action potentials and intracellular calcium transients with high spatiotemporal resolution. The analysis of these complex optical datasets is both time intensive and technically challenging; as such, we have developed a software package for semi-automated image processing and analysis. Herein, we report an updated version of our software package (KairoSight-3.0) with features to enhance the characterization of cardiac parameters using optical signals.MethodsTo test software validity and applicability, we used Langendorff-perfused heart preparations to record transmembrane voltage and intracellular calcium signals from the epicardial surface. Isolated hearts from guinea pigs and rats were loaded with a potentiometric dye (RH237) and/or calcium indicator dye (Rhod-2AM) and fluorescent signals were acquired. We used Python 3.8.5 programming language to develop the KairoSight-3.0 software. Cardiac maps were validated with a user-specified manual mapping approach.ResultsManual maps of action potential duration (30 or 80 % repolarization), calcium transient duration (30 or 80 % reuptake), action potential and calcium transient alternans were constituted to validate the accuracy of software-generated maps. Manual and software maps had high accuracy, with >97 % of manual and software values falling within 10 ms of each other and >75 % within 5 ms for action potential duration and calcium transient duration measurements (n = 1000-2000 pixels). Further, our software package includes additional measurement tools to analyze signal-to-noise ratio, conduction velocity, action potential and calcium transient alternans, and action potential-calcium transient coupling time to produce physiologically meaningful optical maps.ConclusionsKairoSight-3.0 has enhanced capabilities to perform measurements of cardiac electrophysiology, calcium handling, alternans, and the excitation-contraction coupling with satisfactory accuracy.

Dataset Information

POVME 3.0: Software for Mapping Binding Pocket Flexibility.

Publications

POVME 3.0: Software for Mapping Binding Pocket Flexibility.

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