iBIOMES Lite: Summarizing Biomolecular Simulation Data in Limited Settings

Thibault, Julien; Cheatham, Thomas E.; Facelli, Julio C.

doi:10.1021/ci500173w

Cited by 12 publications

(10 citation statements)

References 14 publications

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“…Analogously, user-specified analysis tools can be combined with interactive visualization in a modular fashion. As an example, iBIOMES facilitates searchability and findability by providing a metadata schema for indexing and summarizing MD data in a web-searchable representation [46,47]. In summary, decentralized options may be used by scientists preferring instant, independent and creative solutions for sharing and publication of MD trajectories.…”

Section: Trends In Biochemical Sciencesmentioning

confidence: 99%

Bringing Molecular Dynamics Simulation Data into View

Hildebrand

Rose

Tiemann

2019

Trends in Biochemical Sciences

186

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Molecular dynamics (MD) simulations monitor time-resolved motions of macromolecules. While visualization of MD trajectories allows an instant and intuitive understanding of dynamics and function, so far mainly static representations are provided in the published literature. Recent advances in browser technology may allow for the sharing of trajectories through interactive visualization on the web. We believe that providing intuitive and interactive visualization, along with related protocols and analysis data, promotes understanding, reliability, and reusability of MD simulations. Existing barriers for sharing MD simulations are discussed and emerging solutions are highlighted. We predict that interactive visualization of MD trajectories will quickly be adopted by researchers, research consortiums, journals, and funding agencies to gather and distribute results from MD simulations via the web.

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Section: Trends In Biochemical Sciencesmentioning

confidence: 99%

Bringing Molecular Dynamics Simulation Data into View

Hildebrand

Rose

Tiemann

2019

Trends in Biochemical Sciences

186

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“…The simulations, experiments in iBIOMES nomenclature, 13,17,18 represent seven types of systems as indicated in Table 1. All models except the systems labeled Nuc146 and Nuc147 were based on protein databank entry 1KX5.…”

Section: Modelingmentioning

confidence: 99%

TMB-iBIOMES: An iBIOMES-Lite Database of Nucleosome Trajectories and Meta-Analysis

Sun¹,

Li²,

Bishop³

2019

Preprint

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<div>Here we introduce our TMB-iBIOMES database which serves as both a reference for future comparative, on-demand simulations of nucleosomes and a demonstration of iBIOMES-Lite as a tool for managing a laboratory's simulation inventory. TMB-iBIOMES contains over 20 microseconds of all atom molecular dynamics simulations for over 500 different realizations of the nucleosome. For every simulation, the original input, output, de-watered trajectories, RMSD, and DNA helical parameter data are provided. Closely related simulations are grouped together, and a meta-analysis of each group is provided. The data can be navigated in a file browser format or downloaded directly with command line tools. Collectively the simulations provide a novel view of nucleosomal DNA. Compared to DNA free in solution, DNA on the nucleosome is not highly deformed or tightly restricted as determined by DNA helical parameter analysis. The overall conformation is restricted to a specific left-handed super helix, but the range of conformations explored by individual base pairs is larger than that observed for DNA free in solution. </div>

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“…Coupled with high performance high throughput workflows [62] and our iBIOMES-Lite [63] database of nucleosome simulations [64], a software ecosystem now exists for overnight comparative molecular dynamics simulations of nucleosomes.…”

Section: Nucleosome Modelingmentioning

confidence: 99%

G-Dash: A Genome Dashboard Integrating Modeling and Informatics

Sun

Bishop

2018

Preprint

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Genomics is a sequence based informatics science and a structure based molecular material science. There are few tools available that unite these approaches in a scientifically robust manner. Here we describe G-Dash, a web based prototype of a genomics dashboard, specifically designed to integrate informatics and 3D material studies of chromatin. G-Dash unites our Interactive Chromatin Modeling(ICM) tools with the Biodalliance genome browser and the JSMol molecular viewer to rapidly fold any DNA sequence into atomic or coarse-grained models of DNA, nucleosomes or chromatin. As a chromatin modeling tool, G-Dash enables users to specify nucleosome positions from various experimental or theoretical sources, interactively manipulate nucleosomes, and assign different conformational states to each nucleosome. As an informatics tool, data associated with 3D structures are displayed as tracks in a genome browser. The exchange of data between informatics and structure is bi-directional so any informatics track can inform a molecular structure (e.g. color by function) and structure features can be displayed as informatics tracks in a genome browser(e.g. Roll, Slide, or Twist). As a sample application, models of the CHA1 promoter based on experimentally determined nucleosome positions are explored with G-Dash. Steric clashes and DNA knotting are observed but can be resolved with G-Dash's minimal coarse-grained model without significant variation in structure. Results raise questions about the interpretation of nucleosome positioning data and promoter structures. In this regard, G-Dash is a novel tool for investigating structure-function relationships for regions of the genome ranging from base pairs to chromosomes and for generating, validating and testing mechanistic hypotheses.

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iBIOMES Lite: Summarizing Biomolecular Simulation Data in Limited Settings

Cited by 12 publications

References 14 publications

Bringing Molecular Dynamics Simulation Data into View

Bringing Molecular Dynamics Simulation Data into View

TMB-iBIOMES: An iBIOMES-Lite Database of Nucleosome Trajectories and Meta-Analysis

G-Dash: A Genome Dashboard Integrating Modeling and Informatics

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