Cargando…

FRETraj: integrating single-molecule spectroscopy with molecular dynamics

SUMMARY: Quantitative interpretation of single-molecule FRET experiments requires a model of the dye dynamics to link experimental energy transfer efficiencies to distances between atom positions. We have developed FRETraj, a Python module to predict FRET distributions based on accessible-contact vo...

Descripción completa

Detalles Bibliográficos
Autores principales:	Steffen, Fabio D, Sigel, Roland K O, Börner, Richard
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2021
Materias:	Applications Notes
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10186158/ https://www.ncbi.nlm.nih.gov/pubmed/34478493 http://dx.doi.org/10.1093/bioinformatics/btab615

Ejemplares similares

Site-specific dual-color labeling of long RNAs for single-molecule spectroscopy
por: Zhao, Meng, et al.
Publicado: (2018)

Simulated single molecule microscopy with SMeagol
por: Lindén, Martin, et al.
Publicado: (2016)

Metal ions and sugar puckering balance single-molecule kinetic heterogeneity in RNA and DNA tertiary contacts
por: Steffen, Fabio D., et al.
Publicado: (2020)

Methylscaper: an R/Shiny app for joint visualization of DNA methylation and nucleosome occupancy in single-molecule and single-cell data
por: Knight, Parker, et al.
Publicado: (2021)

PALMsiever: a tool to turn raw data into results for single-molecule localization microscopy
por: Pengo, Thomas, et al.
Publicado: (2015)

SMLocalizer, a GPU accelerated ImageJ plugin for single molecule localization microscopy
por: Bernhem, Kristoffer, et al.
Publicado: (2018)

MD-TASK: a software suite for analyzing molecular dynamics trajectories
por: Brown, David K, et al.
Publicado: (2017)

CoMut: visualizing integrated molecular information with comutation plots
por: Crowdis, Jett, et al.
Publicado: (2020)

GLASSgo in Galaxy: high-throughput, reproducible and easy-to-integrate prediction of sRNA homologs
por: Schäfer, Richard A, et al.
Publicado: (2020)

DyNet: visualization and analysis of dynamic molecular interaction networks
por: Goenawan, Ivan H., et al.
Publicado: (2016)

SCSsim: an integrated tool for simulating single-cell genome sequencing data
por: Yu, Zhenhua, et al.
Publicado: (2020)

MoleculeExperiment enables consistent infrastructure for molecule-resolved spatial omics data in bioconductor
por: Peters Couto, Bárbara Zita, et al.
Publicado: (2023)

PSExplorer: whole parameter space exploration for molecular signaling pathway dynamics
por: Tung, Thai Quang, et al.
Publicado: (2010)

quicksom: Self-Organizing Maps on GPUs for clustering of molecular dynamics trajectories
por: Mallet, Vincent, et al.
Publicado: (2020)

RING-PyMOL: residue interaction networks of structural ensembles and molecular dynamics
por: Del Conte, Alessio, et al.
Publicado: (2023)

Transform-MinER: transforming molecules in enzyme reactions
por: Tyzack, Jonathan D, et al.
Publicado: (2018)

NMRFAM-SPARKY: enhanced software for biomolecular NMR spectroscopy
por: Lee, Woonghee, et al.
Publicado: (2015)

PDBe aggregated API: programmatic access to an integrative knowledge graph of molecular structure data
por: Nair, Sreenath, et al.
Publicado: (2021)

GRACE: a comprehensive web-based platform for integrative single-cell transcriptome analysis
por: Yu, Hao, et al.
Publicado: (2023)

LSMMD-MA: scaling multimodal data integration for single-cell genomics data analysis
por: Meng-Papaxanthos, Laetitia, et al.
Publicado: (2023)

mDCC_tools: characterizing multi-modal atomic motions in molecular dynamics trajectories
por: Kasahara, Kota, et al.
Publicado: (2016)

snakePipes: facilitating flexible, scalable and integrative epigenomic analysis
por: Bhardwaj, Vivek, et al.
Publicado: (2019)

Genoscape: a Cytoscape plug-in to automate the retrieval and integration of gene expression data and molecular networks
por: Clément-Ziza, Mathieu, et al.
Publicado: (2009)

Phenonaut: multiomics data integration for phenotypic space exploration
por: Shave, Steven, et al.
Publicado: (2023)

Correlation-guided Network Integration (CoNI), an R package for integrating numerical omics data that allows multiform graph representations to study molecular interaction networks
por: Monroy Kuhn, José Manuel, et al.
Publicado: (2022)

PACKMAN-Molecule: Python toolbox for structural bioinformatics
por: Khade, Pranav M, et al.
Publicado: (2022)

STACAS: Sub-Type Anchor Correction for Alignment in Seurat to integrate single-cell RNA-seq data
por: Andreatta, Massimo, et al.
Publicado: (2020)

optima: an open-source R package for the Tapestri platform for integrative single cell multiomics data analysis
por: Pei, Dong, et al.
Publicado: (2023)

PyCorrFit—generic data evaluation for fluorescence correlation spectroscopy
por: Müller, Paul, et al.
Publicado: (2014)

CAVER Analyst 2.0: analysis and visualization of channels and tunnels in protein structures and molecular dynamics trajectories
por: Jurcik, Adam, et al.
Publicado: (2018)

ViralFusionSeq: accurately discover viral integration events and reconstruct fusion transcripts at single-base resolution
por: Li, Jing-Woei, et al.
Publicado: (2013)

CellWalkR: an R package for integrating and visualizing single-cell and bulk data to resolve regulatory elements
por: Przytycki, Pawel F, et al.
Publicado: (2022)

scPipe: an extended preprocessing pipeline for comprehensive single-cell ATAC-Seq data integration in R/Bioconductor
por: Amarasinghe, Shanika L, et al.
Publicado: (2023)

ICMA: an integrated cardiac modeling and analysis platform
por: Hussan, Jagir R., et al.
Publicado: (2015)

ADAPT-NMR Enhancer: complete package for reduced dimensionality in protein NMR spectroscopy
por: Lee, Woonghee, et al.
Publicado: (2013)

Photizo: an open-source library for cross-sample analysis of FTIR spectroscopy data
por: Grant-Peters, Melissa, et al.
Publicado: (2022)

Simulations of camera-based single-molecule fluorescence experiments
por: Börner, Richard, et al.
Publicado: (2018)

DDT - Drug Discovery Tool: a fast and intuitive graphics user interface for docking and molecular dynamics analysis
por: Aureli, Simone, et al.
Publicado: (2019)

The ACPYPE web server for small-molecule MD topology generation
por: Kagami, Luciano, et al.
Publicado: (2023)

COSIFER: a Python package for the consensus inference of molecular interaction networks
por: Manica, Matteo, et al.
Publicado: (2020)

Cannot write session to /tmp/vufind_sessions/sess_9h1nhkqkstlpr8p8lg97ui4fht