Cargando…

MODE-TASK: large-scale protein motion tools

SUMMARY: MODE-TASK, a novel and versatile software suite, comprises Principal Component Analysis, Multidimensional Scaling, and t-Distributed Stochastic Neighbor Embedding techniques using Molecular Dynamics trajectories. MODE-TASK also includes a Normal Mode Analysis tool based on Anisotropic Netwo...

Descripción completa

Detalles Bibliográficos
Autores principales:	Ross, Caroline, Nizami, Bilal, Glenister, Michael, Sheik Amamuddy, Olivier, Atilgan, Ali Rana, Atilgan, Canan, Tastan Bishop, Özlem
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2018
Materias:	Applications Notes
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6198866/ https://www.ncbi.nlm.nih.gov/pubmed/29850770 http://dx.doi.org/10.1093/bioinformatics/bty427

Ejemplares similares

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

MDM-TASK-web: MD-TASK and MODE-TASK web server for analyzing protein dynamics
por: Sheik Amamuddy, Olivier, et al.
Publicado: (2021)

Characterizing early drug resistance-related events using geometric ensembles from HIV protease dynamics
por: Sheik Amamuddy, Olivier, et al.
Publicado: (2018)

Improving fold resistance prediction of HIV-1 against protease and reverse transcriptase inhibitors using artificial neural networks
por: Sheik Amamuddy, Olivier, et al.
Publicado: (2017)

Determining the unbinding events and conserved motions associated with the pyrazinamide release due to resistance mutations of Mycobacterium tuberculosis pyrazinamidase
por: Sheik Amamuddy, Olivier, et al.
Publicado: (2020)

Deciphering Isoniazid Drug Resistance Mechanisms on Dimeric Mycobacterium tuberculosis KatG via Post-molecular Dynamics Analyses Including Combined Dynamic Residue Network Metrics
por: Barozi, Victor, et al.
Publicado: (2022)

Designing Molecular Dynamics Simulations to Shift Populations of the Conformational States of Calmodulin
por: Aykut, Ayse Ozlem, et al.
Publicado: (2013)

Integrated Computational Approaches and Tools for Allosteric Drug Discovery
por: Sheik Amamuddy, Olivier, et al.
Publicado: (2020)

Allosteric pockets and dynamic residue network hubs of falcipain 2 in mutations including those linked to artemisinin resistance
por: Okeke, Chiamaka Jessica, et al.
Publicado: (2021)

Novel dynamic residue network analysis approaches to study allosteric modulation: SARS-CoV-2 M(pro) and its evolutionary mutations as a case study
por: Sheik Amamuddy, Olivier, et al.
Publicado: (2021)

Perturbation-Response Scanning Reveals Ligand Entry-Exit Mechanisms of Ferric Binding Protein
por: Atilgan, Canan, et al.
Publicado: (2009)

Slipknot or Crystallographic Error: A Computational Analysis of the Plasmodium falciparum DHFR Structural Folds
por: Tata, Rolland B., et al.
Publicado: (2022)

Assortative Mixing in Close-Packed Spatial Networks
por: Turgut, Deniz, et al.
Publicado: (2010)

DHFR Mutants Modulate Their Synchronized Dynamics with the Substrate by Shifting Hydrogen Bond Occupancies
por: Cetin, Ebru, et al.
Publicado: (2022)

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

A Coarse-Grained Methodology Identifies Intrinsic Mechanisms That Dissociate Interacting Protein Pairs
por: Abdizadeh, Haleh, et al.
Publicado: (2020)

Antiviral Mechanisms of N-Phenyl Benzamides on Coxsackie Virus A9
por: Laajala, Mira, et al.
Publicado: (2023)

MIAMI––a tool for non-targeted detection of metabolic flux changes for mode of action identification
por: Dudek, Christian-Alexander, et al.
Publicado: (2020)

Mechanism of Action of Non-Synonymous Single Nucleotide Variations Associated with α-Carbonic Anhydrase II Deficiency
por: Sanyanga, Taremekedzwa Allan, et al.
Publicado: (2019)

AssociationViewer: a scalable and integrated software tool for visualization of large-scale variation data in genomic context
por: Martin, Olivier, et al.
Publicado: (2009)

Novel features and enhancements in BioBin, a tool for the biologically inspired binning and association analysis of rare variants
por: Basile, Anna O, et al.
Publicado: (2018)

GenRisk: a tool for comprehensive genetic risk modeling
por: Aldisi, Rana, et al.
Publicado: (2022)

CycSim—an online tool for exploring and experimenting with genome-scale metabolic models
por: Le Fèvre, F., et al.
Publicado: (2009)

Cistrome Explorer: an interactive visual analysis tool for large-scale epigenomic data
por: L’Yi, Sehi, et al.
Publicado: (2023)

ecmtool: fast and memory-efficient enumeration of elementary conversion modes
por: Buchner, Bianca, et al.
Publicado: (2023)

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses
por: Capella-Gutiérrez, Salvador, et al.
Publicado: (2009)

SLIDE – a web-based tool for interactive visualization of large-scale – omics data
por: Ghosh, Soumita, et al.
Publicado: (2019)

GSATools: analysis of allosteric communication and functional local motions using a structural alphabet
por: Pandini, Alessandro, et al.
Publicado: (2013)

Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics
por: Bonnal, Raoul J.P., et al.
Publicado: (2012)

CytoModeler: a tool for bridging large-scale network analysis and dynamic quantitative modeling
por: Xia, Tian, et al.
Publicado: (2011)

CImbinator: a web-based tool for drug synergy analysis in small- and large-scale datasets
por: Flobak, Åsmund, et al.
Publicado: (2017)

GEMMER: GEnome-wide tool for Multi-scale Modeling data Extraction and Representation for Saccharomyces cerevisiae
por: Mondeel, Thierry D G A, et al.
Publicado: (2018)

PiMP my metabolome: an integrated, web-based tool for LC-MS metabolomics data
por: Gloaguen, Yoann, et al.
Publicado: (2017)

eBDIMS server: protein transition pathways with ensemble analysis in 2D-motion spaces
por: Orellana, Laura, et al.
Publicado: (2019)

pgainsim: an R-package to assess the mode of inheritance for quantitative trait loci in GWAS
por: Scherer, Nora, et al.
Publicado: (2021)

EvAM-Tools: tools for evolutionary accumulation and cancer progression models
por: Diaz-Uriarte, Ramon, et al.
Publicado: (2022)

Polyphenols Epigallocatechin Gallate and Resveratrol, and Polyphenol-Functionalized Nanoparticles Prevent Enterovirus Infection through Clustering and Stabilization of the Viruses
por: Reshamwala, Dhanik, et al.
Publicado: (2021)

The Scramble conversion tool
por: Bonfield, James K.
Publicado: (2014)

bammds: a tool for assessing the ancestry of low-depth whole-genome data using multidimensional scaling (MDS)
por: Malaspinas, Anna-Sapfo, et al.
Publicado: (2014)

SINE_scan: an efficient tool to discover short interspersed nuclear elements (SINEs) in large-scale genomic datasets
por: Mao, Hongliang, et al.
Publicado: (2017)

Cannot write session to /tmp/vufind_sessions/sess_mmqsa3hulcgbku5gj969253olp