Cargando…

MD-TASK: a software suite for analyzing molecular dynamics trajectories

SUMMARY: Molecular dynamics (MD) determines the physical motions of atoms of a biological macromolecule in a cell-like environment and is an important method in structural bioinformatics. Traditionally, measurements such as root mean square deviation, root mean square fluctuation, radius of gyration...

Descripción completa

Detalles Bibliográficos
Autores principales:	Brown, David K, Penkler, David L, Sheik Amamuddy, Olivier, Ross, Caroline, Atilgan, Ali Rana, Atilgan, Canan, Tastan Bishop, Özlem
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2017
Materias:	Applications Notes
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5860072/ https://www.ncbi.nlm.nih.gov/pubmed/28575169 http://dx.doi.org/10.1093/bioinformatics/btx349

Ejemplares similares

MODE-TASK: large-scale protein motion tools
por: Ross, Caroline, et al.
Publicado: (2018)

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

fqtools: an efficient software suite for modern FASTQ file manipulation
por: Droop, Alastair P.
Publicado: (2016)

OmicsAnalyzer: a Cytoscape plug-in suite for modeling omics data
por: Xia, Tian, et al.
Publicado: (2010)

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)

phippery: a software suite for PhIP-Seq data analysis
por: Galloway, Jared G, et al.
Publicado: (2023)

CAFE: a software suite for analysis of paired-sample transposon insertion sequencing data
por: Abramova, Anna, et al.
Publicado: (2021)

POKY: a software suite for multidimensional NMR and 3D structure calculation of biomolecules
por: Lee, Woonghee, et al.
Publicado: (2021)

SCAFE: a software suite for analysis of transcribed cis-regulatory elements in single cells
por: Moody, Jonathan, et al.
Publicado: (2022)

ISA software suite: supporting standards-compliant experimental annotation and enabling curation at the community level
por: Rocca-Serra, Philippe, et al.
Publicado: (2010)

13CFLUX2—high-performance software suite for (13)C-metabolic flux analysis
por: Weitzel, Michael, et al.
Publicado: (2013)

RIBER/DIBER: a software suite for crystal content analysis in the studies of protein–nucleic acid complexes
por: Chojnowski, Grzegorz, et al.
Publicado: (2012)

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

HiCapTools: a software suite for probe design and proximity detection for targeted chromosome conformation capture applications
por: Anil, Anandashankar, et al.
Publicado: (2018)

The UEA sRNA Workbench (version 4.4): a comprehensive suite of tools for analyzing miRNAs and sRNAs
por: Stocks, Matthew B, et al.
Publicado: (2018)

Modulation of Human Hsp90α Conformational Dynamics by Allosteric Ligand Interaction at the C-Terminal Domain
por: Penkler, David L., et al.
Publicado: (2019)

RapGreen, an interactive software and web package to explore and analyze phylogenetic trees
por: Dufayard, Jean-François, et al.
Publicado: (2021)

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)

GlycanAnalyzer: software for automated interpretation of N-glycan profiles after exoglycosidase digestions
por: Walsh, Ian, et al.
Publicado: (2019)

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

MDContactCom: a tool to identify differences of protein molecular dynamics from two MD simulation trajectories in terms of interresidue contacts
por: Motono, Chie, et al.
Publicado: (2021)

Human, vector and parasite Hsp90 proteins: A comparative bioinformatics analysis
por: Faya, Ngonidzashe, et al.
Publicado: (2015)

SPECTRE: a suite of phylogenetic tools for reticulate evolution
por: Bastkowski, Sarah, et al.
Publicado: (2018)

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)

Asterias: A Parallelized Web-based Suite for the Analysis of Expression and aCGH Data
por: Alibés, Andreu, et al.
Publicado: (2007)

RUbioSeq: a suite of parallelized pipelines to automate exome variation and bisulfite-seq analyses
por: Rubio-Camarillo, Miriam, et al.
Publicado: (2013)

CoCAS: a ChIP-on-chip analysis suite
por: Benoukraf, Touati, et al.
Publicado: (2009)

BEDTools: a flexible suite of utilities for comparing genomic features
por: Quinlan, Aaron R., et al.
Publicado: (2010)

TSUNAMI: Translational Bioinformatics Tool Suite for Network Analysis and Mining
por: Huang, Zhi, et al.
Publicado: (2021)

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)

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)

ontologyX: a suite of R packages for working with ontological data
por: Greene, Daniel, et al.
Publicado: (2017)

MAGETabulator, a suite of tools to support the microarray data format MAGE-TAB
por: Rayner, Tim F., et al.
Publicado: (2009)

CD-HIT Suite: a web server for clustering and comparing biological sequences
por: Huang, Ying, et al.
Publicado: (2010)

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

C2Analyzer: Co-target–Co-function Analyzer
por: Aftabuddin, Md., et al.
Publicado: (2014)

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

Cannot write session to /tmp/vufind_sessions/sess_e2lud3abp6ve6lhdo0fkp9cbmf