Cargando…

Long-timescale dynamics of the Drew–Dickerson dodecamer

We present a systematic study of the long-timescale dynamics of the Drew–Dickerson dodecamer (DDD: d(CGCGAATTGCGC)(2)) a prototypical B-DNA duplex. Using our newly parameterized PARMBSC1 force field, we describe the conformational landscape of DDD in a variety of ionic environments from minimal salt...

Descripción completa

Detalles Bibliográficos
Autores principales:	Dans, Pablo D., Danilāne, Linda, Ivani, Ivan, Dršata, Tomáš, Lankaš, Filip, Hospital, Adam, Walther, Jürgen, Pujagut, Ricard Illa, Battistini, Federica, Gelpí, Josep Lluis, Lavery, Richard, Orozco, Modesto
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Oxford University Press 2016
Materias:	Computational Biology
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4872116/ https://www.ncbi.nlm.nih.gov/pubmed/27084952 http://dx.doi.org/10.1093/nar/gkw264

Ejemplares similares

Kinetics of the Conformational Transformation between B- and A-Forms in the Drew–Dickerson Dodecamer
por: Kovaleva, Natalya A., et al.
Publicado: (2020)

The static and dynamic structural heterogeneities of B-DNA: extending Calladine–Dickerson rules
por: Dans, Pablo D, et al.
Publicado: (2019)

Nucleosome Dynamics: a new tool for the dynamic analysis of nucleosome positioning
por: Buitrago, Diana, et al.
Publicado: (2019)

How accurate are accurate force-fields for B-DNA?
por: Dans, Pablo D., et al.
Publicado: (2017)

PARMBSC1: A REFINED FORCE-FIELD FOR DNA SIMULATIONS
por: Ivani, Ivan, et al.
Publicado: (2015)

BioExcel Building Blocks Workflows (BioBB-Wfs), an integrated web-based platform for biomolecular simulations
por: Bayarri, Genís, et al.
Publicado: (2022)

John Drew
Publicado: (1918)

BIGNASim: a NoSQL database structure and analysis portal for nucleic acids simulation data
por: Hospital, Adam, et al.
Publicado: (2016)

Molecular dynamics simulations: advances and applications
por: Hospital, Adam, et al.
Publicado: (2015)

Mr. Drew, on Inoculation
por: Drew, Walter
Publicado: (1805)

Obituary Gerhart Drews
por: Fuchs, Georg, et al.
Publicado: (2023)

NAFlex: a web server for the study of nucleic acid flexibility
por: Hospital, Adam, et al.
Publicado: (2013)

Unraveling the sequence-dependent polymorphic behavior of d(CpG) steps in B-DNA
por: Dans, Pablo Daniel, et al.
Publicado: (2014)

Modulation of the helical properties of DNA: next-to-nearest neighbour effects and beyond
por: Balaceanu, Alexandra, et al.
Publicado: (2019)

A multi-modal coarse grained model of DNA flexibility mappable to the atomistic level
por: Walther, Jürgen, et al.
Publicado: (2020)

Photocontrolled reversible self-assembly of dodecamer nitrilase
por: Yu, Qiao, et al.
Publicado: (2017)

Drew Heywood's Windows 2000 Network services
por: Heywood, Drew, et al.
Publicado: (2001)

Strain-specific Fibril Propagation by an Aβ Dodecamer
por: Dean, Dexter N., et al.
Publicado: (2017)

Keeping Dr. Charles Richard Drew’s legacy alive
por: Parker-Kelly, Darlene, et al.
Publicado: (2019)

The structural impact of DNA mismatches
por: Rossetti, Giulia, et al.
Publicado: (2015)

Exploring polymorphisms in B-DNA helical conformations
por: Dans, Pablo D., et al.
Publicado: (2012)

Explaining the striking difference in twist-stretch coupling between DNA and RNA: A comparative molecular dynamics analysis
por: Liebl, Korbinian, et al.
Publicado: (2015)

Interstrand cross-linking implies contrasting structural consequences for DNA: insights from molecular dynamics
por: Bignon, Emmanuelle, et al.
Publicado: (2017)

Structure and energy of a DNA dodecamer under tensile load
por: Piana, Stefano
Publicado: (2005)

DNA structure directs positioning of the mitochondrial genome packaging protein Abf2p
por: Chakraborty, Arka, et al.
Publicado: (2017)

Mechanical properties of symmetric and asymmetric DNA A-tracts: implications for looping and nucleosome positioning
por: Dršata, Tomáš, et al.
Publicado: (2014)

Modeling Amyloid-Beta as Homogeneous Dodecamers and in Complex with Cellular Prion Protein
por: Gallion, Steven L.
Publicado: (2012)

Towards a molecular dynamics consensus view of B-DNA flexibility
por: Pérez, Alberto, et al.
Publicado: (2008)

Dodecamer assembly of a metazoan AAA(+) chaperone couples substrate extraction to refolding
por: Gupta, Arpit, et al.
Publicado: (2023)

The complete chloroplast genome of Russian sage Salvia yangii B. T. Drew (Lamiaceae)
por: Cao, Meng-Ting, et al.
Publicado: (2020)

Exploring Early Stages of the Chemical Unfolding of Proteins at the Proteome Scale
por: Candotti, Michela, et al.
Publicado: (2013)

Dodecamer d-AGATCTAGATCT and a Homologous Hairpin form Triplex in the Presence of Peptide REWER
por: Das, Amrita, et al.
Publicado: (2013)

Light Intensity and Temperature Effect on Salvia yangii (B. T. Drew) Metabolic Profile in vitro
por: Kozłowska, Weronika, et al.
Publicado: (2022)

Molecular basis of Arginine and Lysine DNA sequence-dependent thermo-stability modulation
por: Martin, Benjamin, et al.
Publicado: (2022)

The temperature dependence of the helical twist of DNA
por: Kriegel, Franziska, et al.
Publicado: (2018)

Crystal structures of B-DNA dodecamer containing the epigenetic modifications 5-hydroxymethylcytosine or 5-methylcytosine
por: Renciuk, Daniel, et al.
Publicado: (2013)

3dRS, a Web-Based Tool to Share Interactive Representations of 3D Biomolecular Structures and Molecular Dynamics Trajectories
por: Bayarri, Genís, et al.
Publicado: (2021)

A multi-state model of the CaMKII dodecamer suggests a role for calmodulin in maintenance of autophosphorylation
por: Pharris, Matthew C., et al.
Publicado: (2019)

Purification and cryo-EM structure determination of VCP/p97 dodecamers from mammalian and bacterial cells
por: Yu, Guimei, et al.
Publicado: (2022)

Understanding the Connection between Epigenetic DNA Methylation and Nucleosome Positioning from Computer Simulations
por: Portella, Guillem, et al.
Publicado: (2013)

Cannot write session to /tmp/vufind_sessions/sess_lek5i22bdmhrbflreemqs78ckr