Cargando…

Molecular dynamics simulations: advances and applications

Molecular dynamics simulations have evolved into a mature technique that can be used effectively to understand macromolecular structure-to-function relationships. Present simulation times are close to biologically relevant ones. Information gathered about the dynamic properties of macromolecules is...

Descripción completa

Detalles Bibliográficos
Autores principales:	Hospital, Adam, Goñi, Josep Ramon, Orozco, Modesto, Gelpí, Josep L
Formato:	Online Artículo Texto
Lenguaje:	English
Publicado:	Dove Medical Press 2015
Materias:	Review
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4655909/ https://www.ncbi.nlm.nih.gov/pubmed/26604800 http://dx.doi.org/10.2147/AABC.S70333

Ejemplares similares

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

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

NAFlex: a web server for the study of nucleic acid flexibility
por: Hospital, Adam, 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)

Long-timescale dynamics of the Drew–Dickerson dodecamer
por: Dans, Pablo D., et al.
Publicado: (2016)

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

BioExcel Building Blocks, a software library for interoperable biomolecular simulation workflows
por: Andrio, Pau, et al.
Publicado: (2019)

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

Exploring the reasons for the large density of triplex-forming oligonucleotide target sequences in the human regulatory regions
por: Goñi, Josep Ramon, et al.
Publicado: (2006)

Molywood: streamlining the design and rendering of molecular movies
por: Wieczór, Miłosz, et al.
Publicado: (2020)

Molecular Dynamics Study of Naturally Existing Cavity Couplings in Proteins
por: Barbany, Montserrat, et al.
Publicado: (2015)

PMut: a web-based tool for the annotation of pathological variants on proteins, 2017 update
por: López-Ferrando, Víctor, et al.
Publicado: (2017)

Molecular Dynamics Simulations: Advances and Applications
por: Filipe, Hugo A. L., et al.
Publicado: (2022)

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

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

Probing allosteric regulations with coevolution-driven molecular simulations
por: Colizzi, Francesco, et al.
Publicado: (2021)

MMPBSA Decomposition of the Binding Energy throughout a Molecular Dynamics Simulation of Amyloid-Beta (Aß(10−35)) Aggregation
por: Campanera, Josep M., et al.
Publicado: (2010)

A procedure for identifying homologous alternative splicing events
por: Talavera, David, et al.
Publicado: (2007)

Determining promoter location based on DNA structure first-principles calculations
por: Goñi, J Ramon, et al.
Publicado: (2007)

Applications of Molecular Dynamics Simulation in Protein Study
por: Sinha, Siddharth, et al.
Publicado: (2022)

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

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

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

Recent Advances in Molecular Dynamics Simulations of Tau Fibrils and Oligomers
por: Barredo, Prechiel A., et al.
Publicado: (2023)

Application of Molecular Dynamics Simulations in the Analysis of Cyclodextrin Complexes
por: Mazurek, Anna Helena, et al.
Publicado: (2021)

Changes in the free-energy landscape of p38α MAP kinase through its canonical activation and binding events as studied by enhanced molecular dynamics simulations
por: Kuzmanic, Antonija, et al.
Publicado: (2017)

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

Application of molecular dynamics simulation in self-assembled cancer nanomedicine
por: Xu, Xueli, et al.
Publicado: (2023)

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

SEABED: Small molEcule activity scanner weB servicE baseD
por: Fenollosa, Carlos, et al.
Publicado: (2015)

Advances in Molecular Dynamics Simulations and Enhanced Sampling Methods for the Study of Protein Systems
por: Lazim, Raudah, et al.
Publicado: (2020)

Recent Advances of Studies on Cell-Penetrating Peptides Based on Molecular Dynamics Simulations
por: Ouyang, Jun, et al.
Publicado: (2022)

Applications of Molecular Dynamics Simulation in Structure Prediction of Peptides and Proteins
por: Geng, Hao, et al.
Publicado: (2019)

Molecular dynamics modelling of the interaction of a synthetic zinc-finger miniprotein with DNA
por: Rodriguez, Jessica, et al.
Publicado: (2023)

BioSWR – Semantic Web Services Registry for Bioinformatics
por: Repchevsky, Dmitry, et al.
Publicado: (2014)

Exploring the complete mutational space of the LDL receptor LA5 domain using molecular dynamics: linking SNPs with disease phenotypes in familial hypercholesterolemia
por: Angarica, Vladimir Espinosa, et al.
Publicado: (2016)

Algorithms for molecular dynamics simulations: advancing the computational horizon
por: Hedman, Fredrik
Publicado: (2006)

Molecular dynamics simulations and drug discovery
por: Durrant, Jacob D, et al.
Publicado: (2011)

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

Comparison of molecular dynamics and superfamily spaces of protein domain deformation
por: Velázquez-Muriel, Javier A, et al.
Publicado: (2009)

Cannot write session to /tmp/vufind_sessions/sess_tj7dcqvma6icsphoktri8l5rj2