Assessing the Current State of Amber Force Field Modifications for DNA - Test2 - elhamkhani - TriplyDB

Assessing the Current State of Amber Force Field Modifications for DNA

Assessing the Current State of Amber Force Field Modifications for DNA

http://www.wikidata.org/entity/Q27301352

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Interstrand cross-linking implies contrasting structural consequences for DNA: insights from molecular dynamics.Consecutive non-natural PZ nucleobase pairs in DNA impact helical structure as seen in 50 μs molecular dynamics simulations.Exploring the Dynamics of Propeller Loops in Human Telomeric DNA Quadruplexes Using Atomistic Simulations.Evaluating Force Field Performance in Thermodynamic Calculations of Cyclodextrin Host-Guest Binding: Water Models, Partial Charges, and Host Force Field Parameters.Deficiencies in Molecular Dynamics Simulation-Based Prediction of Protein-DNA Binding Free Energy Landscapes.Advances in RNA molecular dynamics: a simulator's guide to RNA force fields.How to understand atomistic molecular dynamics simulations of RNA and protein-RNA complexes?Accuracy limit of rigid 3-point water models.How accurate are accurate force-fields for B-DNA?Insilico direct folding of thrombin-binding aptamer G-quadruplex at all-atom level.RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.In silico structural modeling of multiple epigenetic marks on DNA.Understanding the Relative Flexibility of RNA and DNA Duplexes: Stretching and Twist-Stretch Coupling.A DNA structural alphabet provides new insight into DNA flexibility.Toward an Expanded Genome: Structural and Computational Characterization of an Artificially Expanded Genetic Information System.AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids.Structural and dynamical instability of DNA caused by high occurrence of d5SICS and dNaM unnatural nucleotides.Re-emergence of an orphan therapeutic target for the treatment of resistant prostate cancer - a thorough conformational and binding analysis for ROR-γ protein.Hexahydrated Mg2+ Binding and Outer-Shell Dehydration on RNA Surface.Effect of Methylation on Local Mechanics and Hydration Structure of DNA.Oxidative damage to epigenetically methylated sites affects DNA stability, dynamics and enzymatic demethylation Why are Hoogsteen base pairs energetically disfavored in A-RNA compared to B-DNA?Molecular Modeling Applied to Nucleic Acid-Based Molecule Development

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Assessing the Current State of Amber Force Field Modifications for DNA

http://www.wikidata.org/entity/Q27301352

description

2016 nî lūn-bûn

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2016 թուականի Յունիսին հրատարակուած գիտական յօդուած

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2016 թվականի հունիսին հրատարակված գիտական հոդված

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2016年の論文

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2016年論文

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2016年論文

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2016年論文

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2016年論文

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2016年論文

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2016年论文

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name

Assessing the Current State of Amber Force Field Modifications for DNA

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Assessing the Current State of Amber Force Field Modifications for DNA

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Assessing the Current State of Amber Force Field Modifications for DNA

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type

label

Assessing the Current State of Amber Force Field Modifications for DNA

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Assessing the Current State of Amber Force Field Modifications for DNA

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Assessing the Current State of Amber Force Field Modifications for DNA

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Assessing the Current State of Amber Force Field Modifications for DNA

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Assessing the Current State of Amber Force Field Modifications for DNA

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Assessing the Current State of Amber Force Field Modifications for DNA

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ACS.JCTC.6B00186

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Journal of Chemical Theory and Computation

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Assessing the Current State of Amber Force Field Modifications for DNA

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James C Robertson

http://www.w3.org/2001/XMLSchema#string

Marie Zgarbová

http://www.w3.org/2001/XMLSchema#string

Petr Jurečka

http://www.w3.org/2001/XMLSchema#string

Rodrigo Galindo-Murillo

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P2860

Structure of a B-DNA dodecamer: conformation and dynamics

Convergence and reproducibility in molecular dynamics simulations of the DNA duplex d(GCACGAACGAACGAACGC)

Detection of alkali metal ions in DNA crystals using state-of-the-art X-ray diffraction experiments

Solution structure of an A-tract DNA bend

Overall structure and sugar dynamics of a DNA dodecamer from homo- and heteronuclear dipolar couplings and 31P chemical shift anisotropy

B-DNA structure is intrinsically polymorphic: even at the level of base pair positions

Molecular structure of a left-handed double helical DNA fragment at atomic resolution

3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures

VMD: visual molecular dynamics

The Amber biomolecular simulation programs

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scholarly article

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10.1021/ACS.JCTC.6B00186

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12

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Thomas E Cheatham

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