4.6 Article

Modelling aptamers with nucleic acid mimics (NAM): From sequence to three-dimensional docking

Related references

Note: Only part of the references are listed.
Review Biochemical Research Methods

In silico approach for Post-SELEX DNA aptamers: A mini-review

Nor Azlina Ahmad et al.

Summary: This study utilizes bioinformatics tools to analyze the structural parameters and ligand interaction of DNA aptamers, finding Mfold and RNA Composer to be commonly used tools for secondary and tertiary structure prediction, and ZDOCK and AutoDock as preferred docking simulation tools.

JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2021)

Article Biochemistry & Molecular Biology

DNA aptamers against the DUX4 protein reveal novel therapeutic implications for FSHD

Christian Klingler et al.

FASEB JOURNAL (2020)

Article Chemistry, Physical

Scalable molecular dynamics on CPU and GPU architectures with NAMD

James C. Phillips et al.

JOURNAL OF CHEMICAL PHYSICS (2020)

Article Biochemistry & Molecular Biology

Predictions and analyses of RNA nearest neighbor parameters for modified nucleotides

Melissa C. Hopfinger et al.

NUCLEIC ACIDS RESEARCH (2020)

Article Biochemistry & Molecular Biology

The assessment of three dimensional modelling design for single strand DNA aptamers for computational chemistry application

Mohamad Zulkeflee Sabri et al.

BIOPHYSICAL CHEMISTRY (2020)

Article Biochemistry & Molecular Biology

3dRNA: Building RNA 3D structure with improved template library

Yi Zhang et al.

COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL (2020)

Article Biophysics

QRNAS: software tool for refinement of nucleic acid structures

Juliusz Stasiewicz et al.

BMC STRUCTURAL BIOLOGY (2019)

Review Chemistry, Multidisciplinary

Modeling, Simulations, and Bioinformatics at the Service of RNA Structure

Pablo D. Dans et al.

Review Biochemistry & Molecular Biology

Key Aspects of Nucleic Acid Library Design for in Vitro Selection

Maria A. Vorobyeva et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2018)

Review Biochemistry & Molecular Biology

Biological applications of xeno nucleic acids

Kunihiko Morihiro et al.

MOLECULAR BIOSYSTEMS (2017)

Article Biochemistry & Molecular Biology

HDOCK: a web server for protein-protein and protein-DNA/RNA docking based on a hybrid strategy

Yumeng Yan et al.

NUCLEIC ACIDS RESEARCH (2017)

Article Multidisciplinary Sciences

Three-dimensional modeling of single stranded DNA hairpins for aptamer-based biosensors

Iman Jeddi et al.

SCIENTIFIC REPORTS (2017)

Review Biotechnology & Applied Microbiology

ABCs of DNA aptamer and related assay development

Tarun Kumar Sharma et al.

BIOTECHNOLOGY ADVANCES (2017)

Article Biochemistry & Molecular Biology

Structure of HIV-1 reverse transcriptase bound to a novel 38-mer hairpin template-primer DNA aptamer

Matthew T. Miller et al.

PROTEIN SCIENCE (2016)

Review Biochemical Research Methods

Post-SELEX optimization of aptamers

Shunxiang Gao et al.

ANALYTICAL AND BIOANALYTICAL CHEMISTRY (2016)

Article Biotechnology & Applied Microbiology

Computational approach to analyze isolated ssDNA aptamers against angiotensin II

Mohammad Heiat et al.

JOURNAL OF BIOTECHNOLOGY (2016)

Article Biochemistry & Molecular Biology

Structural basis for specific inhibition of Autotaxin by a DNA aptamer

Kazuki Kato et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2016)

Article Biochemistry & Molecular Biology

Structural basis for specific inhibition of Autotaxin by a DNA aptamer

Kazuki Kato et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2016)

Review Biochemistry & Molecular Biology

The Toolbox for Modified Aptamers

Sergey A. Lapa et al.

MOLECULAR BIOTECHNOLOGY (2016)

Article Biotechnology & Applied Microbiology

Current approaches in SELEX: An update to aptamer selection technology

Mariia Darmostuk et al.

BIOTECHNOLOGY ADVANCES (2015)

Review Chemistry, Medicinal

Aptamers Overview: Selection, Features and Applications

Luiza I. Hernandez et al.

CURRENT TOPICS IN MEDICINAL CHEMISTRY (2015)

Article Chemistry, Physical

Searching the Sequence Space for Potent Aptamers Using SELEX in Silico

Qingtong Zhou et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Chemistry, Multidisciplinary

New Ways to Boost Molecular Dynamics Simulations

Elmar Krieger et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2015)

Article Biochemistry & Molecular Biology

NPDock: a web server for protein-nucleic acid docking

Irina Tuszynska et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Biochemistry & Molecular Biology

PLIP: fully automated protein-ligand interaction profiler

Sebastian Salentin et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Biochemistry & Molecular Biology

Structure analysis of free and bound states of an RNA aptamer against ribosomal protein S8 from Bacillus anthracis

Milya Davlieva et al.

NUCLEIC ACIDS RESEARCH (2014)

Review Biochemistry & Molecular Biology

Characterization of Aptamer-Protein Complexes by X-ray Crystallography and Alternative Approaches

Vincent J. B. Ruigrok et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2012)

Article Biochemistry & Molecular Biology

Automated 3D structure composition for large RNAs

Mariusz Popenda et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Chemistry, Multidisciplinary

Gabedit-A Graphical User Interface for Computational Chemistry Softwares

Abdul-Rahman Allouche

JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)

Article Biochemical Research Methods

RNAstructure: software for RNA secondary structure prediction and analysis

Jessica S. Reuter et al.

BMC BIOINFORMATICS (2010)

Review Biochemical Research Methods

Prediction and design of DNA and RNA structures

Ebbe Sloth Andersen

NEW BIOTECHNOLOGY (2010)

Article Chemistry, Multidisciplinary

AutoDock4 and AutoDockTools4: Automated Docking with Selective Receptor Flexibility

Garrett M. Morris et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2009)

Article Biochemistry & Molecular Biology

3D-DART: a DNA structure modelling server

Marc van Dijk et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Biochemistry & Molecular Biology

New metrics for comparing and assessing discrepancies between RNA 3D structures and models

Marc Parisien et al.

Article Biochemistry & Molecular Biology

RNA2D3D: A program for generating, viewing, and comparing 3-dimensional models of RNA

Hugo M. Martinez et al.

JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS (2008)

Article Biochemistry & Molecular Biology

The Vienna RNA Websuite

Andreas R. Gruber et al.

NUCLEIC ACIDS RESEARCH (2008)

Review Biochemical Research Methods

SELEX-A (r)evolutionary method to generate high-affinity nucleic acid ligands

Regina Stoltenburg et al.

BIOMOLECULAR ENGINEERING (2007)

Article Biochemistry & Molecular Biology

NMR structure of a kissing complex formed between the TAR RNA element of HIV-1 and a LNA-modified aptamer

Isabelle Lebars et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Biochemical Research Methods

Graphical exploratory data analysis of RNA secondary structure dynamics predicted by the massively parallel genetic algorithm

Bruce A. Shapiro et al.

JOURNAL OF MOLECULAR GRAPHICS & MODELLING (2006)

Article Biochemistry & Molecular Biology

GRAMM-X public web server for protein-protein docking

Andrey Tovchigrechko et al.

NUCLEIC ACIDS RESEARCH (2006)

Article Biochemistry & Molecular Biology

Kinefold web server for RNA/DNA folding path and structure prediction including pseudoknots and knots

A Xayaphoummine et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Biochemistry & Molecular Biology

Mfold web server for nucleic acid folding and hybridization prediction

M Zuker

NUCLEIC ACIDS RESEARCH (2003)