4.7 Review

Aptamer Bioinformatics

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Review Biochemistry & Molecular Biology

Evolution of Complex Target SELEX to Identify Aptamers against Mammalian Cell-Surface Antigens

Prabodhika Mallikaratchy

MOLECULES (2017)

Article Biochemistry & Molecular Biology

Structural basis for high-affinity fluorophore binding and activation by RNA Mango

Robert J. Trachman et al.

NATURE CHEMICAL BIOLOGY (2017)

Article Mathematics, Interdisciplinary Applications

Selective Phenome Growth Adapted NK Model: A Novel Landscape to Represent Aptamer Ligand Binding

Andrew Brian Kinghorn et al.

COMPLEXITY (2017)

Article Biochemistry & Molecular Biology

Selection of DNA Aptamers for Ovarian Cancer Biomarker CA125 Using One-Pot SELEX and High-Throughput Sequencing

Delia J. Scoville et al.

JOURNAL OF NUCLEIC ACIDS (2017)

Review Chemistry, Multidisciplinary

Advancements in Aptamer Discovery Technologies

Michael R. Gotrik et al.

ACCOUNTS OF CHEMICAL RESEARCH (2016)

Article Chemistry, Analytical

Aptamer Affinity Maturation by Resampling and Microarray Selection

Andrew B. Kinghorn et al.

ANALYTICAL CHEMISTRY (2016)

Review Genetics & Heredity

Coming of age: ten years of next-generation sequencing technologies

Sara Goodwin et al.

NATURE REVIEWS GENETICS (2016)

Article Biochemistry & Molecular Biology

Structure and possible function of a G-quadruplex in the long terminal repeat of the proviral HIV-1 genome

Beatrice De Nicola et al.

NUCLEIC ACIDS RESEARCH (2016)

Article Multidisciplinary Sciences

Controlling uncertainty in aptamer selection

Fabian Spill et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Article Medicine, Research & Experimental

Galaxy Workflows for Web-based Bioinformatics Analysis of Aptamer High-throughput Sequencing Data

William H. Thiel

MOLECULAR THERAPY-NUCLEIC ACIDS (2016)

Article Medicine, Research & Experimental

In Silico Aptamer Docking Studies: From a Retrospective Validation to a Prospective Case Study'TIM3 Aptamers Binding

Obdulia Rabal et al.

Molecular Therapy-Nucleic Acids (2016)

Article Biochemistry & Molecular Biology

AptaTRACE Elucidates RNA Sequence-Structure Motifs from Selection Trends in HT-SELEX Experiments

Phuong Dao et al.

CELL SYSTEMS (2016)

Article Biochemistry & Molecular Biology

Analysis of In Vitro Aptamer Selection Parameters

Maureen McKeague et al.

JOURNAL OF MOLECULAR EVOLUTION (2015)

Article Biochemical Research Methods

The Phyre2 web portal for protein modeling, prediction and analysis

Lawrence A. Kelley et al.

NATURE PROTOCOLS (2015)

Article Biochemistry & Molecular Biology

Characterisation of aptamer-target interactions by branched selection and high-throughput sequencing of SELEX pools

Daniel M. Dupont et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Biochemistry & Molecular Biology

Large scale analysis of the mutational landscape in HT-SELEX improves aptamer discovery

Jan Hoinka et al.

NUCLEIC ACIDS RESEARCH (2015)

Article Chemistry, Analytical

Single-Round Patterned DNA Library Microarray Aptamer Lead Identification

Jennifer A. Martin et al.

JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY (2015)

Article Biotechnology & Applied Microbiology

Computational Selection of RNA Aptamer against Angiopoietin-2 and Experimental Evaluation

Wen-Pin Hu et al.

BIOMED RESEARCH INTERNATIONAL (2015)

Letter Medicine, Research & Experimental

AptaGUI-A Graphical User Interface for the Efficient Analysis of HT-SELEX Data

Jan Hoinka et al.

MOLECULAR THERAPY-NUCLEIC ACIDS (2015)

Article Medicine, Research & Experimental

FASTAptamer: A Bioinformatic Toolkit for High-throughput Sequence Analysis of Combinatorial Selections

Khalid K. Alam et al.

MOLECULAR THERAPY-NUCLEIC ACIDS (2015)

Article Medicine, Research & Experimental

Aptamer Selection Technology and Recent Advances

Michael Blind et al.

MOLECULAR THERAPY-NUCLEIC ACIDS (2015)

Article Chemistry, Multidisciplinary

Particle Display: A Quantitative Screening Method for Generating High-Affinity Aptamers

Jinpeng Wang et al.

ANGEWANDTE CHEMIE-INTERNATIONAL EDITION (2014)

Article Biochemical Research Methods

Microfluidic approaches to rapid and efficient aptamer selection

Hui Lin et al.

BIOMICROFLUIDICS (2014)

Article Biochemistry & Molecular Biology

Structural basis for activity of highly efficient RNA mimics of green fluorescent protein

Katherine Deigan Warner et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2014)

Article Chemistry, Analytical

Affinity Improvement of a VEGF Aptamer by in Silico Maturation for a Sensitive VEGF-Detection System

Yoshihiko Nonaka et al.

ANALYTICAL CHEMISTRY (2013)

Article Multidisciplinary Sciences

Structural basis for discriminatory recognition of Plasmodium lactate dehydrogenase by a DNA aptamer

Yee-Wai Cheung et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)

Article Biochemistry & Molecular Biology

A Computationally Designed DNA Aptamer Template with Specific Binding to Phosphatidylserine

Md Ashrafuzzaman et al.

NUCLEIC ACID THERAPEUTICS (2013)

Article Multidisciplinary Sciences

A novel protocol for three-dimensional structure prediction of RNA-protein complexes

Yangyu Huang et al.

SCIENTIFIC REPORTS (2013)

Article Biochemical Research Methods

Protein-DNA docking with a coarse-grained force field

Piotr Setny et al.

BMC BIOINFORMATICS (2012)

Article Biotechnology & Applied Microbiology

Isolation and Optimization of Murine IL-10 Receptor Blocking Oligonucleotide Aptamers Using High-throughput Sequencing

Alexey Berezhnoy et al.

MOLECULAR THERAPY (2012)

Article Biochemistry & Molecular Biology

Automated 3D structure composition for large RNAs

Mariusz Popenda et al.

NUCLEIC ACIDS RESEARCH (2012)

Article Mathematical & Computational Biology

Aptamer base: a collaborative knowledge base to describe aptamers and SELEX experiments

Jose Cruz-Toledo et al.

DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION (2012)

Article Biochemical Research Methods

Aptamer selection by high-throughput sequencing and informatic analysis

Shawn Hoon et al.

BIOTECHNIQUES (2011)

Review Biology

Molecular dynamics simulations and drug discovery

Jacob D. Durrant et al.

BMC BIOLOGY (2011)

Article Biochemistry & Molecular Biology

Entropic Fragment-Based Approach to Aptamer Design

Chih-Yuan Tseng et al.

CHEMICAL BIOLOGY & DRUG DESIGN (2011)

Review Biochemistry & Molecular Biology

RNA and DNA complexes with hemin [Fe(III) heme] are efficient peroxidases and peroxygenases: how do they do it and what does it mean?

Dipankar Sen et al.

CRITICAL REVIEWS IN BIOCHEMISTRY AND MOLECULAR BIOLOGY (2011)

Article Multidisciplinary Sciences

Probing the SELEX Process with Next-Generation Sequencing

Tatjana Schuetze et al.

PLOS ONE (2011)

Article Chemistry, Multidisciplinary

Enhanced Functional Potential of Nucleic Acid Aptamer Libraries Patterned to Increase Secondary Structure

Karen M. Ruff et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2010)

Article Biochemistry & Molecular Biology

Genomic SELEX for Hfq-binding RNAs identifies genomic aptamers predominantly in antisense transcripts

C. Lorenz et al.

NUCLEIC ACIDS RESEARCH (2010)

Article Multidisciplinary Sciences

Monitoring Genomic Sequences during SELEX Using High-Throughput Sequencing: Neutral SELEX

Bob Zimmermann et al.

PLOS ONE (2010)

Article Multidisciplinary Sciences

Quantitative selection of DNA aptamers through microfluidic selection and high-throughput sequencing

Minseon Cho et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Article Biochemistry & Molecular Biology

Convergent evolution to an aptamer observed in small populations on DNA microarrays

W. Rowe et al.

PHYSICAL BIOLOGY (2010)

Article Biochemistry & Molecular Biology

Telomeres and Telomerase: From Discovery to Clinical Trials

David R. Corey

CHEMISTRY & BIOLOGY (2009)

Article Biochemistry & Molecular Biology

RazerS-fast read mapping with sensitivity control

David Weese et al.

GENOME RESEARCH (2009)

Article Cell Biology

Analysis of aptamer sequence activity relationships

Mark Platt et al.

INTEGRATIVE BIOLOGY (2009)

Article Biochemistry & Molecular Biology

Array-based evolution of DNA aptamers allows modelling of an explicit sequence-fitness landscape

Christopher G. Knight et al.

NUCLEIC ACIDS RESEARCH (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

In silico selection of RNA aptamers

Yaroslav Chushak et al.

NUCLEIC ACIDS RESEARCH (2009)

Article Biochemical Research Methods

Inferring Binding Energies from Selected Binding Sites

Yue Zhao et al.

PLOS COMPUTATIONAL BIOLOGY (2009)

Article Biochemical Research Methods

DOVIS: an implementation for high-throughput virtual screening using AutoDock

Shuxing Zhang et al.

BMC BIOINFORMATICS (2008)

Article Biotechnology & Applied Microbiology

A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes

Stefan Kurtz et al.

BMC GENOMICS (2008)

Review Biochemistry & Molecular Biology

Molecular dynamics simulations of nucleic acid-protein complexes

Alexander D. MacKerell et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2008)

Article Biochemistry & Molecular Biology

Exploring the sequence space of a DNA aptamer using microarrays

Evaldas Katilius et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Multidisciplinary Sciences

Automated de novo prediction of native-like RNA tertiary structures

Rhiju Das et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2007)

Article Computer Science, Interdisciplinary Applications

Complex SELEX against target mixture: Stochastic computer model, simulation, and analysis

Chi-Kan Chen

COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE (2007)

Article Biology

Subtractive SELEX against two heterogeneous target samples: Numerical simulations and analysis

Chi-Kan Chen et al.

COMPUTERS IN BIOLOGY AND MEDICINE (2007)

Article Chemistry, Multidisciplinary

Geometric formalism for DNA quadruplex folding

Mateus Webba da Silva

CHEMISTRY-A EUROPEAN JOURNAL (2007)

Article Chemistry, Multidisciplinary

Quadruplex-based molecular beacons as tunable DNA probes

A. Bourdoncle et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)

Article Chemistry, Multidisciplinary

Aptamers selected for higher-affinity binding are not more specific for the target ligand

James M. Carothers et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2006)

Article Biochemical Research Methods

The SWISS-MODEL workspace: a web-based environment for protein structure homology modelling

K Arnold et al.

BIOINFORMATICS (2006)

Article Biochemical Research Methods

Structure clustering features on the Sfold Web server

CY Chan et al.

BIOINFORMATICS (2005)

Article Biochemistry & Molecular Biology

In vitro RNA random pools are not structurally diverse: A computational analysis

J Gevertz et al.

Article Chemistry, Analytical

SELEX: Just another separation?

MT Bowser

ANALYST (2005)

Article Biochemistry & Molecular Biology

Abundance of correctly folded RNA motifs in sequence space, calculated on computational grids

R Knight et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Chemistry, Multidisciplinary

Informational complexity and functional activity of RNA structures

JM Carothers et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2004)

Article Biochemistry & Molecular Biology

Sfold web server for statistical folding and rational design of nucleic acids

Y Ding et al.

NUCLEIC ACIDS RESEARCH (2004)

Article Physics, Multidisciplinary

Sequence space localization in the immune system response to vaccination and disease

MW Deem et al.

PHYSICAL REVIEW LETTERS (2003)

Article Biochemistry & Molecular Biology

Mfold web server for nucleic acid folding and hybridization prediction

M Zuker

NUCLEIC ACIDS RESEARCH (2003)

Article Biochemistry & Molecular Biology

ZDOCK: An initial-stage protein-docking algorithm

R Chen et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2003)

Article Multidisciplinary Sciences

Inhibition of rat corneal angiogenesis by a nuclease-resistant RNA aptamer specific for angiopoietin-2

RR White et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2003)

Article Multidisciplinary Sciences

Isolation of high-affinity GTP aptamers from partially structured RNA libraries

JH Davis et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2002)

Article Biochemistry & Molecular Biology

2.8 Å crystal structure of the malachite green aptamer

C Baugh et al.

JOURNAL OF MOLECULAR BIOLOGY (2000)