Predicting aptamer sequences that interact with target proteins using an aptamer-protein interaction classifier and a Monte Carlo tree search approach

Aptamers in nanostructure-based electrochemical biosensors for cardiac biomarkers and cancer biomarkers: A review

(2020) Masoud Negahdary   BIOSENSORS & BIOELECTRONICS

Structure-based development of new RAS-effector inhibitors from a combination of active and inactive RAS-binding compounds

(2019) Abimael Cruz-Migoni et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RPITER: A Hierarchical Deep Learning Framework for ncRNA–Protein Interaction Prediction

(2019) Cheng Peng et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Cancer protein biomarker discovery based on nucleic acid aptamers

(2019) Hongjie Xiong et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

DNA aptamers for the recognition of HMGB1 from Plasmodium falciparum

(2019) Diego F. Joseph et al.   PLoS One

In silico approaches to RNA aptamer design

(2018) Michiaki Hamada   BIOCHIMIE

NGL viewer: web-based molecular graphics for large complexes

(2018) Alexander S Rose et al.   BIOINFORMATICS

Combination of aptamer and drug for reversible anticoagulation in cardiopulmonary bypass

(2018) Ruwan Gunaratne et al.   NATURE BIOTECHNOLOGY

SWISS-MODEL: homology modelling of protein structures and complexes

(2018) Andrew Waterhouse et al.   NUCLEIC ACIDS RESEARCH

PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactions

(2018) Jie Dong et al.   Journal of Cheminformatics

Aptamer-guided nanomedicines for anticancer drug delivery

(2018) Walhan Alshaer et al.   ADVANCED DRUG DELIVERY REVIEWS

Optimal classifier for imbalanced data using Matthews Correlation Coefficient metric

(2017) Sabri Boughorbel et al.   PLoS One

Prediction of aptamer-protein interacting pairs using an ensemble classifier in combination with various protein sequence attributes

(2016) Lina Zhang et al.   BMC BIOINFORMATICS

Random Forests and Kernel Methods

(2016) Erwan Scornet   IEEE TRANSACTIONS ON INFORMATION THEORY

Conformationally selective RNA aptamers allosterically modulate the β2-adrenoceptor

(2016) Alem W Kahsai et al.   Nature Chemical Biology

In silico selection of an aptamer to estrogen receptor alpha using computational docking employing estrogen response elements as aptamer-alike molecules

(2016) Rajesh Ahirwar et al.   Scientific Reports

SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction

(2015) Michal J. Boniecki et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Khalid K Alam et al.   Molecular Therapy-Nucleic Acids

An Aptamer to the MAP Kinase Insert Region

(2014) Sabine Lennarz et al.   ACS Chemical Biology

PseKNC: A flexible web server for generating pseudo K-tuple nucleotide composition

(2014) Wei Chen et al.   ANALYTICAL BIOCHEMISTRY

ZDOCK server: interactive docking prediction of protein-protein complexes and symmetric multimers

(2014) B. G. Pierce et al.   BIOINFORMATICS

Structural Features of β2 Adrenergic Receptor: Crystal Structures and Beyond

(2014) Injin Bang et al.   MOLECULES AND CELLS

Progress in Aptamer-Mediated Drug Delivery Vehicles for Cancer Targeting and Its Implications in Addressing Chemotherapeutic Challenges

(2014) Jie Zhu et al.   Theranostics

propy: a tool to generate various modes of Chou’s PseAAC

(2013) Dong-Sheng Cao et al.   BIOINFORMATICS

Molecular Docking: A Powerful Approach for Structure-Based Drug Discovery

(2012) Xuan-Yu Meng et al.   Current Computer-Aided Drug Design

Automated 3D structure composition for large RNAs

(2012) Mariusz Popenda et al.   NUCLEIC ACIDS RESEARCH

Conformational Locking upon Cooperative Assembly of Notch Transcription Complexes

(2012) Sung Hee Choi et al.   STRUCTURE

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

(2012) Jose Cruz-Toledo et al.   Database-The Journal of Biological Databases and Curation

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

Toward the estimation of the absolute quality of individual protein structure models

(2010) Pascal Benkert et al.   BIOINFORMATICS

A new taxonomy-based protein fold recognition approach based on autocross-covariance transformation

(2009) Qiwen Dong et al.   BIOINFORMATICS

In silico selection of RNA aptamers

(2009) Y. Chushak et al.   NUCLEIC ACIDS RESEARCH