Binding interface and impact on protease cleavage for an RNA aptamer to HIV-1 reverse transcriptase

IsRNA: An Iterative Simulated Reference State Approach to Modeling Correlated Interactions in RNA Folding

(2018) Dong Zhang et al.   Journal of Chemical Theory and Computation

Effect of tRNA on the Maturation of HIV-1 Reverse Transcriptase

(2018) Tatiana V. Ilina et al.   JOURNAL OF MOLECULAR BIOLOGY

Poly-Target Selection Identifies Broad-Spectrum RNA Aptamers

(2018) Khalid K. Alam et al.   Molecular Therapy-Nucleic Acids

RNA–protein interactions govern antiviral specificity and encapsidation of broad spectrum anti-HIV reverse transcriptase aptamers

(2017) Margaret J. Lange et al.   NUCLEIC ACIDS RESEARCH

ATSAS 2.8: a comprehensive data analysis suite for small-angle scattering from macromolecular solutions

(2017) D. Franke et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

Conformational Plasticity of the NNRTI-Binding Pocket in HIV-1 Reverse Transcriptase: A Fluorine Nuclear Magnetic Resonance Study

(2016) Naima G. Sharaf et al.   BIOCHEMISTRY

Performance of MDockPP in CAPRI rounds 28-29 and 31-35 including the prediction of water-mediated interactions

(2016) Xianjin Xu et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

Structural Maturation of HIV-1 Reverse Transcriptase—A Metamorphic Solution to Genomic Instability

(2016) Robert London   Viruses-Basel

Differential Isotopic Enrichment To Facilitate Characterization of Asymmetric Multimeric Proteins Using Hydrogen/Deuterium Exchange Mass Spectrometry

(2015) Devrishi Goswami et al.   ANALYTICAL CHEMISTRY

Interaction between Reverse Transcriptase and Integrase Is Required for Reverse Transcription during HIV-1 Replication

(2015) Shewit S. Tekeste et al.   JOURNAL OF VIROLOGY

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

(2015) Matthew T. Miller et al.   PROTEIN SCIENCE

Insight into HIV-1 reverse transcriptase–aptamer interaction from molecular dynamics simulations

(2014) Niran Aeksiri et al.   JOURNAL OF MOLECULAR MODELING

Selective unfolding of one Ribonuclease H domain of HIV reverse transcriptase is linked to homodimer formation

(2014) Xunhai Zheng et al.   NUCLEIC ACIDS RESEARCH

A knowledge-based scoring function for protein-RNA interactions derived from a statistical mechanics-based iterative method

(2014) Sheng-You Huang et al.   NUCLEIC ACIDS RESEARCH

Vfold: A Web Server for RNA Structure and Folding Thermodynamics Prediction

(2014) Xiaojun Xu et al.   PLoS One

Examining the Role of the HIV-1 Reverse Transcriptase p51 Subunit in Positioning and Hydrolysis of RNA/DNA Hybrids

(2013) Suhman Chung et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Potent Inhibition of HIV-1 Reverse Transcriptase and Replication by Nonpseudoknot, “UCAA-motif” RNA Aptamers

(2013) Angela S Whatley et al.   Molecular Therapy-Nucleic Acids

HDX Workbench: Software for the Analysis of H/D Exchange MS Data

(2012) Bruce D. Pascal et al.   JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY

Robust Suppression of HIV Replication by Intracellularly Expressed Reverse Transcriptase Aptamers Is Independent of Ribozyme Processing

(2012) Margaret J Lange et al.   MOLECULAR THERAPY

HIV-1 reverse transcriptase complex with DNA and nevirapine reveals non-nucleoside inhibition mechanism

(2012) Kalyan Das et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

High-throughput sequence analysis reveals structural diversity and improved potency among RNA inhibitors of HIV reverse transcriptase

(2012) Mark A. Ditzler et al.   NUCLEIC ACIDS RESEARCH

Allosteric Suppression of HIV-1 Reverse Transcriptase Structural Dynamics upon Inhibitor Binding

(2011) James M. Seckler et al.   BIOPHYSICAL JOURNAL

Identification of amino acid residues in HIV-1 reverse transcriptase that are critical for the proteolytic processing of Gag-Pol precursors

(2011) Hironori Nishitsuji et al.   FEBS LETTERS

Physics-Based De Novo Prediction of RNA 3D Structures

(2011) Song Cao et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Broad-spectrum aptamer inhibitors of HIV reverse transcriptase closely mimic natural substrates

(2011) Mark A. Ditzler et al.   NUCLEIC ACIDS RESEARCH

Selective killing of human immunodeficiency virus infected cells by non-nucleoside reverse transcriptase inhibitor-induced activation of HIV protease

(2010) Dirk Jochmans et al.   Retrovirology

CHARMM: The biomolecular simulation program

(2009) B. R. Brooks et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Structure and Function of HIV-1 Reverse Transcriptase: Molecular Mechanisms of Polymerization and Inhibition

(2008) Stefan G. Sarafianos et al.   JOURNAL OF MOLECULAR BIOLOGY

Footprinting protein–DNA complexes using the hydroxyl radical

(2008) Swapan S Jain et al.   Nature Protocols

Conservation Patterns of HIV-1 RT Connection and RNase H Domains: Identification of New Mutations in NRTI-Treated Patients

(2008) André F. A. Santos et al.   PLoS One