Molecular dynamics simulations of aptamer-binding reveal generalized allostery in thrombin

Visualizing ensembles in structural biology

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Importance of long-time simulations for rare event sampling in zinc finger proteins

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PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models

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Thrombosis: a major contributor to the global disease burden

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The ensemble nature of allostery

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Development of Aptamer oligonucleotides as Anticoagulants and Antithrombotics for Cardiovascular Diseases: Current Status

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A Unified View of “How Allostery Works”

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Non-specificity and synergy at the binding site of the carboplatin-induced DNA adduct via molecular dynamics simulations of the MutSα–DNA recognition complex

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Conformational and Oligomeric Effects on the Cysteine pKaof Tryparedoxin Peroxidase

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Insights into Protein—DNA Interactions, Stability and Allosteric Communications: A Computational Study of Mutsα-DNA Recognition Complexes

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Structural and Electrostatic Asymmetry at the Active Site in Typical and Atypical Peroxiredoxin Dimers

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High-resolution structures of two complexes between thrombin and thrombin-binding aptamer shed light on the role of cations in the aptamer inhibitory activity

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Rational Design and Characterization of D-Phe-Pro-D-Arg-Derived Direct Thrombin Inhibitors

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Interrelation between inflammation, thrombosis, and neuroprotection in cerebral ischemia

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An overview of the Amber biomolecular simulation package

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Thrombin plasticity

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Rigidification of the autolysis loop enhances Na+ binding to thrombin

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Nucleic Acid Aptamers: Clinical Applications and Promising New Horizons

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The binding effect of aptamers on thrombin

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Engineered Thrombin Aims to Take on Heparin

(2010) Jeanne Erdmann   CHEMISTRY & BIOLOGY

Molecular dynamics simulations of protein dynamics and their relevance to drug discovery

(2010) Freddie R Salsbury Jr   CURRENT OPINION IN PHARMACOLOGY

Aptamers as therapeutics

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Harmonic and anharmonic aspects in the dynamics of BPTI: A normal mode analysis and principal component analysis

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Blood Coagulation: Hemostasis and Thrombin Regulation

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Long Range Communication between Exosites 1 and 2 Modulates Thrombin Function

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ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale

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An Implementation of the Smooth Particle Mesh Ewald Method on GPU Hardware

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CHARMM: The biomolecular simulation program

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The anticoagulants market

(2009) Irena Melnikova   NATURE REVIEWS DRUG DISCOVERY

Synergistic effect of aptamers that inhibit exosites 1 and 2 on thrombin

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How Na+ activates thrombin – a review of the functional and structural data

(2008) James A. Huntington   BIOLOGICAL CHEMISTRY

Role of the A chain in thrombin function

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Small molecule induction of MSH2-dependent cell death suggests a vital role of mismatch repair proteins in cell death

(2008) Aksana Vasilyeva et al.   DNA REPAIR

Molecular dynamic simulations of the metallo-beta-lactamase from Bacteroides fragilis in the presence and absence of a tight-binding inhibitor

(2008) Freddie R. Salsbury et al.   JOURNAL OF MOLECULAR MODELING

Thrombin

(2008) Enrico Di Cera   MOLECULAR ASPECTS OF MEDICINE