Mechanistic insights into thrombin's switch between “slow” and “fast” forms

Uncovering Large-Scale Conformational Change in Molecular Dynamics without Prior Knowledge

(2016) Ryan L. Melvin et al.   Journal of Chemical Theory and Computation

Evaluation of Methods for the Calculation of the pKa of Cysteine Residues in Proteins

(2016) Ernest Awoonor-Williams et al.   Journal of Chemical Theory and Computation

Visualizing ensembles in structural biology

(2016) Ryan L. Melvin et al.   JOURNAL OF MOLECULAR GRAPHICS & MODELLING

All-Atom Molecular Dynamics Reveals Mechanism of Zinc Complexation with Therapeutic F10

(2016) Ryan L. Melvin et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Na+ Binding Is Ineffective in Forming a Primary Substrate Pocket of Thrombin

(2016) Ikuo Kurisaki et al.   JOURNAL OF PHYSICAL CHEMISTRY B

MDTraj: A Modern Open Library for the Analysis of Molecular Dynamics Trajectories

(2015) Robert T. McGibbon et al.   BIOPHYSICAL JOURNAL

Colon Cancer Growth and Dissemination Relies upon Thrombin, Stromal PAR-1, and Fibrinogen

(2015) G. N. Adams et al.   CANCER RESEARCH

Allostery without a conformational change? Revisiting the paradigm

(2015) Ruth Nussinov et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

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

(2015) Martin K. Scherer et al.   Journal of Chemical Theory and Computation

Toward Understanding Allosteric Activation of Thrombin: A Conjecture for Important Roles of Unbound Na+ Molecules around Thrombin

(2015) Ikuo Kurisaki et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Assessing the accuracy of physical models used in protein-folding simulations: quantitative evidence from long molecular dynamics simulations

(2014) Stefano Piana et al.   CURRENT OPINION IN STRUCTURAL BIOLOGY

Practical Aspects of Free-Energy Calculations: A Review

(2014) Niels Hansen et al.   Journal of Chemical Theory and Computation

The ensemble nature of allostery

(2014) Hesam N. Motlagh et al.   NATURE

Effects of histidine protonation and rotameric states on virtual screening of M. tuberculosis RmlC

(2013) Meekyum Olivia Kim et al.   JOURNAL OF COMPUTER-AIDED MOLECULAR DESIGN

Correlated Motions and Residual Frustration in Thrombin

(2013) Brian Fuglestad et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Biomolecular Simulation: A Computational Microscope for Molecular Biology

(2012) Ron O. Dror et al.   Annual Review of Biophysics

An ensemble view of thrombin allostery

(2012) Bernhard C. Lechtenberg et al.   BIOLOGICAL CHEMISTRY

The Dynamic Structure of Thrombin in Solution

(2012) Brian Fuglestad et al.   BIOPHYSICAL JOURNAL

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

(2012) Irene Russo Krauss et al.   NUCLEIC ACIDS RESEARCH

H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations

(2012) R. Anandakrishnan et al.   NUCLEIC ACIDS RESEARCH

Thrombin plasticity

(2011) James A. Huntington   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

PROPKA3: Consistent Treatment of Internal and Surface Residues in Empirical pKaPredictions

(2011) Mats H. M. Olsson et al.   Journal of Chemical Theory and Computation

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

(2011) Naveen Michaud-Agrawal et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Protonation, Tautomerization, and Rotameric Structure of Histidine: A Comprehensive Study by Magic-Angle-Spinning Solid-State NMR

(2011) Shenhui Li et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Assessing the fractions of tautomeric forms of the imidazole ring of histidine in proteins as a function of pH

(2011) J. A. Vila et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2010) Freddie R Salsbury Jr   CURRENT OPINION IN PHARMACOLOGY

NMR resonance assignments of thrombin reveal the conformational and dynamic effects of ligation

(2010) B. C. Lechtenberg et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events

(2010) Peter Csermely et al.   TRENDS IN BIOCHEMICAL SCIENCES

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

(2009) M. J. Harvey et al.   Journal of Chemical Theory and Computation

Thrombin allosteric modulation revisited: a molecular dynamics study

(2009) Hermes Luís Neubauer de Amorim et al.   JOURNAL OF MOLECULAR MODELING

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

(2008) James A. Huntington   BIOLOGICAL CHEMISTRY

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

Benchmarking pKaPrediction Methods for Residues in Proteins

(2008) Courtney L. Stanton et al.   Journal of Chemical Theory and Computation

Thrombin

(2008) Enrico Di Cera   MOLECULAR ASPECTS OF MEDICINE

Structural identification of the pathway of long-range communication in an allosteric enzyme

(2008) P. S. Gandhi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA