Probing light chain mutation effects on thrombin via molecular dynamics simulations and machine learning

Molecular dynamics of a far positioned SOD1 mutant V14M reveals pathogenic misfolding behavior

(2017) Dharma Rao Tompa et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

In silico prediction of drug resistance due to S247R mutation of Influenza H1N1 neuraminidase protein

(2017) Rahul Shubhra Mandal et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Effects of helix and fingertip mutations on the thermostability of xyn11A investigated by molecular dynamics simulations and enzyme activity assays

(2017) Thana Sutthibutpong et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Mutations in Antibody Fragments Modulate Allosteric Response Via Hydrogen-Bond Network Fluctuations

(2016) Amit Srivastava et al.   BIOPHYSICAL JOURNAL

In silico analysis of the effect of mutation on epidermal growth factor receptor in non-small-cell lung carcinoma: from mutational analysis to drug designing

(2016) Fu-Li Zhao et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Influence of V54M mutation in giant muscle protein titin: a computational screening and molecular dynamics approach

(2016) D. Thirumal Kumar et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Impact of disease-causing mutations on inter-domain interactions in cMyBP-C: a steered molecular dynamics study

(2016) Navaneethakrishnan Krishnamoorthy et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

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

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

Visualizing ensembles in structural biology

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

Prediction of allosteric sites and mediating interactions through bond-to-bond propensities

(2016) B. R. C. Amor et al.   Nature Communications

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

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

Recovering the number of clusters in data sets with noise features using feature rescaling factors

(2015) Renato Cordeiro de Amorim et al.   INFORMATION SCIENCES

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

(2015) Ryan Godwin et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

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

Dynamics Govern Specificity of a Protein-Protein Interface: Substrate Recognition by Thrombin

(2015) Julian E. Fuchs et al.   PLoS One

Correlated Motions and Residual Frustration in Thrombin

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

The Dynamic Structure of Thrombin in Solution

(2012) Brian Fuglestad et al.   BIOPHYSICAL JOURNAL

Oral Anticoagulant Therapy

(2012) Walter Ageno et al.   CHEST

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

MDAnalysis: A toolkit for the analysis of molecular dynamics simulations

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

Impact of Chemotherapy on Thrombin Generation and on the Protein C Pathway in Breast Cancer Patients

(2011) Som D. Mukherjee et al.   pathophysiology of haemostasis and thrombosis

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

(2010) Freddie R Salsbury Jr   CURRENT OPINION IN PHARMACOLOGY

The refined 1.9-Å X-ray crystal structure of d-Phe-Pro-Arg chloromethylketone-inhibited human α-thrombin: Structure analysis, overall structure, electrostatic properties, detailed active-site geometry, and structure-function relationships

(2010) Wolfram Bode et al.   PROTEIN SCIENCE

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

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

Fast determination of the optimal rotational matrix for macromolecular superpositions

(2009) Pu Liu et al.   JOURNAL OF COMPUTATIONAL CHEMISTRY

Allosteric Communication Occurs via Networks of Tertiary and Quaternary Motions in Proteins

(2009) Michael D. Daily et al.   PLoS Computational Biology

Role of the A chain in thrombin function

(2008) M. E. Papaconstantinou et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

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