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2 results for “benzamidine”
Representative structures for Trypsin-Benzamidine conformation-space network
<p>These structures were used for the analysis presented in the paper "Multiple Ligand Unbinding Pathways and Ligand-Induced Destabilization Revealed by WExplore" published in Biophysical Journal, 112, February 28, 2017. There is a tar ball (allframes.tgz) containing 4000 structures in PDB format, as well as a PDF file of the network with labels for each of the 4000 states (network_labels.pdf). Unpack the tar ball with: "tar xzf allframes.tgz".</p> <p> </p>
Molecular dynamics dataset of Trypsin-Benzamidine
<p>This dataset contains all-atom molecular dynamics trajectories of Trypsin-Benzamidine. All details regarding the molecular dynamics setup are given in references [1, 2]. The dataset consists of two parts and comes with a time step of 100 ps.</p> <p><strong>long-trajs.tar</strong>: cumulative of 100 µs of MD data in trajectories of 48 x 2 µs and 4 x 1 µs. Generated and used in [1].</p> <p><strong>gpugrid-trajs.tar</strong>: cumulative of 49.5 µs of MD data in trajectories of 495 x 100 ns. Generated for [2] and used in [1, 2].</p> <p>[1] Plattner, N.; Noé, F. Protein Conformational Plasticity and Complex Ligand-Binding Kinetics Explored by Atomistic Simulations and Markov Models. <em>Nature Communications</em> <strong>2015</strong>, <em>6</em>, 7653. <a href="https://doi.org/10.1038/ncomms8653">https://doi.org/10.1038/ncomms8653</a>. </p> <p>[2] Buch, I.; Giorgino, T.; De Fabritiis, G. Complete Reconstruction of an Enzyme-Inhibitor Binding Process by Molecular Dynamics Simulations. <em>Proc. Natl. Acad. Sci. U.S.A.</em> <strong>2011</strong>, <em>108</em> (25), 10184–10189. <a href="https://doi.org/10.1073/pnas.1103547108">https://doi.org/10.1073/pnas.1103547108</a>.</p>
ScienceDex guides
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OpenNeuro
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