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300 ns md simulation trajectories  (AUTODOCK GmbH)
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AUTODOCK GmbH 300 ns md simulation trajectories
The C- rmsd of monomer insulin (black) and insulin in the complex <t>with</t> <t>LVEALYL</t> (color curves) was obtained during <t>300</t> ns MD simulations at pH 7. The structure resolved at pH 2.1 remains stable at pH 7. Arrow roughly refers to equilibration time ns, when the system reaches equilibrium (curve saturation).
300 Ns Md Simulation Trajectories, supplied by AUTODOCK GmbH, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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The C- rmsd of monomer insulin (black) and insulin in the complex with LVEALYL (color curves) was obtained during 300 ns MD simulations at pH 7. The structure resolved at pH 2.1 remains stable at pH 7. Arrow roughly refers to equilibration time ns, when the system reaches equilibrium (curve saturation).

Journal: PLoS ONE

Article Title: Oligomerization of Peptides LVEALYL and RGFFYT and Their Binding Affinity to Insulin

doi: 10.1371/journal.pone.0065358

Figure Lengend Snippet: The C- rmsd of monomer insulin (black) and insulin in the complex with LVEALYL (color curves) was obtained during 300 ns MD simulations at pH 7. The structure resolved at pH 2.1 remains stable at pH 7. Arrow roughly refers to equilibration time ns, when the system reaches equilibrium (curve saturation).

Article Snippet: Four 300 ns MD simulation trajectories have been carried out for insulin-LVEALYL complex using the conformation generated by Autodock Vina in the best mode ( ) as the initial configuration.

Techniques:

Beta-content of each residue of insulin in the absence (black) and presence (red) of LVEALYL. Red and blue indices refer to chain A and B, respectively. The results are averaged over snapshots collected in equilibrium during one and four 300 ns MD simulations for insulin and insulin-LVEALYL complex, respectively.

Journal: PLoS ONE

Article Title: Oligomerization of Peptides LVEALYL and RGFFYT and Their Binding Affinity to Insulin

doi: 10.1371/journal.pone.0065358

Figure Lengend Snippet: Beta-content of each residue of insulin in the absence (black) and presence (red) of LVEALYL. Red and blue indices refer to chain A and B, respectively. The results are averaged over snapshots collected in equilibrium during one and four 300 ns MD simulations for insulin and insulin-LVEALYL complex, respectively.

Article Snippet: Four 300 ns MD simulation trajectories have been carried out for insulin-LVEALYL complex using the conformation generated by Autodock Vina in the best mode ( ) as the initial configuration.

Techniques: Residue

Structure of the most populated cluster (96%) from 12 clusters obtained by the clustering technique with tolerance of 0.2 nm. The result was obtained using snapshots collected in equilibrium during 300 ns MD simulations. LVEALYL peptide and fragment B11-17 are highlighted in yellow. Fragment B22-27 becomes a -strand in the presence of LVEALYL, but not B11-17. LVEALYL forms the beta sheet with insulin having 4 backbone-backbone HBs.

Journal: PLoS ONE

Article Title: Oligomerization of Peptides LVEALYL and RGFFYT and Their Binding Affinity to Insulin

doi: 10.1371/journal.pone.0065358

Figure Lengend Snippet: Structure of the most populated cluster (96%) from 12 clusters obtained by the clustering technique with tolerance of 0.2 nm. The result was obtained using snapshots collected in equilibrium during 300 ns MD simulations. LVEALYL peptide and fragment B11-17 are highlighted in yellow. Fragment B22-27 becomes a -strand in the presence of LVEALYL, but not B11-17. LVEALYL forms the beta sheet with insulin having 4 backbone-backbone HBs.

Article Snippet: Four 300 ns MD simulation trajectories have been carried out for insulin-LVEALYL complex using the conformation generated by Autodock Vina in the best mode ( ) as the initial configuration.

Techniques:

Hydrogen bond (A) and side chain (B) contact maps of LVEALYL peptdie and insulin. Results were obtained in 300 ns MD simulations. Arrows refer to fragment B11-17 and B22-27.

Journal: PLoS ONE

Article Title: Oligomerization of Peptides LVEALYL and RGFFYT and Their Binding Affinity to Insulin

doi: 10.1371/journal.pone.0065358

Figure Lengend Snippet: Hydrogen bond (A) and side chain (B) contact maps of LVEALYL peptdie and insulin. Results were obtained in 300 ns MD simulations. Arrows refer to fragment B11-17 and B22-27.

Article Snippet: Four 300 ns MD simulation trajectories have been carried out for insulin-LVEALYL complex using the conformation generated by Autodock Vina in the best mode ( ) as the initial configuration.

Techniques: