Molecular dynamics

MD basics

• Jianhan's recommendations
• Thermodynamics of chemical equilibrium
• van der Waals forces
• NMR Spectroscopy
• Capping

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Docking

• Rosetta
• AutoDock

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Visualization and analyses

• How to make images for publication using VMD
• Nifty MD tricks

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Databases and servers

• Protein Ensemble Database (IDPs)
• IDP
• SCOP
• CIDER
• PONDR
• CDPro
• PD2 ca2main
• Multi-sequence alignment: Clustal Omega
• Calmodulin Target Database
• QM basis set
• GROMACS topology

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MD packages

• AMBER
• GROM
• Tinker