Dr. Sherman works closely with researchers using Schrödinger software for molecular modeling and drug design projects. All of the scripts discussed here can be downloaded free of charge from the Schrödinger Script Center, or by using 'Update...' from the Scripts menu in Maestro.
Q. I am working on a large-scale cross docking experiment. What scripts can help automate the process?
A. Under normal circumstances, we highly encourage users to interactively prepare target structures in Maestro using the Protein Preparation Wizard. This interactive process helps ensure that you have an accurate target structure, but occasionally there are instances when you have too many proteins to do this manually. In such cases, the script XGlide (Docking->Glide Cross Docking) can prepare protein-ligand complexes, generate Glide grids, perform docking of all ligands into all proteins, and analyze the results. There are many additional options, such as aligning all of the proteins, running SiteMap to predict binding sites, and applying docking constraints.
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Q. I have been running replica exchange (REMD) in Desmond and would like to visualize the transitions between the replicas. Is there a way to do that?
A. Yes, we now have a graphical interface for plotting exchanges from a REMD simulation. The script, called Replica Exchange Review (available under the Molecular Dynamics menu), shows the transitions for each temperature as a function of time.
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Q. I often find myself having to split a receptor-ligand complex into separate ligand and receptor files, or else I need to create a single receptor-ligand complex from a poseviewer file. I currently do this manually, but is there an automated way?
A. The command line tool pv_convert.py can convert a poseviewer file into a series of receptor-ligand complexes. It can also convert complexes into ligand-only, receptor-only, or poseviewer files.
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Q. I would like to show the distances between an atom of interest and all nearby atoms. Is there an easier alternative to using Maestro’s Measure tool to define atom pairs?
A. The script “Display Distances from Atom,” available under the Workspace Tools menu, will do just that. The script allows you to click on any atom in the Workspace and see the distances to all atoms within the cutoff distance.
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Q. I just ran a MacroModel conformational search and would like to color each structure based on the energy. How can I do this?
A. This is easily accomplished using the “Color by Relative Energy” script from the Project Table menu. The script operates on selected entries in the Project Table and colors based on the automatically detected MacroModel energy property. Atom colors will not be changed for structures without a MacroModel energy property.
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Q. I want to get the most recent version of everything from the Script Center, but when I update from the Scripts menu in Maestro I am asked for a password. I do not think I have a Schrödinger password. What should I do?
A. As of Suite 2011 a password is no longer required for script updates. However, getting a Schrödinger account gives you access to many useful training and documentation resources on our website, so you may still want to get an account. To do so, navigate to the Request Logon page under the “Resources & Downloads” menu at www.schrodinger.com.
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