Dr. Sherman works closely with researchers using Schrödinger software for molecular modeling and drug design projects. All of the scripts discussed here may be downloaded free of charge from the Schrödinger Script Center, or by using 'Update...' from the Scripts menu in Maestro.
Q:I just completed a retrospective virtual screening study and would like to compute enrichments. Do you have a tool to do this?
A:Yes, we recently posted a script called enrichment.py that computes a number of the more common enrichment factors, such as standard enrichment factors (EF), area under the receiver-operating characteristic curve (AUC), robust initial enhancement (RIE), and Boltzmann-Enhanced Discrimination of Receiver-Operating Characteristic (BEDROC).
Q: I read a recent paper by Guo et al. on applying replica exchange molecular dynamics (REMD) to a series of P53 stapled peptides. I would like to run REMD in Desmond – how can I determine what temperature I should use?
A: The optimal temperature schedule depends on the size of your system and desired temperature range. We have a script called predict_remd_temp.py to predict a reasonable temperature schedule. The script has an option to effectively freeze atoms (by assigning very large masses), permitting the use of a smaller number of replicas.
Q: I just ran a molecular dynamics simulation with Desmond and would like to cluster the frames in order to choose representative structures. How can this be done?
A: The script trajectory_cluster.py will perform hierarchical clustering on structures from a Desmond trajectory. Clustering is based on the RMSD matrix of a specified set of atoms, and each cluster is written to a separate file. An additional file with a single representative structure from each cluster is also created.