Have a question about modeling software that needs an answer? Schrödinger’s recently created Knowledge Base is an easily searchable online compendium of articles that answer a variety of scientific, technical, and how-to questions for anyone using Schrödinger software.
At over one thousand articles and constantly growing, the Knowledge Base distills real-life issues encountered by Schrödinger technical support, applications scientists, and your fellow users. We encourage you to check it out here, and save it in your bookmarks for easy future reference.
Although it’s impossible to succinctly describe all the content in the Knowledge Base, if you’re using Glide, Induced Fit Docking, Prime, Phase, or Canvas then you might be interested in a few of the articles listed below:
Knowledge Base articles about target preparation
- How should I treat water molecules in the active site while preparing my structure, and how does Glide treat water molecules in the active site?
- How are the partial charges assigned to metal complexes for the impref minimization stage of protein preparation?
Knowledge Base articles about flexible receptor docking with Induced Fit Docking (IFD)
- I'm running an IFD run with a metal-containing system. The metal moves during the calculation. How can I force the metal to stay fixed?
Knowledge Base articles about Glide ligand docking
- What are the main differences between HTVS (high throughput virtual screening), SP (standard precision), and XP (extra precision) Glide docking?
Knowledge Base articles about protein structure prediction with Prime
- I have built my GPCR homology model and I am confident the alignment is correct. However, I want to rotate a helix to help orient a known key residue into the binding site. Can I do this in Maestro?
Knowledge Base articles about pharmacophore modeling with Phase
- If I create a hypothesis manually using Create Hypothesis, how do I add excluded volumes before searching for hits?
- In Phase, how do I modify the way rings are defined? I want the rings to be perceived as hydrophobes.
- While generating pharmacophores using 5 actives, I got the following warning message: WARNING No hypotheses survived the scoring job. Try relaxing the scoring parameters. Can you tell me how to change the scoring parameters, or what else I can do?
Knowledge Base articles about running cheminformatics experiments with Canvas