scipion-chem-schrodinger

Schrodinger is a platform that platform leverages a deep understanding of physics, chemistry, and predictive modeling to accelerate innovation. It contains numerous tools for molecular modelling, including drug discovery and molecular dynamics.

Installation

A) Requirements

In order to use this plugin, you need to install first scipion-chem.

B) Installation steps

• Install the stable version

  Through the plugin manager GUI by launching Scipion and following Others >> Plugin Manager, or

scipion3 installp -p scipion-chem-schrodinger

• Developer’s version

  1. Download repository:

  git clone https://github.com/scipion-chem/scipion-chem-schrodinger.git

  2. Install:

  scipion3 installp -p /path/to/scipion-chem-schrodinger --devel

Warning

Installation of the stable version through the Plugin Manager or with the command provided above is not available yet.

Please install the developer version until a stable version is released, or install the latest stable version with the following steps:

cd /path/to/scipion-chem-schrodinger && git checkout master && scipion3 installp -p . --devel

Notice that Schrodinger is a licensed software, so from Scipion Chem we only provide tools for using their programs, but we do not provide the software itself, which must be separately installed by the user.

Protocols

A) Virtual Drug Screening

It includes several tools from Schrodinger for Virtual Drug Screening. The user will be able to prepare both the target and the ligands, predict or define the binding sites and perform a docking analysis.

• Schrödinger Receptor Preparation: Prepares an AtomStruct object containing a protein file to make it ready for Schrodinger tools using the Prepwizard Schrodinger utility.

• Schrödinger Ligand Preparation: Prepares a SetOfSmallMolecules to make it ready for Schrodinger tools using the Ligprep Schrodinger program.

• Schrödinger Binding Site Prediction (SiteMap): Predicts the most promising binding sites on the structure using SiteMap .

• Grid Preparation: Generates the grids used by the docking Schrodinger program: Glide.

• Schrödinger Glide Docking: Uses Glide for docking a set of ligands to a receptor.

B) Molecular Dynamics

It includes protocols able to handle Molecular Dynamics simulations in Schrodinger.

The following protocols allow the user to prepare, run and analyze these simulations.

• Schrödinger System Preparation (Desmond): Prepares a Schrodinger MD system using Desmond prior to its simulation from a AtomStruct or a SmallMolecule object.

• Schrödinger MD Simulation (Desmond): Takes the prepared Schrodinger system and uses Desmond to run a defined simulation.

C) Utils

It includes other util protocols that can be used in any of the previous fields.

• Schrödinger Format Conversion: Uses Schrodinger scripts to convert an AtomStruct or a SetOfSmallMolecules to the desired format.

• Schrödinger Fix Structure: Allows the user to use Prime for fixing an atomic structure.

• Schrödinger Split Structure: Allows the user to use the split_structure.py script from Schrodinger mmShare.