Prime User Manual - ISP

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Chapter 1: Introduction
Covalent Docking is a facility for “docking” ligands that are covalently bound to the receptor.
It uses designated reactive bonds in the ligand and a receptor bond to sample the possible
attachment points, and performs a loop prediction to sample the ligand and specified parts of
the receptor. The result is a set of “poses” of the ligand, docked to the receptor.
Prime MM-GBSA is a facility for calculating ligand binding energies within the MM-GBSA
continuum solvation model.
1.2 Prime Documentation
The Prime User Manual describes the Prime suite, including information about:
• Essentials of using the Prime–SP module: runs and projects, job control, and the layout
and common features of step panels
• Starting a structure prediction: the Input Sequence and Find Homologs steps
• Using the Comparative Modeling path, including the Edit Alignment and Build Structure
steps
• Using Fold Recognition
• Using the Prime–Refinement module
• Running Prime MM-GBSA calculations
• Running Prime jobs from the command line
This document expands on the information provided in the Maestro online help. In addition to
describing steps, features, and options, this document suggests ways to determine which
choices are the most useful, describes results, and provides some background and technical
detail. Terms pertinent to Prime are defined in the Glossary.
For a tutorial introduction to Prime, see the Prime Quick Start Guide. For information on
installing Prime, see the Installation Guide.
For information about Schrödinger’s Induced Fit Docking protocol, which uses Prime and
Glide to optimize docking by including ligand-induced flexibility in the receptor active site,
see the document Induced Fit Docking.
Maestro online help includes topics for Prime. See page 131 for a discussion of help in
Maestro, including tooltips (Balloon Help) and technical support contacts. For a fuller description
of the help facility, see Chapter 15 of the Maestro User Manual.
Prime 2.1 User Manual