Prime User Manual - ISP

Prime User Manual
Chapter 1: Introduction
Chapter 1
Prime 2.1 is a highly accurate protein structure prediction suite of programs that integrates
Comparative Modeling and Fold Recognition into a single user-friendly, wizard-like interface.
The Comparative Modeling path incorporates the complete protein structure prediction process
from template identification, to alignment, to model building. Refinement can then be done
from a separate panel, and involves side-chain prediction, loop prediction, and minimization.
The Prime interface was designed to accommodate both novice and expert users, while the
underlying programs were designed to produce superior results in a variety of applications,
including:
• High-resolution homology modeling
• Refinement of active sites
• Induced-fit optimization
• Fold Recognition
• Structure-based functional annotation
• Generation of alternate loop conformations
1.1 The Prime Suite in Maestro
To run Prime you use Maestro, the graphical user interface (GUI) for all of Schrödinger’s products.
For an introduction to Maestro, see the Maestro Overview. For help with a Maestro panel,
click the Help button. For more information, see the Maestro User Manual.
The Prime submenu of the Maestro Applications menu has four items, Structure Prediction,
Refinement, Covalent Docking, and MM-GBSA, which provide access to the Structure Prediction
(Prime–SP), Refinement, covalent docking and MM-GBSA modules of the Prime suite.
Prime–SP consists of a series of steps leading from a protein sequence through Comparative
Modeling to the construction of a 3D structure. If a template of sufficiently high sequence
identity exists in the database of known structures, the Comparative Modeling path is used. If a
suitable template cannot be identified using sequence information, however, Fold Recognition
can be used to identify potential templates.
Prime–Refinement is a facility for refining protein structures that have been imported into
Maestro or added to the Project Table from the Comparative Modeling workflow or another
Schrödinger application.
Prime 2.1 User Manual 1