PrimeX
A comprehensive package for accurate protein crystal structure refinement
Overview
PrimeX is an advanced tool to facilitate protein crystal structure refinement and produces accurate structures more compatible with computational chemistry applications than those produced by other protein refinement programs.
Traditional protein crystallography introduces issues for downstream modeling due to high-energy contacts and missing hydrogens. PrimeX addresses these concerns by restraining protein geometry to OPLS-AA, adding hydrogens during refinement, and improving non-bonded interactions for better structure accuracy.
Key Capabilities
Loop building and refinement
Builds loops up to 40-residues in length, using technologies in the well-validated Prime protein modeling program and guided by electron density fit.
Ligand placement
Places ligands and other small molecules into electron density using technologies in the Glide docking program, which has demonstrated superior accuracy in ligand-receptor docking.
Accurate all-atom force field
Utilizes the OPLS-AA force field with state-of-the-art computational technologies to refine protein structures that are immediately ready for all computational simulations.
Advanced refinement techniques
Provides simulated annealing for reciprocal space refinement.
Choice of minimizers
Offers conjugate gradient, truncated Newton, and quasi-Newton (LBFGS) to optimize performance and accuracy.
Automatic parameter generation
Generates parameters for ligands and other small molecules, as well as modified residues, automatically without requiring user intervention.
Treatment of hydrogens
Automatically adds hydrogens, which are included during refinement according to physical chemistry as prescribed by the OPLS-AA force field.
Easy to use
Intuitive user interface is integrated into Maestro with step-by-step organization of refinement statistics in the Project Table and convenient analysis of protein structure geometry through interactive tables and plots.
Advanced calculation controls
Allows command-line input as well as scripting with Python for added control and customizable operations.
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Publications
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Training & Resources
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