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A comprehensive package for accurate protein crystal structure refinement



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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A powerful and innovative solution for accurate protein structure prediction


Industry-leading ligand-receptor docking solution


Browse the list of peer-reviewed publications using Schrödinger technology in related application areas.

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Investigating Protein-Peptide Interactions Using the Schr’dinger Computational Suite
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PrimeX and the Schrödinger computational chemistry suite of programs
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Allosteric Inhibition of the NS2B-NS3 Protease from Dengue Virus
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Significant reduction in errors associated with non-bonded contacts in protein crystal structures: Automated all-atom refinement with PrimeX
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The crystal structure of DehI reveals a new ‘-haloacid dehalogenase fold and active-site mechanism
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Structure of the Arabidopsis thaliana TOP2 oligopeptidase
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A Structure-Based Model for Predicting Serum Albumin Binding

Training & Resources

Online Certification Courses

Level up your skill set with hands-on, online molecular modeling courses. These self-paced courses cover a range of scientific topics and include access to Schrödinger software and support.


Learn how to deploy the technology and best practices of Schrödinger software for your project success. Find training resources, tutorials, quick start guides, videos, and more.