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Prime

A powerful and innovative solution for accurate protein structure prediction

Prime

Overview

Prime is a fully-integrated protein structure prediction solution that incorporates homology modeling and fold recognition into a single solution. Prime includes an intuitive step-by-step interface that takes users through the workflow of structure prediction by supplying helpful default settings for each stage of the process.

Webinars

Discover how Schrödinger technology is being used to solve real-world research challenges.

Homology modeling with the Schrödinger Biologics Suite
Antibody modeling with the Schrödinger Platform

Key Capabilities

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Refine experimental structures obtained through X-ray crystallography, NMR or Cryo-EM for accurate and detailed starting points for subsequent simulations
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Accurately predict protein structures from sequence to obtain a high-quality model when an experimental structure is not available 
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Predict and refine side chain positions to create a complete, all-atom protein mode. 
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Predict membrane permeability and conformations of macrocycles
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Rapidly calculate energetics system of interest using MM-GBSA
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Benefit from an intuitive step-by-step interface that takes users through the full workflow of structure prediction 
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Create backbone models for early structural investigations or functional annotation in cases of low- or no-sequence identity
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Rapidly scan thousands of protein mutations, with tight integration to FEP+ that allows for an accurate and thorough screening cascade for protein optimization.
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Related Products

Learn more about the related computational technologies available to progress your research projects.

IFD-MD

Accurate ligand binding mode prediction for novel chemical matter, for on-targets and off-targets

FEP+

High-performance free energy calculations for drug discovery

Membrane Permeability

Physics-based solution for rapid and accurate prediction of passive membrane permeability

PrimeX

Comprehensive package for accurate protein crystal structure refinement

Publications

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

Life Science
Disulfide Bond Engineering of an Endoglucanase from Penicillium verruculosum to Improve Its Thermostability
Life Science
Target-template relationships in protein structure prediction and their effect on the accuracy of thermostability calculations
Life Science
A novel method for in silico assessment of Methionine oxidation risk in monoclonal antibodies: Improvement over the 2-shell model
Life Science
A Descriptor Set for Quantitative Structure-Property Relationship Prediction in Biologics
Life Science
Accurate Prediction of Protein Thermodynamic Stability Changes upon Residue Mutation using Free Energy Perturbation
Life Science
A Reliable and Accurate Solution to the Induced Fit Docking Problem for Protein-Ligand Binding
Life Science
Relative Binding Affinity Prediction of Charge-Changing Sequence Mutations with FEP in Protein-Protein Interfaces
Life Science
High throughput evaluation of macrocyclization strategies for conformer stabilization
Life Science
Investigating Protein-Peptide Interactions Using the Schr’dinger Computational Suite
Life Science
Improving Accuracy, Diversity, and Speed with Prime Macrocycle Conformational Sampling

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.

Tutorials

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.