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Structure Prediction & Target Enablement

Harness the structural biology revolution

Structure Prediction & Target Enablement

Unlock your protein target for high-precision, structure-based design

We are in the midst of a revolution in structural biology, with a proliferation of available structures across protein classes now possible due to advances in cryo-EM and technologies such as AlphaFold. However, significant refinement and accurate ligand placement is required to use these models in physics-based simulations including docking and free energy perturbation.

Schrödinger’s comprehensive suite of solutions for protein model refinement, ligand placement, and binding site analysis allows you to unlock a broader range of targets for structure-based design.


Solutions to generate design-ready structures from a broad range of starting points

Enable both on-targets and off-targets for rigorous structure-based design

High resolution structures

Prepare high resolution X-ray crystal or cryo-EM structures for structure-based design

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Quickly and reliably prepare high-quality, all-atom protein models suitable for physics-based simulations
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Predict the binding mode of novel ligands in existing structures at near experimental accuracy
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Understand competitor binding modes without needing to obtain an experimental structure for each series

Low resolution structures

Refine and validate low resolution X-ray crystal or cryo-EM structures

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Correct common structural problems and create reliable, all-atom protein models
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Dock ligands into ambiguous density, such as in cryo-EM structures, using a best-in-class force field to resolve uncertainty
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Place cofactors and solvent to convert low resolution models into complete, all-atom representations

No structure

Create and validate structures from homologous protein sequence or make use of available AlphaFold structures

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Harness the power of genomic data to easily create homology models of pharmaceutically relevant targets
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Reliably and accurately dock ligands into template-based homology models or AlphaFold structures
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Quantitatively validate structural models using known SAR and a highly accurate in silico binding affinity assay
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Identify and assess the druggability of protein binding sites

Binding site identification

Rapidly identify and rank a protein’s probable binding sites with confidence

Cryptic pocket exploration

Elucidate cryptic binding pockets and reveal binding hot spots using metadynamics accelerated sampling workflow for mixed solvent simulations

Hydration site analysis

Discover new possibilities for ligand design by predicting the location and thermodynamic potential of hydration sites in the binding site

Case studies & webinars

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

Structure-based drug discovery without a structure: Enabling accurate FEP+ predictions for challenging targets and ADMET anti-targets

Opening new worlds for structure-based drug discovery with advanced computational methods

Improving protein-ligand modeling into cryo-EM data and the use of those models in drug discovery efforts

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Key Products

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


Complete modeling environment for your molecular discovery


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


High-performance free energy calculations for drug discovery


Industry-leading ligand-receptor docking solution

OPLS4 & OPLS5 Force Field

A modern, comprehensive force field for accurate molecular simulations


A powerful and innovative solution for accurate protein structure prediction


Fast, accurate, and intuitive binding site identification


State-of-the-art, structure-based method for assessing the energetics of water solvating ligand binding sites for ligand optimization


High-performance molecular dynamics (MD) engine providing high scalability, throughput, and scientific accuracy


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

Using AlphaFold and Experimental Structures for the Prediction of the Structure and Binding Affinities of GPCR Complexes via Induced Fit Docking and Free Energy Perturbation

Coskun, D. et al. J. Chem. Theory Comput. 2024, 20(1), 477–489

Benchmarking Refined and Unrefined AlphaFold2 Structures for Hit Discovery

Zhang, Y. et al. J. Chem. Inf. Model. 2023, 63(6), 1656–1667

Induced-Fit Docking Enables Accurate Free Energy Perturbation Calculations in Homology Models

Xu, T. et al. J. Chem. Theory Comput. 2022, 18(9), 5710–5724

Software and services to meet your organizational needs

Software Platform

Deploy digital drug discovery workflows using a comprehensive and user-friendly platform for molecular modeling, design, and collaboration.

Research Services

Leverage Schrödinger’s computational expertise and technology at scale to advance your projects through key stages in the drug discovery process.

Support & Training

Access expert support, educational materials, and training resources designed for both novice and experienced users.