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Enzyme Engineering

Efficiently optimize enzymes using structure-based design

Efficiently optimize enzymes using structure-based design

Capabilities for in silico enzyme design

Easily build 3D enzyme structures directly from sequence and understand substrate binding to the active site

  • Import, analyze, and edit protein sequences, including quick sequence alignment and annotation with Multiple Sequence Viewer
  • Create high-quality homology models from sequence using a fully automated workflow
  • Perform structural refinement with Prime or equilibration via molecular dynamics with Desmond
  • Predict high fidelity experimental binding poses with advanced, fully flexible docking

Understand substrate binding to the active site

  • Perform quick docking
  • Predict high fidelity experimental binding poses with advanced, fully flexible docking

Improve kinetic performance and reactivity

  • Gain valuable insights into reaction mechanism through quantum mechanics (QM) calculations
  • Understand the transition state and reaction barriers
  • Combine the accuracy of quantum mechanics with the speed of molecular mechanics (QM/MM)

Improve specificity, selectivity and substrate range

  • Obtain accurate and efficient pKa predictions for titratable protein residues in complex interfaces or active sites using constant pH simulations
  • Perform fast and quick residue mutation scan with residue scanning
  • Engineer enzymes for thermostability, substrate selectivity and specificity with FEP+

Engineer enzymes with improved chemical and physical stability

  • Identify chemically labile residues on the protein surface
  • Accurately predict relative thermostability of mutational variants at elevated temperature
  • Predict residue mutations best suited to mitigate chemical liabilities
  • Predict aggregation propensity of surface residues of the enzyme

Key Products

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


Comprehensive modeling platform for biologics discovery


A powerful and innovative solution for accurate protein structure prediction


Industry-leading ligand-receptor docking solution


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


Quantum mechanics solution for rapid and accurate prediction of molecular structures and properties


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.

A Computational Approach to Enzyme Design: Predicting ω-Aminotransferase Catalytic Activity Using Docking and MM-GBSA Scoring

Sirin, S. et al. J. Chem. Inf. Model. 2014, 54(8), 2334-2346

Physics-based enzyme design: Predicting binding affinity and catalytic activity

Sirin, S. et al. Proteins. 2014, 82(12), 3397-3409

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.