Schrödinger Suite

The Schrodinger suite of software has a large number of applications for a variety modeling, analysis and computational tasks. In general the program is run on your local computer and there are installers for OS X, Linux and Windows. In addition to running locally many if not all of the programs can be run on the cluster using the job submission utilities within the suite.

The Department of Biochemistry and Molecular Biology and Center for World Health and Medicine pay a yearly subscription fee for the software and the shared token library that allows certain special applications to run. Tokens are distributed from a license server in the Department of Biochemistry and Molecular Biology. The main set of tools (such as Maestro) have a large pool of tokens. We also have unlimited licenses for running the Desmond Molecular Dynamics program. Other applications/tasks in the suite check out licenses from the token library. The exact number varies by task.

Because of the limited number of application specific tokens, priority is given to the groups who cover the cost of maintaining the software.

To get a copy of the program installers contact David Gohara. Additional setup will be needed in order to check out licenses.

Biologics Suite

Comprehensive Protein Modeling

  • Complete set of homology modeling tools, including both rapid and advanced methods
  • Chimeric and multimeric models
  • Advanced sequence tools for multiple alignment, with extensive annotation options
  • Protein structure quality analysis
  • Identification of consensus elements in structural families/homologs

Advanced features for protein engineering

  • Protein aggregation prediction
  • Identification of hot spots for proteolysis, glycosylation, deamidation, and oxidation
  • Residue-based analysis of energies, solvent-accessible surface areas, and hydropathy
  • Cysteine scanning to identify residue mutations for potential cysteine-cysteine disulfide bonds
  • Automated residue scanning to predict relative stabilities as well as changes in solvent‑accessible surface area, pKa, and hydropathy

Antibody modeling

  • Automated intuitive workflow
  • Prediction of CDR from sequence
  • Rapid prediction using curated antibody database
  • Advanced ab initio loop prediction using Prime
  • Database management tools for simple incorporation of new/proprietary structures, and allows use of multiple databases in modeling

State-of-the-art protein-protein docking

  • Well-validated docking code, PIPER; for more information please visit the PIPER website.
  • Special antibody and multimer modes

Advanced simulations

  • Access to Schrödinger simulation tools
  • Advanced molecular dynamics (MD)
  • Extensive Free Energy Perturbation (FEP) tools
  • Large-scale, low mode (normal) search for domain movement
  • Quantum mechanics/molecular mechanics (QM/MM) predictions of binding site reactivity

Small-Molecule Drug Discovery Suite

Wide range of virtual screening options, spanning the spectrum of speed vs. accuracy tradeoffs

  • 2D/3D QSAR with a large selection of fingerprint options
  • Shape-based screening, with or without atom properties
  • Ligand-based pharmacophore modeling
  • e-Pharmacophore modeling incorporating ligand-receptor interaction energies
  • Flexible ligand docking with industry-leading Glide
  • SIFt — structure interaction fingerprint analysis
  • Induced-fit docking with receptor flexibility
  • Covalent docking
  • 2D ligand interaction diagrams

Advanced computations to estimate binding affinity and to rank-order compounds

  • Embrace post-docking refinement
  • Prime MM/GBSA
  • Free energy perturbation (FEP) theory
  • Linear interaction approximation (LIA)
  • QM-polarized ligand docking

Analyses to predict, prepare, refine, and characterize target structureand binding modes

  • Protein crystal structure refinement
  • Protein structure analysis and homology modeling
  • GPCR and hERG modeling
  • Protein binding site identification and analysis
  • Multiple binding mode prediction

Complete set of utilities to prepare, analyze, and filter ligand structures and to create and design ligand libraries

  • 2D to 3D structure conversion, with emphasis on bioactive conformers
  • Tautomeric state enumeration and analysis
  • Ligand interaction diagram
  • Commercially-available compound database
  • Flexible ligand superposition
  • Combinatorial library creation
  • Core hopping
  • Filter compound libraries based on predicted ADME properties
  • R-group analysis

General modeling tools that can be applied across a wide range of chemical systems

  • High-performance QM calculations, in gas phase and in solution
  • MM/MD simulations, with implicit or explicit solvents
  • Small molecule and macromolecular conformational analyses
  • Mixed-mode QM/MM calculations for ground state and reactivity studies

Fully supported by state-of-the-art visualization and workflow automation tools

  • Unified graphical user interface, Maestro, that serves all computations
  • Publication-quality graphics and flexible analysis
  • KNIME Extensions and customizable workflows
  • Python API