White Paper
Life Science
- Tutorial
Generating ternary complex structures to enable rational design of targeted protein degraders
Generate and score structures for a target-PROTAC-ligase complex to enable linker optimization.
- Documentation
Learning Path: Virtual Screening
A structured overview of how to construct a virtual screening pipeline.
- Tutorial
Conformational Analysis for Small Molecules Using MacroModel and ConfGen
Investigate torsional profiles for related small molecules and how conformation affects intra- and intermolecular interactions.
- Publication
- Oct 2, 2017
Benchmarking Commercial Conformer Ensemble Generators
Friedrich, et al. J. Chem. Inf. Model., 2017, Article ASAP, DOI: 10.1021/acs.jcim.7b00505
- Publication
- Nov 19, 2014
Exploring Conformational Search Protocols for Ligand-based Virtual Screening and 3-D QSAR Modeling
Cappel, et al. J. Comput. Aided Mol. Des., 2015, 29(2), 165-182
- Publication
- Dec 12, 2013
Optimization, Pharmacophore Modeling and 3D-QSAR Studies of Sipholanes as Breast Cancer Migration and Proliferation Inhibitors
Foudah, et al. Eur. J. Med. Chem., 2014, 73, 310-324
- Publication
- Oct 1, 2013
Bioguided discovery and pharmacophore modeling of the mycotoxic indole diterpene alkaloids penitrems as breast cancer proliferation, migration, and invasion inhibitors
Sallam, et al. Med. Chem. Commun., 2013, 4, 1360-1369
- Publication
- Jun 26, 2013
Improved docking of polypeptides with Glide
Tubert-Brohman, et al. J. Chem. Inf. Model., 2013, 53(7), 1689-1699
- Publication
- Jun 19, 2013
Boosting virtual screening enrichments with data fusion: Coalescing hits from two-dimensional fingerprints, shape, and docking
Sastry, et al. J. Chem. Inf. Model., 2013, 53, 1531-1542
- Publication
- Apr 27, 2010
Drug-like Bioactive Structures and Conformational Coverage with the LigPrep/ConfGen Suite: Comparison to Programs MOE and Catalyst
Chen, et al. J.Chem. Inf. Model., 2010, 50, 822-839
Events
Webinar
Life Science
- Feb 18, 2026
Schrödinger デジタル創薬セミナー: Into the Clinic ~計算化学がもたらす創薬プロセスの変貌~ 第22回
Predictive toxicology solutions: Actionable, structure-based insights to dial-out tox liabilities early
Webinar
Life Science
- Feb 19, 2026
Introducing RetroSynth: Breaking the synthesis bottleneck with AI and physics-based modeling
Join us for the introduction of RetroSynth, Schrödinger’s AI-driven synthesis planning platform. RetroSynth is engineered to accelerate and scale conventional retrosynthesis by harnessing advanced deep learning algorithms.
Event
Materials Science
- Feb 25th-26th, 2026
InventU Sustainable Future Congress 2026
Schrödinger is excited to be participating in the InventU Sustainable Future Congress conference taking place on February 25th – 26th in Amsterdam, Netherlands.
Webinars
Webinar
Life Science
- Feb 18, 2026
Schrödinger デジタル創薬セミナー: Into the Clinic ~計算化学がもたらす創薬プロセスの変貌~ 第22回
Predictive toxicology solutions: Actionable, structure-based insights to dial-out tox liabilities early
Webinar
Life Science
- Feb 19, 2026
Introducing RetroSynth: Breaking the synthesis bottleneck with AI and physics-based modeling
Join us for the introduction of RetroSynth, Schrödinger’s AI-driven synthesis planning platform. RetroSynth is engineered to accelerate and scale conventional retrosynthesis by harnessing advanced deep learning algorithms.
Webinar
Life Science
- Feb 26, 2026
Building a biotech: Enabling a successful digital drug discovery program with a connected platform AMER
Join us to see how this powerful solution can accelerate your DMTA cycles and enable your teams – this isn’t about complex simulations, it’s about giving your team the tools they need to make better decisions, faster.
Documentation
- Documentation
Learning Path: Oligonucleotide Modeling
A structured overview of tools and workflows for nucleic acids in drug discovery.
- Documentation
WaterMap
Efficiently converged MD simulations are run with explicit water molecules, and resultant trajectories are analyzed to cluster hydration sites.
- Documentation
SiteMap
Identify binding sites, including allosteric binding sites and protein-protein interfaces, and evaluate their druggability.
Tutorials
- Tutorial
Structure-Based Virtual Screening using Glide
Prepare receptor grids for docking, dock molecules and examine the docked poses.
- Tutorial
Ligand Binding Pose Generation for FEP+
Generate starting poses for FEP simulations for a series of BACE1 inhibitors using core constrained docking.
- Tutorial
Homology Modeling of Protein-Ligand Binding Sites with IFD-MD
Create a homology model of TYK2 from JAK3 and including a bound ligand. Compare this model with the crystal structure for TYK2 bound to 4GIH.
Training Videos
Video
Life Science
Getting Going with Maestro BioLuminate
A free video series introducing the basics of using Maestro Bioluminate.
Video
Life Science
- Video
Introducing Ligand Designer
An overview of the LigandDesigner workflow, Editing in 2D and 3D, using display options and overlays, and accessing the Admin Panel.
Publications
- Publication
- Oct 13, 2025
Accelerated in silico discovery of SGR-1505: A potent MALT1 allosteric inhibitor for the treatment of mature B-cell malignancies
Nie Z, et al. J. Med. Chem., 2025
- Publication
- Oct 12, 2025
Discovery of highly potent noncovalent inhibitors of SARS-CoV-2 main protease through computer-aided drug design
Okabe A, et al. J Med Chem, 2025
- Publication
- Sep 17, 2025
Accurate hydration free energy calculations for diverse organic molecules with a machine learning force field
Xie, et al. ChemRxiv, 2025, 1, Preprint
Case Studies
Case Study
Life Science
Materials Science
Case Study
Life Science
Case Study
Life Science
White Papers
White Paper
Life Science
- Jan 29, 2026
FEP+ Pose Builder — maximizing utility and productivity in FEP simulations
FEP+ Pose Builder is a methodological advancement introduced as an integrated feature to drastically enhance accessibility, user-friendliness, and productivity within the FEP+ pipeline.
White Paper
Life Science
- Oct 29, 2024
20 Years of Glide: A Legacy of Docking Innovation and the Next Frontier with Glide WS
Glide has long set the gold standard for commercial molecular docking software due to its robust performance in both binding mode prediction and empirical scoring tasks, ease of use, and tight integration with Schrödinger’s Maestro interface and molecular discovery workflows.
White Paper
Life Science
Quick Reference Sheets
- Quick Reference Sheet
Force Field Builder
A one-page guide to calculate missing torsion parameters for ligands using the Force Field Builder panel.
- Quick Reference Sheet
Ligand Interaction Diagram
A one-page guide to using the Ligand Interaction Diagram for examining ligand-receptor interactions.
- Quick Reference Sheet
GlideMap
A one-page guide to using the GlideMap GUI for ligand placement guided by experimental density.
Latest insights from Extrapolations blog
With FEP+, “The Experiment is the Limit.”
Over the past century, small molecule drugs have represented the dominant modality in drug research, enabling medical breakthroughs that have saved countless lives.
Tackling Drug Solubility: AbbVie and Schrödinger Collaborate to Advance Accurate Prediction Methods
The complexity and size of drug candidates has grown in recent years as scientists pursue novel targets once considered undruggable.
Blog
Can AlphaFold Models be Used for Structure-Based Drug Design? A Perspective Two Years In
We recently sat down with Edward Miller, Senior Director of Protein Structure Modeling at Schrödinger, to discuss his experience using AlphaFold models for SBDD.
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.
Free learning resources
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.
Other Resources