- Publication
- Aug 12, 2019
Reaction-based Enumeration, Active Learning, and Free Energy Calculations to Rapidly Explore Synthetically Tractable Chemical Space and Optimize Potency of Cyclin Dependent Kinase 2 Inhibitors
Konze, et al. J. Chem. Inf. Model., 2019, 59, 9, 3782-3793
- Publication
- Aug 9, 2019
Protein-Ligand Binding Free Energy Calculations with FEP+
Wang, et al. Biomolecular Simulations, 2019, 2022, 201-232
- Publication
- Jul 30, 2019
Promoting transparency and reproducibility in enhanced molecular simulations
Bonomi, et al. Nature Methods, 2019, 16 (8), 670-673
- Publication
- Jun 30, 2019
Channelrhodopsin-2 function is modulated by residual hydrophobic mismatch with the surrounding lipid environment
Richards, et al. Applied Sciences (Switzerland), 2019, 9 (13), 2674
- Publication
- Jun 30, 2019
Two PKA RI’ holoenzyme states define ATP as an isoform-specific orthosteric inhibitor that competes with the allosteric activator, cAMP
Lu, et al. PNAS, 2019, 116 (33), 16347-16356
- Publication
- Jun 20, 2019
Noncovalent inhibitors reveal BTK gatekeeper and auto-inhibitory residues that control its transforming activity
Wang, et al. JCI Insight, 2019, 4(12), e127566
- Publication
- Jun 19, 2019
Small-molecule targeting of MUSASHI RNA-binding activity in acute myeloid leukemia
Minuesa, et al. Nature Communications, 2019, 10, 2691 (2019)
- Publication
- May 30, 2019
Application of Free Energy Perturbation (FEP+) to Understanding Ligand Selectivity: A Case Study to Assess Selectivity Between Pairs of Phosphodiesterases (PDE-s)
Moraca, et al. J. Chem. Inf. Model., 2019, 59(6), 2729-2740
- Publication
- May 22, 2019
Conformational communication mediates the reset step in t6A biosynthesis
Luthra, et al. Nucleic Acids Res., 2019, 47 (12), 6551-6567
- Publication
- May 17, 2019
Multi-Granulin Domain Peptides Bind to Pro-Cathepsin D and Stimulate Its Enzymatic Activity More Effectively Than Progranulin in Vitro
Butler, et al. Biochemistry, 2019, 58 (23), 2670-2674
- Publication
- May 9, 2019
Generation of Tautomers Using Micro-pKa-s
Watson, et al. J. Chem. Inf. Model., 2019, 59(6), 2672-2689
- Publication
- Apr 16, 2019
A Structural Change in Butyrophilin upon Phosphoantigen Binding Underlies Phosphoantigen-Mediated V’9V’2 T Cell Activation
Yang, et al. Immunity, 2019, 50 (4), 1043
Events
Webinar
Life Science
- Mar 18, 2026
デジタル創薬セミナー ~計算化学がもたらす創薬プロセスの変貌~ 第23回
Rethinking the rules: Exploiting solvent exposed salt-bridge interactions with free energy perturbation simulations for the discovery of potent inhibitors of SOS1
Webinar
Materials Science
- Mar 18, 2026
The Importance of Human Know-How in AI Execution for Materials R&D
Join us to explore how Schrödinger’s domain experts integrate these three pillars to streamline material optimization.
Event
Life Science
- Mar 18th-20th, 2026
AI Convergence 2026
Schrödinger is excited to be participating in the AI Convergence: Small Molecule Drug Discovery Summit 2026 taking place on March 18th – 20th in Boston, Massachusetts.
Webinars
Webinar
Life Science
- Mar 18, 2026
デジタル創薬セミナー ~計算化学がもたらす創薬プロセスの変貌~ 第23回
Rethinking the rules: Exploiting solvent exposed salt-bridge interactions with free energy perturbation simulations for the discovery of potent inhibitors of SOS1
Webinar
Life Science
- Mar 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
- Mar 26, 2026
Embracing a new era of toxicity screening: Atomic-resolution modeling to mitigate off-target liabilities
Join us for a technical overview of Schrödinger’s Predictive Toxicology solution. This session will demonstrate how physics-based, atomic-resolution modeling transforms toxicology from a reactive “filter” into a proactive “design tool.”
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