- Publication
- Mar 19, 2013
Close intramolecular sulfur-oxygen contacts: Modified force field parameters for improved conformation generation
Lupyan, et al. J. Comput. Aided Mol. Des., 2012, 26, 1195-1205
- Publication
- Mar 6, 2013
Contributions of water transfer energy to protein-ligand association and dissociation barriers: WaterMap analysis of a series of p38′ MAP kinase inhibitors
Pearlstein, et al. Proteins, 2013, 81(9), 1509-1526
- Publication
- Feb 25, 2013
Optimization of peptide hydroxamate inhibitors of insulin-degrading enzyme reveals marked substrate-selectivity
Abdul-Hay, et al. J. Med. Chem., 2013, 56(6), 2246-2255
- Publication
- Feb 19, 2013
Long-range electrostatic complementarity governs substrate recognition by human chymotrypsin C, a key regulator of digestive enzyme activation
Batra, et al. J. Biol. Chem., 2013, 288(14), 9848-9859
- Publication
- Feb 18, 2013
Selective targeting of dendritic cell-specific intercellular adhesion molecule-3-grabbing nonintegrin (DC-SIGN) with mannose-based glycomimetics: Synthesis and interaction studies of bis(benzylamide) derivatives of a pseudomannobioside
Varga, et al. Chem. Eur. J., 2013, 19, 4786-4797
- Publication
- Feb 7, 2013
Prediction of Long Loops with Embedded Secondary Structure Using the Protein Local Optimization Program
Miller, et al. J. Chem. Theory Comput., 2013, 9(3), 1846-1864
- Publication
- Feb 5, 2013
Type II kinase inhibitors show an unexpected inhibition mode against Parkinson-s disease-linked LRRK2 mutant G2019S
Liu, et al. Biochemistry, 2013, 52, 1725-1736
- Publication
- Jan 16, 2013
Modeling Local Structural Rearrangements Using FEP/REST: Application to Relative Binding Affinity Predictions of CDK2 Inhibitors
Wang, et al. J. Chem. Theory Comput., 2013, 9, 1282-1293
- Publication
- Nov 15, 2012
Discovery of new non-steroidal FXR ligands via a virtual screening workflow based on Phase shape and induced fit docking
Fu, et al. Bioorg. Med. Chem. Lett., 2012, 22(22), 6848-6853
- Publication
- Nov 1, 2012
Steric hindrance mutagenesis in the conserved extracellular vestibule impedes allosteric binding of antidepressants to the serotonin transporter
Plenge, et al. J. Biol. Chem., 2012, 287, 39316-39326
- Publication
- Nov 1, 2012
Novel inverse binding mode of indirubin derivatives yields improved selectivity for DYRK kinases
Myrianthopoulos, et al. ACS Med Chem Lett, 2013, 4(1), 22-26
- Publication
- Oct 31, 2012
Scaffold-based pan-agonist design for the PPAR’, PPAR’ and PPAR’ receptors
Zhang L.S.; Wang S.Q.; Xu W.R.; Wang R.L.; Wang J.F., PLos ONE, 2012, 7(10), DOI: 10.1371/journal.pone.0048453
Events
Event
Life Science
Materials Science
- May 18th-20th, 2026
17th Global Drug Delivery & Formulation Summit
Schrödinger is excited to be participating in the 17th Global Drug Delivery & Formulation Summit taking place on May 18th – 20th in Berlin, Germany.
Event
Life Science
- May 19th-21st, 2026
24th Schrödinger European User Group Meeting 2026
This year’s UGM event will feature an engaging mix of scientific presentations, hands-on workshops, and a panel discussion spanning the full scope of Schrödinger’s life science molecular design platform.
Event
Materials Science
- May 19th-20th, 2026
Suppliers’ Day 2026
Schrödinger is excited to be participating in the Supplier’s Day 2026 conference taking place on May 19th – 20th in New York, New York.
Webinars
Webinar
Life Science
- May 27th – Jun 3rd, 2026
Biologics modeling for wet lab scientists: Detecting and deprioritizing dead ends before they reach the bench
Join us to learn how to detect and deprioritize high-risk candidates, effectively discarding developability dead-ends before they ever reach the bench.
Webinar
Life Science
- Jun 4th-11th, 2026
Generative Glide: AI-driven ultra-large virtual screening for real-world drug discovery
Join us as we go beyond slides and run a demo of the workflow, showing how Generative Glide performs in practice from setup through results.
Webinar
Life Science
- May 6, 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.
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
- Dec 3, 2025
Glide WS: Methodology and Initial Assessment of Performance for Docking Accuracy and Virtual Screening
Friesner, et al. Journal of Chemical Theory and Computation, 2025, 21(24), 12696–12708
- 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
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