- Publication
- Jun 29, 2011
Replica Exchange with Solute Scaling: A more efficient version of Replica Exchange with Solute Tempering (REST2)
Wang, et al. J. Phys Chem B., 2011, 115(30), 9431-9438
- Publication
- Jun 28, 2011
Water in the active site of ketosteroid isomerase
Hanoian, et al. Biochemistry., 2011, 50, 6689-6700
- Publication
- Aug 14, 2010
Prediction of Absolute Solvation Free Energies using Molecular Dynamics Free Energy Perturbation and the OPLS Force Field
Shivakumar, et al. J. Chem. Theory Comput., 2010, 6, 1509-1519
- Publication
- Dec 9, 2009
A Role for a Specific Cholesterol Interaction in Stabilizing the Apo Configuration of the Human A2A Adenosine Receptor
Lyman, et al. Structure, 2009, 17, 1660-1668
- Publication
- Jan 6, 2009
A Conserved Protonation-Dependent Switch Controls Drug Binding in the Abl Kinase
Shan, et al. Proc. Natl. Acad. Sci. USA, 2009, 106, 139-144
- Publication
- Nov 11, 2006
Scalable Algorithms for Molecular Dynamics Simulations on Commodity Clusters
Kevin J. Bowers, et al. Proceedings of the ACM/IEEE Conference on Supercomputing (SC06), Tampa, Florida, 2006, November 11-17
- Publication
- May 25, 2005
Molecular determinants of selectivity and efficacy at the dopamine D3 receptor
Newman, et al. J. Med. Chem., 2012, 55(15), 6689-6699
Events
Event
Materials Science
- Jul 15, 2026
IFT FIRST 2026
Schrödinger is excited to be participating in the IFT First Annual Event and Expo 2026 conference taking place on July 12th – 15th in Chicago, Illinois.
Event
Materials Science
- Jul 14th-16th, 2026
Battery Seminar 2026
Schrödinger is excited to be participating in the Battery Seminar 2026 conference taking place on July 14th – 16th in San Jose, California.
Webinar
Materials Science
- Jul 23, 2026
Accelerating sustainable chemical innovation with physics-powered AI and predictive modeling
Join us for a webinar with Innovation Research Interchange and learn how the Fast-Moving Consumer Goods (FMCG) sector is currently navigating a significant transition driven by a global consumer shift toward “clean label” products and high-transparency ingredient lists.
Webinars
Webinar
Life Science
- Jul 29, 2026
Standing out in a competitive landscape: The power of structure-based biologics design
Join our upcoming webinar to learn how to leverage advanced in silico methods to de-risk your molecules and increase your experimental success rates.
Webinar
Life Science
- May 27, 2026
Biologics modeling for wet lab scientists: Detecting and deprioritizing dead ends before they reach the bench recording
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
- Apr 30, 2026
Educator’s Week 2026
Join us for a series of live webinar presentations from leading educators at top academic institutions, as well as talks by Schrödinger scientists.
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
- Tutorial
- Video
The LiveDesign Assistant
Learn how to build and adjust coloring rules, create Freeform and Formula columns, and plot data using the LiveDesign Assistant.
Publications
- Publication
- May 8, 2026
Discovery of 2H-Pyrrolo[3,4-c]pyridin-3-one Derivatives as Type-III c-MET Inhibitors Enabled by Free-Energy Perturbation CalculationsCl
Therrien, et al. ACS Medicinal Chemistry Letters, 2026
- Publication
- Apr 8, 2026
Structure-Based Discovery of Imidazo[4,5-c]pyridine SARM1 Modulators Showing Paradoxical Activation
Albanese, et al. Journal of Medicinal Chemistry, 2026, 69(8), 9521–9536
- Publication
- Mar 21, 2026
Structure-Based Calculation of Excipient Effects on the Viscosity of Concentrated Antibody Solutions
Shelley, et al. mAbs, 2026, 18(1)
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