- 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
- Nov 1, 2006
Long Loop Prediction Using the Protein Local Optimization Program
Zhu, et al. Proteins: Structure, Function, and Bioinformatics, 2006, 65, 438-452
- Publication
- Nov 1, 2006
PIPER: An FFT-based protein docking program with pairwise potentials
Kozakov, et al. Proteins, 2006, 65, 392-406
- Publication
- Oct 6, 2006
Conformational flexibility, internal hydrogen bonding, and passive membrane permeability: Successful in silico prediction of the relative permeabilities of cyclic peptides
Rezai, et al. J. Am. Chem. Soc, 2006, 128, 14073-14080
- Publication
- Oct 4, 2006
2,6-Disubstituted N-Arylsulfonyl Piperidines as Gamma-Secretase Inhibitors
Pissarnitski, et al. Bioorganic & Medicinal Chemistry Letters, 2007, 17, 57-62
- Publication
- Sep 27, 2006
Quantum chemistry applied to the mechanisms of transition metal containing enzymes — cytochrome c oxidase, a particularly challenging case
Blomberg, et al. J. Comput. Chem., 2006, 27, 1373-1384
- Publication
- Sep 23, 2006
Extra Precision Glide: Docking and Scoring Incorporating a Model of Hydrophobic Enclosure for Protein-Ligand Complexes
Friesner, et al. J. Med. Chem., 2006, 49, 6177-6196
- Publication
- Sep 1, 2006
Molecular mechanics methods for predicting protein-ligand binding
Huang, et al. Phys. Chem. Chem. Phys., 2006, 8, 5166-5177
- Publication
- Aug 1, 2006
Predicting Enantioselectivity: Computation as an Efficient “Experimental” Tool for Probing Enantioselectivity
Ragusa, et al. Eur. J. Org. Chem., 2006, 16, 3545-3549
- Publication
- Jul 19, 2006
Accurate Prediction of the Relative Potencies of Members of a Series of Kinase Inhibitors Using Molecular Docking and MM-GBSA Scoring
Lyne, et al. J. Med. Chem., 2006, 49, 4805-4808
- Publication
- Jul 11, 2006
Identification of a putative binding site for 5-alkyl-benzothiadiazides in the AMPA receptor dimer interface
Harps’e, et al. J. Mol. Graph. Model., 2007, 26, 213-225
- Publication
- Jun 23, 2006
Furan-2-ylmethylene thiazolidinediones as novel, potent, and selective inhibitors of phosphoinositide 3-kinase gamma
Pomel, et al. J. Med. Chem., 2006, 3857-3871
Events
Event
Life Science
- Sep 6th-10th, 2026
EFMC Medicinal Chemistry 2026
Schrödinger is excited to be participating in the EFMC Medicinal Chemistry 2026 conference taking place on September 6th – 10th in Basel, Switzerland.
Webinar
Life Science
- Sep 10, 2026
Is structure-based drug design and toxicology ready for ion channels and transporters?
In this webinar, we will answer this question by presenting the results of a large scale study of potency prediction for seven clinically relevant ion channels and two transporters.
Event
Life Science
- Sep 13th-16th, 2026
30th National Meeting on Medicinal Chemistry 2026
Schrödinger is excited to be participating in the 30th National Meeting on Medicinal Chemistry 2026 conference taking place on September 13th – 16th in Messina, Italy.
Webinars
Webinar
Life Science
- Sep 10, 2026
Is structure-based drug design and toxicology ready for ion channels and transporters?
In this webinar, we will answer this question by presenting the results of a large scale study of potency prediction for seven clinically relevant ion channels and two transporters.
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.
Webinar
Life Science
- Apr 24, 2026
Schrödinger 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24回
APR 24, 2026 | Diverse computational strategies enable the discovery of p38α-MK2 molecular glues
Documentation
- Documentation
Predicitive Tox Documentation
Documentation covering the panel help for Predictive Tox.
- 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.
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