- Publication
- Mar 28, 2001
Activation of the C-H bond of Methane by Intermediate Q of Methane Monoozygenase: A Theoretical Study
Gherman, et al. J. Am. Chem. Soc., 2001, 123, 3836-3837- Publication
- Mar 20, 2001
Solvent Models for Protein-Ligand Binding: Comparison of Implicit Solvent Poisson and Surface Generalized Born Models with Explicit Solvent Simulations
Zhang, et al. J. Comput. Chem., 2001, 22, 591-607- Publication
- Feb 15, 2001
Large Scale Ab Initio Quantum Chemical Calculations on Biological Systems
Friesner, et al. Accounts of Chemical Research, 2001, 34, 351-358- Publication
- Jan 1, 2001
Molecular Modeling of Bifunctional Chelate Peptide Conjugates. 1. Copper and Indium Parameters for the AMBER Force Field
Reichert, et al. Inorg. Chem., 2001, 40, 5223-5230- Publication
- Dec 6, 2000
Hessian-Free Low-Mode Conformational Search for Large-Scale Protein Loop Optimization: Application to c-jun N-Terminal Kinase JNK3
Kolossvary, et al. J. Comp. Chem., 2001, 22, 21-30- Publication
- Dec 1, 2000
Design, Synthesis and Binding Properties of Novel and Selective 5-HT3 and 5-HT4 Receptor Ligands
Modica, et al. Eur. J. Med. Chem., 2000, 35, Erratum: ibid 2001, 36 287-301- Publication
- Nov 14, 2000
A Mixed Quantum Mechanics/Molecular Mechanics (QM/MM) Method for Large-scale Modeling of Chemistry in Protein Environments
Murphy, et al. J. Comp. Chem., 2000, 21, 1442-1457- Publication
- Nov 5, 2000
Protonation states of the chromophore of denatured green fluorescent proteins predicted by ab initio calculations
El Yazal, et al. J. Am. Chem. Soc., 2000, 122, 11411-11415- Publication
- Oct 24, 2000
Design, Synthesis, and Solution Structure of a Pyrrolinone-Based ‘-Turn Peptidomimetic
Smith, et al. J. Am. Chem. Soc., 2000, 122, 11037-11038- Publication
- Jun 6, 2000
Structures of Protonated Arginine Dimer and Bradykinin Investigated by Density Functional Theory: Further Support for Stable Gas-Phase Salt Bridges
Strittmatter, et al. J. Phys. Chem. A., 2000, 104, 6069-6076- Publication
- Jun 5, 2000
Prediction of Drug Solubility from Monte Carlo Simulations
Jorgensen, et al. Bioorg. Med. Chem. Lett., 2000, 10, 1155-8- Publication
- May 4, 2000
Improved Treatment of Cyclic Beta-Amino Acids and Successful Prediction of Beta-Peptide Secondary Structure using a Modified Force Field: AMBER*C
Christianson, et al. J. Comput. Chem., 2000Case Studies
Case Study
Life Science
Materials Science
Case Study
Life Science
Case Study
Life Science
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.
Events
Webinar
Materials Science
- Oct 29, 2025
Advancing battery materials innovation using charge-aware machine learning force fields
In this webinar, we will demonstrate how Schrödinger is utilizing an integrated computational approach combining physics-based molecular modeling with machine learning force fields (MLFFs) to address key challenges in battery materials design.
Webinar
Life Science
- Oct 31, 2025
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20回
In silico cryptic binding site detection and prioritization
Event
Life Science
- Nov 3rd-5th, 2025
BIO Europe 2025
Schrödinger is excited to be participating in the BIO Europe 2025 conference taking place on November 3rd – 5th in Vienna, Austria.
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, PreprintQuick Reference Sheets
- Quick Reference Sheet
GlideMap
A one-page guide to using the GlideMap GUI for ligand placement guided by experimental density.
- Quick Reference Sheet
Synthesis Queue LiveReport
Use Freeform columns to track the status of compounds in a synthesis queue.
- Quick Reference Sheet
Modeling Queue LiveReport
Learn how to use Freeform columns and an Auto-Update Search to create compound progression workflows.
Tutorials
- Tutorial
Structure-Based Virtual Screening using Glide
Prepare receptor grids for docking, dock molecules and examine the docked poses.
- Tutorial
Ligand Binding Pose Prediction for FEP+ using Core-Constrained Docking
Generate starting poses for FEP simulations for a series of BACE1 inhibitors using core constrained docking.
- Tutorial
Antibody Visualization and Modeling in BioLuminate
Visualize, build, and evaluate antibody models, analyze an antibody for various characteristics, dock an antigen to an antibody.
Webinars
Webinar
Life Science
- Oct 31, 2025
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20回
In silico cryptic binding site detection and prioritization
Webinar
Life Science
- Oct 9, 2025
6th EFMC² Tandem Talks
Schrödinger is excited to be participating in the 6th EFMC² Tandem Talks virtual event taking place on October 9th.
Webinar
Life Science
- Oct 8, 2025
Structure-based discovery of highly potent dihydroorotate dehydrogenase inhibitors for once-monthly malaria chemoprevention
In this webinar, Zhe Nie, medicinal chemist and project leader at Schrödinger, and Margaret Phillips, professor at UT Southwestern Medical School, Dallas, share in conversation how their teams worked collaboratively towards the discovery of novel DHODH inhibitors.
White Papers
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
White Paper
Life Science
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