Schrödinger

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The Stanford Libraries are very pleased to announce that we have licensed a number of software programs from Schrödinger.   These programs are available to all current students, faculty, and staff at Stanford University for not-for-profit, academic research, and for instructional use.  Commercial use is explicitly prohibited for this product.  Please see license terms.

This is collaborative effort with the Stanford Research Computing Center and the Vice Provost for Teaching and Learning who are providing computing support for Schrödinger software on campus. 

Be sure to check out the Schrodinger@Stanford at the ChEM-H Macromolecular Structure Knowledge Center.  This blog contains practical information, tips, and news about Schrödinger software to help Stanford users.

The Citations page on Schrödinger's website has information about citing the software in publications.

About Schrödinger software at Stanford

An alphabetical list describing each software program is available at the bottom of this page.

Biologics logoBiologics Suite - All the tools that are important in modeling biologics, antibodies, and proteins. 

This new, easy-to-use suite is designed form the ground up to be the first complete collection of all the tools that are important in modeling biologics, antibodies, and proteins. 

Software available: BioLuminate, Desmond, KNIME Extensions, Maestro, OPLS3, PIPER, Prime, Protein Preparation Wizard, SiteMap.

Small-molecule logoSmall-Molecule Drug Discovery Suite - A comprehensive suite to accelerate lead discovery and lead optimization. 

From quantitative structure activity relationships (QSAR) to virtual screening to binding affinity predictions, the comprehensive Small-Molecule Drug Discovery Suite contains all the tools necessary for fragment-, ligand-, and structure-based drug design for lead discovery and optimization. 

Software available: AutoQSAR, Canvas, ConfGen, Core Hopping, CovDock, Desmond, Epik, Field-Based QSAR, Glide, Induced Fit, Jaguar, KNIME Extensions, LigPrep, MacroModel, Maestro, MOPAC2012, OPLS3, P450 Site of Metabolism Prediction, Phase, PLDB, Prime, PrimeX, Protein Preparation Wizard, QikProp, QM-Polarized Docking, QSite, Shape Screening, and SiteMap.  MOPAC2012 must be installed separately.

Materials Science suiteMaterials Science Suite - A diverse set of tools for computing the structure, reactivity, and properties of chemical systems. 

This innovative new suite provides versatile and powerful tools for the quantum mechanics-based simulation of chemical systems, enabling the analysis and optimization of systems with applications in speciality chemicals and materials science. 

Software available: Canvas, Desmond, KNIME Extensions, MacroModel, Maestro, MOPAC2012, MS Combi, MS Jaguar, OPLS3.  MOPAC2012 must be installed separately.

PyMOL logoPyMOL - High-performance molecular graphics for communicating structural results.

Software available: PyMOL and AxPyMOL (Win).

Options for using Schrödinger software

Personal computers: All current students, faculty, and staff at Stanford can install Schrödinger software on their personal computer.

High Performance Computing Cluster: The Stanford Research Computing Center has installed Schrödinger software on Sherlock 2.0, a High Performance Computing Linux cluster, which supports sponsored or departmental research.  Please note that Sherlock 2.0 is only for research, not instructional use.  

Accounts are created for lab groups, not individuals.   To request a group account for using Schrödinger, a Principal Investigator (PI) should send email to Grace Baysinger that includes their name and SUNet ID.   PIs should also send names and SUNet IDs for others in their group that should have access to Schrödinger on Sherlock.  Thanks to the Vice Provost and Dean of Research, there is no charge to PIs for using Schrödinger software on Sherlock.

Computer Clusters: The Vice Provost for Teaching and Learning has Maestro and MacroModel installed on the 700 cluster computers located in the libraries, dorms, and computer clusters to help support instructional use.   Maestro is the interface for using MacroModel.

Key contacts for help

  • Install the software, get license info for desktop/laptops, and request Sherlock accounts, contact Grace Baysinger
  • Download software problems or for technical support on how to use Schrödinger software, fill out contact support form on Schrödinger's website.
  • How to use Sherlock 2, contact the Stanford Research Computer Center

Training and support

A-Z description of the software

An alphabetical list of the software we have licensed plus the product suite name(s) they are part of is below.

 

Description

Product Suites

AutoQSAR

AutoQSAR - Automated creation and application of predictive QSAR models following best practices.   AutoQSAR automates the creation of high-quality, predictive QSAR models and makes their application trivially simple.

Small-Molecule Drug Discovery
 BioLuminate

BioLuminate - Providing a comprehensive modeling solution for biologics.  BioLuminate is a brand-new, intuitive user interface that is specifically designed for examining biologics and protein systems with seamless access to superior scientific modeling algorithms.  

Biologics

 Canvas

Canvas - A comprehensive cheminformatics computing environment.  Canvas is a powerful suite of cheminformatics tools built on innovative technologies that achieve unmatched performance and versatility. Canvas offers solutions to a wide range of problems faced by researchers

Small-Molecule Drug Discovery, and Materials Science
 Confgen

ConfGen - Accurate and efficient bioactive conformational searching.  Reproducing bioactive ligand geometries in minimally sized conformer sets, accurate results from high-performance ConfGen calculations save time and effort in downstream applications.

Small-Molecule Drug Discovery
 Core Hopping

Core Hopping - Comprehensive ligand- and receptor-based scaffold exploration for lead optimization.  In addition to more conventional ligand-based methods, Core Hopping offers receptor-based scaffold hopping, exploiting information about the active site and known binding poses to guide the search for novel cores.

Small-Molecule Drug Discovery
 CovDock

CovDock - An all-in-one workflow for pose prediction and scoring of covalently bound ligands.  With the recent resurgence in covalent drug research, computational insight into covalent docking is becoming key to understanding how covalent inhibitors can be used to address selectivity and potency challenges.  Covalent inhibitors derive their activity not only from the formation of a covalent bond between the target and the ligand but also from stabilizing non-covalent forces in the binding pocket. CovDock selects the top covalent complexes using the extensively validated Prime energy model, and calculates an apparent affinity score that captures the essential elements of a successful covalent docking process.

Small-Molecule Drug Discovery
 Desmond

Desmond - High-performance molecular dynamics simulations.  Desmond's combined speed and accuracy make possible long time scale molecular dynamics simulations, allowing users to examine events of great biological and pharmaceutical importance. Seamlessly integrated with Maestro, Desmond provides comprehensive setup, simulation, and analysis tools.

Biologics, Small-Molecule Drug Discovery, and Materials Science
 Epik

Epik - Rapid and robust pKa predictions. Combining the proven reliability of Hammett and Taft methods with powerful tautomerization tools, Epik is the program of choice for accurate enumeration of ligand protonation states in biological conditions.

Small-Molecule Drug Discovery
 Field_Based_QSAR

Field-Based QSAR - Discover and optimize new lead compounds using quantitative predictions of binding-site chemistry.  Field-Based QSAR opens up new possibilities in ligand-based drug discovery projects. Supplied with an aligned training set of active and inactive compounds, Field-Based QSAR predicts drug activity on the basis of either force fields or Gaussian fields that describe ligand chemistry.

Small-Molecule Drug Discovery
 Glide_XP_Visualizer

Glide - A complete solution for ligand-receptor docking. Glide offers the full spectrum of speed and accuracy from high-throughput virtual screening of millions of compounds to extremely accurate binding mode predictions, providing consistently high enrichment at every level.

Small-Molecule Drug Discovery
 Glide_XP_Visualizer

Glide XP Visualizer – a tool for viewing Glide descriptors.  Glide offers the full range of speed vs. accuracy options, from the HTVS (high-throughput virtual screening) mode for efficiently enriching million compound libraries, to the SP (standard precision) mode for reliably docking tens to hundreds of thousands of ligand with high accuracy, to the XP (extra precision) mode where further elimination of false positives is accomplished by more extensive sampling and advanced scoring, resulting in even higher enrichment. The size of the dataset that needs to be studied at each level of accuracy is approximately an order of magnitude smaller than that of the previous, faster step. XP provides the most accurately docked poses and the highest level of enrichment.  The XP Visualizer is in Glide.

Small-Molecule Drug Discovery

 Induced_Fit

Induced Fit - A novel method for fast and accurate prediction of ligand induced conformational changes in receptor active sites. The active site geometry of a protein complex depends heavily upon conformational changes induced by the bound ligand. However, resolving the crystallographic structure of a protein-ligand complex requires a substantial investment of time, and is frequently infeasible or impossible. Schrödinger's Induced Fit protocol solves this problem by using Glide and Prime to exhaustively consider possible binding modes and the associated conformational changes within receptor active sites.

Small-Molecule Drug Discovery
 Jaguar

Jaguar - Rapid ab initio electronic structure package. Jaguar is a high-performance ab initio package for both gas and solution phase simulations, with particular strength in treating metal containing systems, making it the most practical quantum mechanical tool for solving real-world problems.

Small-Molecule Drug Discovery, and Materials Science
 Jaguar pKa

Jaguar pKa: A KNIME Workflow to evaluate the pKa of specified atoms using Jaguar.

Small-Molecule Drug Discovery
 KNIME_Extensions

KNIME Extensions  - A modular, highly configurable framework for easy workflow automation and data analysis.  Using the popular open-source KNIME interface, researchers can easily assemble individual "nodes" into a complete workflow — from structure preparation and selection to a validated predictive model. Expediting a wide variety of common tasks, Schrödinger KNIME Extensions are an indispensable tool for modeling and cheminformatics.

Biologics, Small-Molecule Drug Discovery, and Materials Science
 LigPrep

LigPrep - Versatile generation of accurate 3D molecular models.  LigPrep goes far beyond simple 2D to 3D structure conversions by including tautomeric, stereochemical, and ionization variations, as well as energy minimization and flexible filters to generate fully customized ligand libraries for further computational analyses.

Small-Molecule Drug Discovery
 MacroModel

MacroModel - Versatile, full-featured program for molecular modeling.  MacroModel combines leading force fields, accurate effective solvation models, and advanced conformational searching methods to provide the most complete molecular modeling package suitable for a wide array of research.

Small-Molecule Drug Discovery, and Materials Science
 Maestro

Maestro 11 - The completely reimagined all-purpose molecular modeling environment. Maestro 11 is the completely redesigned interface for all Schrödinger software. Significantly enhanced usability built on Maestro’s long-standing impressive visualization and analysis tools makes Maestro 11 a versatile modeling environment for all researchers.

Biologics, Small-Molecule Drug Discovery, and Materials Science
 Membrane_Permeability

Membrane Permeability - Physics-based, accurate predictions of passive membrane permeability. The Prime physics-based membrane predictor combines conformational sampling with Schrödinger’s advanced force field and solvent models within a physics-based framework to produce more accurate predictions of passive membrane permeability.

Biologics, and Small-Molecule Drug Discovery
 MOPAC

MOPAC2012 - Fast, accurate quantum chemistry for large structures and condensed phase.   Schrödinger provides access to MOPAC2012 for basic semiempirical NDDO (neglect of diatomic differential overlap) capabilities. With this tool you can calculate heats of formation, optimized geometries, force constants, and a selection of properties as indicated below. This semiempirical NDDO program can be run from Maestro or from the command line.

Produced by Stewart Computational Chemistry and free to academic users, MOPAC2012 has been integrated to work with Schrödinger software but only MOPAC2016 is available for downloading. Instructions for modifying 2016 to 2012: Copy MOPAC2016.exe and rename the copy MOPAC2012.exe.   Copy "password for MOPAC2016" and rename the copy "password for MOPAC2012" You should then have two MOPAC executables and two passwords.  Then try running the Schrodinger software.

Small-Molecule Drug Discovery, and Materials Science
 MS_Maestro

MS Maestro – A specialized interface to enable efficient and systematic exploration of chemical design space for key technology applications including optoelectronics and reactive systems. 

Materials Science
 OPLS3

OPLS3 Force Field - A revolutionary advance in modern force fields. OPLS3 is the culmination of a significant, large-scale effort to create the most accurate force field with the most comprehensive coverage of chemical space.

Biologics, Small-Molecule Drug Discovery, and Materials Science
 Cytochrome P450 Oxidase

P450 Site of Metabolism (SOM) Prediction - A tool is used for identifying likely sites of metabolism based on Hammet and Taft- type rules and 3D spatial information in several P450 isoforms.  For a given atom of a molecule to be a significant site of metabolism by a P450 enzyme, it must have some degree of reactivity in the absence of the enzyme and also be accessible to the reactive heme iron center. To address both of these requirements, the P450 Site of Metabolism workflow combines induced-fit docking (IFD) for the determination of accessibility to the reactive center with a rule-based approach to intrinsic reactivity.  Note: password required to link in this description.

Small-Molecule Drug Discovery
 Phase

Phase - An easy-to-use pharmacophore modeling solution for ligand- and structure-based drug design.  Phase is a complete, user-friendly pharmacophore modeling solution designed to maximize performance in virtual screening and lead optimization. Fast, accurate, and easy-to-use, Phase includes a novel, scientifically validated common pharmacophore perception algorithm.

Biologics, and Small-Molecule Drug Discovery
 Piper

PIPER - A state of the art protein-protein docking program. PIPER is a state-of-the-art protein-protein docking program based on a multi-staged approach and advanced numerical methods that reliably generates accurate structures of protein-protein complexes.

Biologics
 Prime

Prime - A powerful and innovative package for accurate protein structure predictions. Prime is a fully-integrated protein structure prediction program. It provides an easy-to-use interface that takes a novice user intuitively from sequence to alignment to refined structure. Prime also provides expert users complete control over calculational settings to maximize accuracy of predictions. Prime is a powerful and complete tool for generating accurate receptor models for structure-based drug design.

Biologics, and Small-Molecule Drug Discovery
 PrimeX

PrimeX - A comprehensive package for accurate protein crystal structure refinement.  PrimeX uses state-of-the-art technologies to refine protein crystal structures for computational drug discovery.

Small-Molecule Drug Discovery
 Protein_Ligand_Database

Protein-Ligand Database (PLDB) - An active knowledge base of structural data and protein-ligand interactions. PLDB is an active structural data store that can be pipelined in any custom workflow, while flexibly allowing searches using advanced structure motifs and protein-ligand interaction patterns.

Small-Molecule Drug Discovery
 Protein_Prep_Wizard

Protein Preparation Wizard - An easy-to-use tool for correcting common structural problems and creating reliable, all-atom protein models. Successful structure-based modeling projects demand not only accurate software, but accurate starting structures as well. Left untreated, common problems with experimentally-derived structures can lead to wasted time and resources. Schrödinger’s Protein Preparation Wizard is designed to help researchers ensure structural correctness at the outset of a project, equipping them with a high-confidence structure ideal for use with a wide variety of modeling applications.

Biologics, and Small-Molecule Drug Discovery
 PyMOL

PyMOL - Stunning high-performance molecular graphics for communicating structural results.  Tens of thousands of scientists worldwide choose PyMOL to view, share, and analyze their molecular data. In addition to being lightweight and fast, PyMOL can create images of peerless visualization quality, while offering the flexibility of Python-based development and scalability.  AxPyMOL - plugin for Windows PowerPoint that enables presentation of 3-D molecular data without having to "tab out" of PowerPoint slides.   Stanford's site license includes PyMOL and AxPyMOL.

PyMOL and AxPyMOL
 QikProp

QikProp - Rapid ADME predictions of drug candidates. QikProp efficiently evaluates pharmaceutically relevant properties for over half a million compounds per hour, making it an indispensable lead generation and lead optimization tool.

Small-Molecule Drug Discovery
 QM_Polarized_Ligand_Docking

QM Polarized Ligand Docking - A novel research solution that combines the power of Glide with the accuracy of QSite.  Accurate treatment of electrostatic charges is crucial to the success of any docking algorithm. Although contemporary force fields are capable of modeling partial atomic charges on ligands with reasonable accuracy, they are generally incapable of considering charge polarization induced by the protein environment. The greater the role charge polarization plays in determining a ligand's bound conformation, the more difficult it will be for MM docking algorithms to perceive the correct binding mode. For research applications that demand the highest level of docking accuracy, Schrödinger introduces QM-Polarized Ligand Docking (QPLD), which uses ab inito charge calculations to overcome this limitation.

Small-Molecule Drug Discovery
 QSite

QSite - A high-performance QM/MM program. QSite applies quantum mechanics to the reactive center of a protein active site and molecular mechanics to the rest of the system. Its accuracy allows detailed understanding of reactions involving proteins, making it a powerful tool for lead optimization.

Small-Molecule Drug Discovery
Schrodinger_Python_API

Schrödinger API - interface that allows python code to be used with our software.  It is accessed using the unlimited MMLIBS token.

Access API module and documentation
 Shape_Screening

Shape Screening - A fast and efficient tool for shape-based superposition and similarity searching. Shape Screening is capable of screening large databases of compounds to identify new leads with similar shape and electrostatic properties to a lead query molecule.

Small-Molecule Drug Discovery
 Site_Map

SiteMap - Fast, accurate, and practical binding site identification. Combining a novel algorithm for rapid binding site identification and evaluation with easy-to-use property visualization tools, SiteMap provides researchers with an efficient means to find and better exploit the characteristics of ligand binding sites.

Biologics, and Small-Molecule Drug Discovery
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