| Schrödinger |
Maestro7
|
|
√ |
workhorse platform for all-purpose
molecular modeling |
https://www.schrodinger.com/maestro |
| AutoQSAR8
|
√ |
|
automated creation and application
of predictive QSAR models |
https://www.schrodinger.com/autoqsar |
| ConfGen9
|
|
√ |
accurate and efficient bioactive
conformational searching |
https://www.schrodinger.com/confgen |
| Desmond10
|
|
√ |
high-performance MD simulations |
https://www.schrodinger.com/desmond |
| FEP+11
|
|
√ |
high-performance free energy
calculations for drug discovery |
https://www.schrodinger.com/fep |
| Glide12
|
|
√ |
solution for ligand–receptor
docking |
https://www.schrodinger.com/glide |
| Induced
Fit13
|
|
√ |
fast and
accurate prediction
of ligand-induced changes in receptor active sites |
https://www.schrodinger.com/induced-fit |
| LigPrep14
|
|
√ |
versatile generation of
accurate 3D molecular models |
https://www.schrodinger.com/ligprep |
| MacroModel15
|
|
√ |
molecular modeling platform |
https://www.schrodinger.com/macromodel |
| Phase16
|
|
√ |
easy-to-use pharmacophore
modeling solution for ligand- and structure-based drug design |
https://www.schrodinger.com/phase |
| PyMOL17
|
|
√ |
high-performance molecular
graphics platform for 3D visualization |
https://www.schrodinger.com/pymol |
| QSite18
|
|
√ |
high-performance QM/MM program |
https://www.schrodinger.com/qsite |
| Shape
Screening19
|
|
√ |
VLS using
3D shape-based
similarity |
https://www.schrodinger.com/shape-screening |
| Core
Hopping20
|
|
√ |
comprehensive
ligand- and
receptor-based scaffold exploration tool for lead optimization |
https://www.schrodinger.com/core-hopping |
| e-Pharmacophores21
|
|
√ |
energetically optimized
structure-based pharmacophores |
https://www.schrodinger.com/e-pharmacophores |
| Field-Based
QSAR22
|
√ |
√ |
discover and optimize new
lead compounds using quantitative predictions of binding-site chemistry |
https://www.schrodinger.com/field-based-qsar |
| Jaguar23
|
|
√ |
rapid ab initio QM electronic
structure package |
https://www.schrodinger.com/jaguar |
| LiveDesign24
|
√ |
√ |
next-generation platform
for collaborative drug design |
https://www.schrodinger.com/livedesign/drug-discovery |
| QikProp25
|
√ |
|
rapid ADME prediction of
drug candidates |
https://www.schrodinger.com/qikprop |
| WaterMap26
|
|
√ |
solution for desolvation
thermodynamics |
https://www.schrodinger.com/watermap |
| SiteMap27
|
|
√ |
fast, accurate, and practical
binding site predictor |
https://www.schrodinger.com/sitemap |
| Canvas28
|
√ |
|
comprehensive cheminformatics
computing environment |
https://www.schrodinger.com/canvas |
| EPIK29
|
√ |
|
fast and robust pKa predictions |
https://www.schrodinger.com/epik |
| CovDock30
|
|
√ |
work-flow for pose prediction
for covalently bound ligands |
https://www.schrodinger.com/covdock |
| |
| Cresset |
Forge31
|
√ |
√ |
ligand-based workbench for
molecular design and SAR analysis |
https://www.cresset-group.com/software/forge/ |
| Activity
Atlas32
|
|
√ |
component
of Forge for SAR
interpretation and visualization |
https://www.cresset-group.com/software/forge-activity-atlas/ |
| Activity
Miner32
|
|
√ |
component
of Forge to find
and understand activity cliffs |
https://www.cresset-group.com/software/forge-activity-miner/ |
| FieldTemplater32
|
√ |
√ |
component of Forge to generate
the most accurate field pharmacophores available |
https://www.cresset-group.com/software/field-templater/ |
| Flare33
|
|
√ |
protein–ligand analysis
platform for advanced SBDD |
https://www.cresset-group.com/software/flare/ |
| Spark32
|
√ |
√ |
scaffold hopping and R-group
replacement for innovative molecular design |
https://www.cresset-group.com/software/spark/ |
| Blaze34
|
|
√ |
ligand-based virtual screening |
https://www.cresset-group.com/software/blaze/ |
| PickR32
|
√ |
|
advanced electrostatic diversity
monomer selection tool for library design |
https://www.cresset-group.com/software/pickr/ |
| Lead
Finder35
|
|
√ |
high-throughput
docking
and scoring for VLS |
https://www.cresset-group.com/software/lead-finder/ |
| Torx32
|
√ |
|
next-generation platform
for smallmolecules team-working and collaboration |
https://www.cresset-group.com/software/torx/ |
| |
| Open-Eye |
cheminformatics tool kits |
| FastROCS TK36
|
√ |
|
real-time shape similarity
for VLS, lead hopping, and shape clustering |
https://www.eyesopen.com/molecular-modeling-fastrocs |
| OEChem
TK40
|
√ |
|
core chemistry handling
and representation |
https://www.eyesopen.com/oechem-tk |
| OEDepict
TK |
√ |
|
2D molecule rendering and
depiction |
https://www.eyesopen.com/oedepict-tk |
| Grapheme
TK |
√ |
|
Advanced molecule rendering
and report generation |
https://www.eyesopen.com/grapheme-tk |
| GraphSim
TK41
|
√ |
|
2D molecular similarity
(e.g., fingerprints) |
https://www.eyesopen.com/graphsim-tk |
| Lexichem
TK42
|
√ |
|
name-to-structure and structure-to-name
translator |
https://www.eyesopen.com/lexichem-tk |
| MolProp
TK |
√ |
|
molecular property calculation
and filtering |
https://www.eyesopen.com/molprop-tk |
| Quacpac
TK43
|
√ |
|
tautomer enumeration and
charge assignment |
https://www.eyesopen.com/quacpac-tk |
| MedChemTK |
√ |
|
matched molecular pair analysis,
fragmentation, and molecular complexity metrics |
https://www.eyesopen.com/oemedchem-tk |
| modeling
tool kits |
| OEDocking TK44
|
|
√ |
molecular
docking and scoring |
https://www.eyesopen.com/oedocking-tk |
| Omega
TK45
|
|
√ |
conformer
generation |
https://www.eyesopen.com/omega-tk |
| Shape
TK46
|
|
√ |
3D shape
description, manipulators,
and interrogation |
https://www.eyesopen.com/shape-tk |
| Spicoli
TK |
|
√ |
surface generation, manipulation,
and interrogation |
https://www.eyesopen.com/spicoli-tk |
| Szmap
TK |
|
√ |
understanding water interactions
in binding sites |
https://www.eyesopen.com/szmap-tk |
| Zap
TK47
|
|
√ |
calculate
Poisson–Boltzmann
electrostatic potentials |
https://www.eyesopen.com/zap-tk |
| Szybki
TK48
|
|
√ |
general
purpose optimization
with MMFF94 |
https://www.eyesopen.com/szybki-tk |
| Orion |
√ |
√ |
cloud-based platform to
develop custom computational drug discovery workflows and visualizations |
https://www.eyesopen.com/orion |
| |
| BioSolve-IT |
SeeSAR49
|
√ |
√ |
visual compound prioritization
and evolution; structure-based design work supporting MPO; visualize
binding affinity at interfaces |
https://www.biosolveit.de/SeeSAR/ |
| infiniSee50
|
√ |
|
finds molecules chemically
similar to given molecule or template; navigates through “almost
infinite space” and employs FTrees technology |
https://www.biosolveit.de/infiniSee/ |
| FlexX51
|
|
√ |
structure-based docking;
binding mode prediction |
https://www.biosolveit.de/FlexX/ |
| HYDE52
|
√ |
√ |
structure-based scoring;
compound classification |
https://www.biosolveit.de/HYDE/ |
| FlexS53
|
√ |
√ |
ligand-based alignment in
3D; prep for 3D QSAR; find scaffold/compound mimics; virtual screening |
https://www.biosolveit.de/FlexS/ |
| FTrees54
|
√ |
|
ligand-based similarity;
fuzzy matching to detect novel molecular scaffolds |
https://www.biosolveit.de/FTrees/ |
| ReCore54
|
√ |
|
fragment-based; replace
central elements in known bioactive molecules to create new custom
3D scaffold |
https://www.biosolveit.de/ReCore/ |
| FTrees-FS54
|
√ |
|
combinatorial fragment space
extension module for FTrees; builds up compounds from fragments while
still comparing and searching for similarity |
https://www.biosolveit.de/products/#FTrees |
| CoLibri54
|
√ |
|
toolkit for chemical space
exploration; generate chemical space; focus on synthetically accessible
entities |
https://www.biosolveit.de/CoLibri/ |
| REAL
Space Navigator |
√ |
|
collaboration with Enamine,
“world’s largest, ultrafast” searchable chemical
space; 13 billion compounds |
https://www.biosolveit.de/REALSpaceNavigator/ |
| GalaXi |
√ |
|
explore chemical space commercially
available on demand from Wuxi |
https://www.biosolveit.de/2019/10/10/launch-of-galaxi/ |
| KnowledgeSpace |
√ |
|
virtual chemical space containing
100+ literature reactions to produce likely synthetically accessible
compounds |
https://www.biosolveit.de/CoLibri/spaces.html |
| |
| Dotmatics |
Browser |
√ |
|
searching and browsing across
all corporate scientific databases |
https://www.dotmatics.com/products/browser |
| D40 |
√ |
|
“Dotmatics for Microsoft
Office” connector to integrate with Microsoft Office suite |
https://www.dotmatics.com/products |
| Blueprint |
√ |
|
Web-based platform for visualization
and scientific data analysis for small-molecule design |
https://www.dotmatics.com/products/blueprint |
| Vortex |
√ |
|
chemically intuitive data
visualization and analysis’ expansion on the “spreadsheet”;
can do statistical analysis and create visualizations |
https://www.dotmatics.com/products/vortex/ |
| |
| Discngine |
Assay |
√ |
|
design and manage cellular,
molecular, and high-content screening campaigns |
https://www.discngine.com/assay |
| 3Decision |
|
√ |
store, analyze, and share
protein–ligand structures, sequences, and associated data |
https://3decision.discngine.com/ |
| Chemistry
Collection |
√ |
|
generate and visualize scaffold
networks, perform molecular fragmentation, or use Pharmacophore Graph
to design matched molecule pairs analysis |
https://www.discngine.com/chemistry-collection |
| Network
Collection |
√ |
|
represent, manage, and analyze
complex network structures using advanced graph theory |
https://www.discngine.com/network-collection |
| |
| Optibrium |
Stardrop |
√ |
|
small-molecule design, optimization,
and data analysis; can do predictive modeling and QSAR |
https://www.optibrium.com/stardrop/stardrop-features.php |
| Asteris |
√ |
|
iPad app for drug discovery |
https://www.asteris-app.com/ |
| Ocura |
√ |
|
load and browse molecular
structures; data viewer |
https://www.optibrium.com/ocura/ |
| |
| TIBCO |
Spotfire |
√ |
|
AI-powered search-driven
experience; built-in data wrangling and advanced analytics |
https://www.tibco.com/products/tibco-spotfire |
| TIBCO
Data Science |
√ |
|
share and deploy analytics
models across organizations for increased collaboration |
https://www.tibco.com/products/data-science |
| |
| Dassault Systemes |
Biovia Pipeline Pilot |
√ |
|
data pipelining tool for
creating simple as well as advanced workflows for various data science
initiatives such as cheminformatics, bioinformatics, ML, etc. |
https://www.3ds.com/products-services/biovia/products/data-science/pipeline-pilot/ |
| Discovery
Studio |
|
√ |
data pipelining tool for
advanced 3D design such as molecular mechanics, free energy calculations,
biotherapeutics developability, and more in a common environment |
https://www.3ds.com/products-services/biovia/products/molecular-modeling-simulation/biovia-discovery-studio/ |
| |
| CCDC |
mercury |
|
√ |
knowledge-based geometry
and interaction preferences |
https://www.ccdc.cam.ac.uk/mercury/ |
| GOLD |
|
√ |
protein–ligand
docking |
https://www.ccdc.cam.ac.uk/solutions/csd-discovery/components/gold/ |
| CSD-CrossMiner |
√ |
|
discovery-oriented data
mining of protein and small-molecule crystal structures |
https://www.ccdc.cam.ac.uk/solutions/csd-discovery/components/csd-crossminer |
| SuperStar |
√ |
|
knowledge-based pharmacophore
prediction |
https://www.ccdc.cam.ac.uk/solutions/csd-discovery/components/superstar/ |
| CSD
Python API |
√ |
|
Python-based programmatic
access to the tools |
https://www.ccdc.cam.ac.uk/solutions/csd-materials/components/csd-python-api/ |
| Mogul |
|
√ |
knowledge-based library
of molecular geometry derived from the Cambridge Structural Database
(CSD) |
https://www.ccdc.cam.ac.uk/solutions/csd-system/components/mogul/ |
| |
| CCG |
Molecular Operating Environment
(MOE)55
|
|
√ |
integrated
computer-aided
molecular design platform; includes 3D visualization, structure-based
design, SAR explorer, data modeling, virtual screening, simulations,
QSAR, etc. for small molecules as well as antibody–drug conjugates
and biologics |
https://www.chemcomp.com/Products.htm |
| MOESaic55
|
√ |
|
allows small-molecule SAR
analysis such as MMPs, R-group, etc. |
https://www.chemcomp.com/Products.htm#MOEsaic-SAR_Explorer |
| PSILO55
|
|
√ |
data repository and visualization
application to store curated RCSB protein structures, pocket similarity,
and other features for data analysis |
https://www.chemcomp.com/Products.htm#PSILO-Structure_Database |
| |
| Medchemica |
MCPairs |
|
√ |
AI/ML-based
SAR analysis
application to generate match pairs and new ideas |
https://www.medchemica.com/products/ |
| |
| ChemAlive |
ConstruQt |
√ |
|
high-throughput quantum
chemistry for molecular design; allows automated library-scale deployment
of quantum chemical calculations |
https://www.chemalive.com/construqt/ |
| |
| CDD Vault |
CDD Vault |
√ |
|
informatics platform; molecular/data
viewing and browsing |
https://www.collaborativedrug.com/benefits/ |
| |
| BioSymetrics |
Augusta |
√ |
|
biomedical-specific ML framework;
drug discovery through small-molecule activity prediction |
https://www.biosymetrics.com/products/moa-prediction/ |
| |
| Eidogen Sertanty |
Target Informatics Platform
(TIP) |
√ |
|
interrogate the druggable
genome from a structural perspective; bridge the gap between bio-
and cheminformatics |
https://www.eidogen.com/tip.php |
| TIP
Calculation Engine (STRUCTFAST,
SiteSeeker, SiteSorter, SLiC) |
|
√ |
structure
determination;
binding site annotation; similarity assessment |
https://www.eidogen.com/tae.php |
| Eidogen
Visualization Environment
(EVE) |
|
√ |
visualize and compare small-molecule
binding sites of targets of interest |
https://www.eidogen.com/eve.php |
| Oncology
Knowledgebase (OKB) |
√ |
|
database of structure–activity
data across targets of oncological interest |
https://www.eidogen.com/oncologykb.php |
| Kinase Knowledgebase (KKB) |
√ |
|
database of kinase structure–activity
and chemical synthesis data |
https://www.eidogen.com/kinasekb.php |
| ChIP |
√ |
|
algorithm-driven enumeration
engine for automated generation of medicinally relevant, novel molecules
with proven synthetic access |
https://www.eidogen.com/chip.php |
| |
| VeraChem |
VM2 |
|
√ |
software package for molecular-binding
free energy calculations |
http://www.verachem.com/products/vm2 |
| VConf |
√ |
|
2D-to-3D small-molecule
conversion |
http://www.verachem.com/products/vconf |
| VCharge |
|
√ |
accurate partial atomic
charges of drug-like molecules |
http://www.verachem.com/products/vcharge |
| VFilter |
√ |
√ |
analyze ensembles of molecular
conformations and remove repeats |
http://www.verachem.com/products/vfilter |
| Vrms |
√ |
√ |
provides symmetry-corrected
root-mean-square deviation between molecular conformers |
https://www.verachem.com/products/vrms/ |
| VDisplay |
|
√ |
3D molecular viewer |
https://www.verachem.com/products/vdisplay/ |
| |
| NextMove |
Arthor56
|
√ |
|
fast, state-of-the-art substructure
and chemical similarity search capabilities for ultra-large databases
of 100s of millions of compounds, using SMARTS optimization, Just-In-Time
compilation, and/or GPUs |
https://www.nextmovesoftware.com/arthor.html |
| Matsy57
|
√ |
|
set of tools for creating
and analyzing matched molecular series (the general form of MMPS);
In particular, can be used to suggest what compound to make next in
a med-chem program |
https://www.nextmovesoftware.com/matsy.html |
| MPSearch57
|
√ |
|
rapidly searches a database
to find matched pairs related to a query molecule This type of search
is used to explore previous medicinal chemistry strategies |
https://www.nextmovesoftware.com/mpsearch.html |
| Patsy58
|
√ |
|
speed up SMARTS pattern
matching by creating optimized SMARTS patterns of source code; speed
gains are particularly large when multiple SMARTS patterns are matched
against a single structure |
https://www.nextmovesoftware.com/patsy.html |
| SmallWorld59
|
√ |
|
index of chemical space
based on more than 230 billion substructures; can be used to measure
similarity based on graph-edit distance, find the maximum common subgraph
of two or more molecules, analyze HTS results, and more |
https://www.nextmovesoftware.com/smallworld.html |
| CaffeineFix60
|
√ |
|
rapidly match chemical names
or terms against a dictionary of grammar (e.g., a grammar for IUPAC
names); use in text mining; can be used to provide autocomplete functionality
and spell-correction |
https://www.nextmovesoftware.com/caffeinefix.html |
| LeadMine61
|
√ |
|
extracts chemical names
and terms from text; incorporates CaffeineFix technology to find terms
that match appropriate dictionaries or grammars; has enhanced functionality
to handle patent literature |
https://www.nextmovesoftware.com/leadmine.html |
| Casandra62
|
√ |
|
server for delivering real-time
safety warning of experimental hazards straight to pharmaceutical
ELNs |
https://www.nextmovesoftware.com/casandra.html |
| HazELNut63
|
√ |
|
suite of tools used to extract,
normalize, and analyze information in ELNs; can be used to implement
a search interface, find/eliminate duplicates, find similar reactions,
etc. |
https://www.nextmovesoftware.com/hazelnut.html |
| NameRxn64
|
√ |
|
used to classify and name
reactions; particularly useful in the context of ELN analysis but
also as a plug-in to chemical drawing software; builds on NextMove
Patsy technology |
https://www.nextmovesoftware.com/namerxn.html |
| Pistachio65
|
√ |
|
reaction dataset browser
providing loading, querying, and analytics of chemical reactions;
with over 9 million chemical reactions extracted from U.S. and EPO
patents, it demonstrates an AI interface to faceted (structure) search |
https://www.nextmovesoftware.com/pistachio.html |
| |
| Alvascience |
alvaMolecule |
√ |
|
visual analytics platform
allowing users to standardize and organize chemistry project data |
https://www.alvascience.com/alvamolecule/ |
| alvaModel |
√ |
|
build and deploy QSAR/QSPR
regression models; consists of two pieces of software: alvaModel and
alvaRunner |
https://www.alvascience.com/alvamodel/ |
| alvaDesc |
√ |
|
allows calculation of over
5000 0D/1D/2D/3D molecular descriptors |
https://www.alvascience.com/alvadesc/ |
| alvaBuilder |
√ |
|
molecule design platform
utilizing user-selected property criteria |
https://www.alvascience.com/alvabuilder/ |
| |
| Datagrok |
Datagrok for Cheminformatics |
√ |
|
chemistry data visualization
and analytics; provides a structure/substructure search as well as
mechanism to build ML models |
https://datagrok.ai/cheminformatics |
| |
| Molsoft |
ICM Chemist Pro |
√ |
|
allows scientists to draw
and edit chemicals, create and view chemical spreadsheets, and perform
chemical searching, chemical clustering, and many other routine cheminformatics
functionalities |
https://www.molsoft.com/icm-chemist-pro.html |
| ICM
Pro |
|
√ |
desktop software environment
for high-quality protein structure analysis, modeling, and docking |
https://www.molsoft.com/icm_pro.html |
