Ligand-Based Drug Design integrates ICM Chemist Pro and ICM RIDE for pharmacophore modeling, similarity search, and lead optimization. Combined with ChemAxon’s calculators and predictors, it enables early evaluation of properties and drug-likeness to guide smarter decisions.
Structure-Based Drug Design
Structure-Based Drug Design solutions from MolSoft LLC leverage the powerful ICM platform for high-accuracy docking, molecular dynamics, protein modeling, and binding site analysis. These tools enable researchers to rationally design and optimize drug candidates using detailed 3D structural insights.
ICM PRO
ICM Pro
ICM-Pro is MolSoft’s primary desktop modeling software offering most of the core functionalities like:
- ICM Pocket Finder
- Docking
- Ligand- Protein
- Induced Fit
- Protein-Protein
- Peptide Docking

- RNA Docking
- ICM 3D Interactive Editor
- 2D ligand-receptor interaction diagrams
- PROTAC Modeling
- Molecular Dynamics
- Predict Effect of Mutation
- Crystallographic Analysis Tool
- Protein Structure Prediction and Analysis
- Sequence Analysis & Alignments and many other functionalities
To know more click here
ICM Pro is a comprehensive tool for structure-based drug design and offers high-quality protein structure analysis, modeling, docking, PROTAC Modeling, RNA Docking, MD, Mutation studies and much more.
ICM VLS
ICM Virtual Ligand Screening
ICM-VLS ( Virtual Ligand Screening) is MolSoft’s efficient virtual screening methodology in which ligands are fully and continuously flexible, some of the core functionalities include:
- Ligand Docking – Batch
- Covalent Docking
- Structure-based VLS
- Virtual Ligand Screening Physics/AI based scores

- Ligand-based VLS (APF)
- Fragment-based VLS
- Dock on the fly Markush generated libraries
- ICM 3D Interactive Editor
- Atomic Property Fields (APF)
- RIDE (CPU version)
- Pharmacophore Searching
- Includes all Functionalities of ICM Chemist – Pro
To know more click here.
ICM VLS is a high-accuracy virtual ligand screening platform enabling hit identification. It combines advanced docking, flexible receptor modeling, and robust scoring functions to prioritize promising candidates efficiently.
ICM – Homology
ICM Homology
ICM-Homology offers a methodology for conformational modeling of protein side chains and loops, implemented in ICM, relies on internal coordinate definition of the molecular object combined with computationally efficient ICM Biased Probability Monte Carlo
- Sensitive sequence search for template identification.
- Fast model building – the algorithm builds the model with all loops in seconds.

- Loop prediction using a loop PDB database.
- Loop prediction through local energy optimization.
- Multi-template modeling.
- Loop grafting.
- Protein sculpting.
- Peptide modeling.
- Search the PDB for similar loop conformation.
- Calculate relative residue frequency in similar loops from the PDB.
- Prediction of Disulfide bonds.
- Local reliability prediction and model validation features.
- Model refinement using ICM global optimization.
- Membrane protein modeling.
- High-throughput homology modeling.
To know more click here.
The ICM-Homology modeling algorithm has proved to be one of the more robust modeling tools for conformational modeling of protein side chains and loops as well as single and multi-template modeling.
Ligand-Based Drug Design
ICM Chemist Pro
ICM Chemist-Pro
ICM-Pro is MolSoft’s primary desktop modeling software offering most of the core functionalities like:
- 2D/3D Molecular Editor
- Chemical Spreadsheet Environment
- Substructure & Similarity Search

- 2D → 3D Conversion
- 3D Ligand Superposition
- Pharmacophore Modeling (APF)
- QSAR Modeling & Validation
- Combinatorial Library Enumeration
- Stereoisomer & Tautomer Generation
- ADMET Property Calculations & Plotting
- Clustering & Chemical Space Analysis
- Local Compound Database Support
- Interactive 3D Ligand Editing
To know more click here.
ICM Chemist Pro is a standalone chemoinformatics tool offering a wide set of 3D chemical tools, chemical superposition, 3D interactive ligand-receptor editing, and QSAR.
Calculator & Predictors
Calculators and Predictors
Chemaxon’s Calculators and Predictors allow users to execute high quality physico-chemical calculations and predictions.
- Physicochemical Property Calculations
- LogP / LogD Prediction

- pKa & Protonation State Estimation
- Solubility Prediction
- ADMET Risk Prediction (e.g., hERG)
- Elemental Analysis & Mass Calculation
- Polar Surface Area (PSA)
- Structural Descriptors
- Tautomer & Microspecies Distribution
- Applicability Domain & Confidence Metrics
- API & Command-line Integration
To know more click here.
Chemaxon’s Calculators and Predictors estimate physicochemical, ADMET, and drug-likeness properties like lipophilicity, pKa, permeability, and other critical parameters with high accuracy.
ICM – RIDE -GPU
RIDE (GPU)
RIDE is a fast 3D molecular similarity search method based on Atomic Property Fields. RIDE searches databases of compound conformers for molecules that are isosteric to the query
- Can screen 1.5Million conformers/sec/GPU
- GPU-Accelerated 3D Similarity Search
- Bioisosteric Replacement Engine
- Rapid Lead Optimization Assistance
- Scaffold Hopping at Scale
- Flexible Conformer Matching
- High-Throughput Virtual Replacement
- Structure-Aware Chemical Space Exploration
- Integrates with ICM Design Workflows
- Supports Large Compound Libraries
- Fast Performance via Parallel GPU Compute
To know more click here.
RIDE is a fast 3D molecular similarity search method based on Atomic Property Fields. RIDE searches databases of compound conformers for molecules that are isosteric to the query
AI/ML Based tools – Ultra Large Library Screening
Ultra-Large Library Screening solutions from MolSoft enable rapid exploration of billions of virtual compounds using advanced docking, AI-driven scoring, and high-performance computing. Powered by ICM technology, they help researchers efficiently identify high-quality hit candidates with improved accuracy and speed.
RIDGE
RIDGE (Rapid Docking GPU Engine)
Below are concise feature bullets for RIDGE (Rapid Docking GPU Engine):
- GPU-accelerated structure-based docking
- Ultra-fast virtual ligand screening (~100 compounds/sec on RTX GPUs)
- ~1000× speed of a single CPU core
- Screens 10 Million compounds on a desktop GPU in a day

- Supports multiple GPUs for parallel jobs
- Compatible with existing ICM docking projects
- Uses highly-compressed conformer libraries
- Neural-network scoring (RTCNN)
- Option to apply physics-based docking scores
- Minimal setup from standard ICM dock projects
- Efficient for ultra-large library screening
- Works on Linux and Windows platforms
To know more click here.
RIDGE (Rapid Docking GPU Engine) enables you to perform 3D structure-based screening of ultra-large libraries. It can screen around 100 compounds/ sec on a single consumer-grade GPU.
GigaScreen
GigaScreen
The GigaScreen method combines machine learning and deep learning tools to tackle the computational intensity of screening very large chemical databases. Key features include:
- Ultra-large library screening framework
- Deep learning-guided hit prioritization
- Combines ML models with GPU docking

- Uses RIDGE GPU acceleration for speed
- Screens billions of virtual compounds
- Iterative model training and scoring
- Reduces compute costs and data volume
- Adjustable score thresholds for filtering
- Automated batch processing workflows
- Scales on single workstation or GPU cluster
- Hybrid physics + AI scoring strategies
- Active learning loop for model refinement
- Efficient candidate selection from giga-sized libraries
- Supports custom filtering rules and constraints
- Integrates with existing ICM workflows
- Includes trillions of pre-prepared libraries from multiple vendors
To know more click here.
The GigaScreen method combines machine learning and deep learning tools to tackle the computational intensity of screening very large chemical databases. Capable of screening 1 billion molecules/day.
CombiRIDGE
CombiRIDGE
CombiRIDGE is a new innovative GPU-accelerated solution for high-throughput ligand docking and screening which leverages MolSoft’s generative neural network conformer enumeration method GINGER, ultra-fast GPU docking technology RIDGE and advanced graph neural network scoring ( RTCNN ). The approach allows you to optimize specific R-groups and screen vast ultra-large or combinatorial libraries efficiently.
- Reaction-based combinatorial library generation

- Synthesizable compound design
- Applies known chemical transformation rules
- Generates diverse, focused libraries
- Preserves synthetic feasibility
- Customizable reaction templates
- Flexible scaffold and building block selection
- Supports enumerations with stereochemistry
- Integrates with ICM design workflows
- Enables rapid ideation of analog series
- Automated combinatorial enumeration
- Structural filtering and property constraints
- Facilitates hit expansion strategies
- High-throughput library creation
- Supports custom compound rules
- Enhances medicinal chemistry productivity
- Efficiently explores chemical neighborhoods
To know more click here.
CombiRIDGE is a new innovative GPU-accelerated solution for high-throughput ligand docking and screening which leverages MolSoft’s generative neural network conformer enumeration method GINGER.
V-SYNTHES
V-SYNTHES
V-SYNTHES is a hierarchical synthon-based virtual screening platform that enables efficient exploration of ultra-large, synthetically accessible chemical libraries using flexible ICM docking.
- Hierarchical synthon-based virtual screening strategy
- Efficient navigation of ultra-large make-on-demand libraries
- Screens tens of billions of compounds
- Uses ICM docking for flexible, accurate scoring

- Fragment-based initial screening and enumeration
- Minimal Enumeration Library (MEL) generation
- Iterative docking and hit refinement
- 4D flexible-receptor representation support
- Accelerated docking via hierarchical protocol
- Applicable to gigascale chemical spaces
- Prioritizes synthetically accessible candidates
- Scales on desktop or cluster environments
- Integrates with ICM-Pro and VLS workflows
- Supports complex target classes like GPCRs and kinases
To know more click here
V-SYNTHES is a hierarchical, synthon-based virtual screening strategy that efficiently navigates gigascale make-on-demand chemical libraries by iteratively assembling and docking scaffold–synthon combinations.
ICM – RIDE -GPU
RIDE (GPU)
RIDE is a fast 3D molecular similarity search method based on Atomic Property Fields. RIDE searches databases of compound conformers for molecules that are isosteric to the query
- Can screen 1.5Million conformers/sec/GPU
- GPU-Accelerated 3D Similarity Search
- Bioisosteric Replacement Engine
- Rapid Lead Optimization Assistance
- Scaffold Hopping at Scale
- Flexible Conformer Matching
- High-Throughput Virtual Replacement
- Structure-Aware Chemical Space Exploration
- Integrates with ICM Design Workflows
- Supports Large Compound Libraries
- Fast Performance via Parallel GPU Compute
To know more click here.
RIDE is a fast 3D molecular similarity search method based on Atomic Property Fields. RIDE searches databases of compound conformers for molecules that are isosteric to the query
GINGER
GINGER
- GPU-accelerated conformer generation
- Neural network-based internal coordinate model
- Rapid production of diverse, low-energy 3D conformers

- Highly scalable for very large libraries
- Generates high-quality conformers with energy refinement
- Efficiently handles millions of compounds per day
- Produces smaller, high-accuracy conformer sets
- Ideal for 3D workflows (screening, docking, similarity)
- Integrates with ICM-Pro, RIDE, and RIDGE
Memory-efficient and robust conformer processing
To know more click here.
GINGER (Graph Internal-coordinate Neural-network conformer Generator with Energy Refinement) is Molsoft’s new cutting-edge software designed for lightning-fast high quality conformer library generation on GPUs.
AI Driven Drug Design
AI-driven drug design integrates predictive modeling, virtual screening, and curated chemical intelligence to accelerate hit discovery and lead optimization. By combining data-driven insights with advanced computational methods, researchers can prioritize high-quality candidates faster and with greater confidence.
LigandAIDE
LigandAIDE
Ligand AIDE is a de novo ligand generation workflow based on Artificial Intelligent Design Evolution. It uses an iterative evolutionary strategy to grow and optimize ligands directly in the context of a protein binding site.
- AI-driven de novo ligand generation workflow
- Iterative evolutionary design directly in a protein binding site

- Begins from docked fragment population and grows ligands
- Uses groupGen neural network for R-group addition and replacement
- Atom-level substitution via neural atom predictor
- Re-docks new designs each generation for optimized fit
- Multi-objective selection using AI score, docking score, and drug-like filters
- Synthesizability criteria enforce practical chemical designs
- Typically uses multiple evolutionary cycles (e.g., 3-5)
- Efficient exploration of chemical space with binding quality focus
- Integrates with docking workflows for automated design refinement
To know more click here.
Ligand AIDE is a de novo ligand generation workflow based on Artificial Intelligent Design Evolution. It uses an iterative evolutionary strategy to grow and optimize ligands directly in the context of a protein binding site.
MolScreen
MolScreen
MolScreen is a set of high quality 2D fingerprint and 3D pharmacophore models for a broad range of pharmacology and toxicology targets.
- Panel of >2,500 high-quality 2D & 3D AI/ML models for pharmacology & toxicity targets
- Models cover ~1,200 distinct targets
- Includes 2D fingerprint ML classifiers & regressors

- 3D Atomic Property Field (APF) pharmacophore models
- ADMET prediction models (e.g., CYP, hERG, half-life)
- Supports lead identification & profiling workflows
- Useful for target identification & drug repurposing
- Fast scoring with validated performance metrics (e.g., high AUCs for key model types)
- Works with ICM-Pro + VLS screening automation
- Enables multi-target vs. multi-compound profiling
- Models can be run directly or via batch jobs in ICM GUI/CLI
- Includes classification & regression scoring outputs
- Adaptable for lead optimization and SAR analysis
To know more click here.
MolScreen is a set of high quality 2D fingerprint and 3D pharmacophore models for a broad range of pharmacology and toxicology targets. The models can be used for lead discovery or counter screening.
Reaxys
Reaxys
Trusted data, technology and expertise to support chemistry research
- Expert-curated chemistry database integrating reactions, substances, properties, and literature.

- Contains data from ≈125 million documents from 18,000 journals
- Includes ~49 million patent documents from 105 patent offices
- Contains ~353 million chemical substances and ~500 million associated properties.
- Includes ~51 million bioactivity data points linked to ~43,000 biological targets.
- Powerful structure, substructure, and multi-field search capabilities.
- Supports synthesis planning, AI-driven retrosynthesis, and experiment design insights.
- Weekly data updates and API access for integration into workflows.
- Covers historical and modern authoritative chemical information back to the 18th century.
- Weekly data updates to keep substance, reaction, and property records current.
- Powerful structure, substructure, and multi-field search capabilities.
- Supports synthesis planning, retrosynthesis insights, and experimental design.
To know more click here.
Reaxys is a comprehensive chemical database and chemistry search engine that combines a billion chemistry data points with AI search and retrosynthesis tools. Reaxys helps chemists accelerate synthesis planning, competitive analysis and the DMTA cycle.
AI-Enabled Life Science Database
AI-enabled life science databases integrate chemical, biological, pharmacological, and clinical intelligence into a unified, searchable knowledge ecosystem. By combining curated data with advanced analytics and AI-driven insights, researchers can make faster, evidence-based decisions across discovery and development.
Reaxys
Reaxys
Trusted data, technology and expertise to support chemistry research
- Expert-curated chemistry database integrating reactions, substances, properties, and literature.

- Contains data from ≈125 million documents from 18,000 journals
- Includes ~49 million patent documents from 105 patent offices
- Contains ~353 million chemical substances and ~500 million associated properties.
- Includes ~51 million bioactivity data points linked to ~43,000 biological targets.
- Powerful structure, substructure, and multi-field search capabilities.
- Supports synthesis planning, AI-driven retrosynthesis, and experiment design insights.
- Weekly data updates and API access for integration into workflows.
- Covers historical and modern authoritative chemical information back to the 18th century.
- Weekly data updates to keep substance, reaction, and property records current.
- Powerful structure, substructure, and multi-field search capabilities.
- Supports synthesis planning, retrosynthesis insights, and experimental design.
To know more click here.
Reaxys is a comprehensive chemical database and chemistry search engine that combines a billion chemistry data points with AI search and retrosynthesis tools. Reaxys helps chemists accelerate synthesis planning, competitive analysis and the DMTA cycle.
Embiology
Embiology
EmBiology uncovers millions of biological relationships to help you better understand disease biology. Get targeted data using relation and concept filters.
- AI-curated biological knowledge graph linking genes, proteins, diseases, pathways, cells, tissues, and processes.
- Contains structured cause-and-effect relationships extracted from millions of scientific articles.
- Integrates semantic biological associations rather than simple co-mentions.
- Supports multi-entity query exploration (e.g., gene sets, disease lists).
- Visual network and pathway views for interactive relationship mapping.
- Advanced filtering by relationship type, organism, evidence strength, and publication date.
- Enables identification of upstream regulators and downstream effects for mechanistic insight.
- Facilitates target identification & prioritization with contextual evidence scoring.
- Supports biomarker discovery through biologically relevant associations.
- Provides evidence scoring and provenance tracking to link relationships back to source literature.
- Regular updates to ensure current biological knowledge and ongoing curation.
- API and export support for integration into bioinformatics and data science workflows.
- Designed to accelerate translational research and systems biology interpretation.
- Enables exploration of disease mechanisms, signaling pathways, and regulatory networks.
To know more click here
EmBiology provides a clear view of biological relationships to optimize drug research. EmBiology uncovers millions of biological relationships to help you better understand disease biology. Get targeted data using relation and concept filters.
Embase
Embase
ICM-Pro is MolSoft’s primary desktop modeling software offering most of the core functionalities like:
- ~40+ million biomedical records from 1947–present
- Daily updates with newly published literature

- 8,500 peer-reviewed journals indexed globally
- Extensive conference abstract coverage
- ~2,900+ journals unique to Embase (not in MEDLINE)
- EMtree controlled vocabulary with 90,000+ terms
- Deep drug, disease, and medical device indexing
- Advanced Boolean, proximity, and field-specific search
- PICO search builder and query translation tools
- Strong pharmacovigilance & adverse event coverage
- Medical device surveillance and regulatory insights
- Alerts, saved searches, and export tools
- API and data delivery options for integration
- Supports systematic reviews, HEOR, regulatory & clinical research
To know more click here.
Embase is the biomedical database for systematic reviews, drug safety monitoring and evidence-based research and practice. Regulators and researchers worldwide rely on Embase for biomedical literature that is comprehensive and current.
PharmPendium
PharmaPendium
PharmaPendium supports drug safety and efficacy decisions for better drug outcomes.
- Full-text FDA & EMA regulatory documents
- Extracted safety, PK, metabolism & efficacy data

- Millions of curated regulatory pages
- Integrated FAERS real-world adverse event data
- MedDRA-coded safety terminology
- Drug benchmarking vs approved/withdrawn compounds
- Drug–Drug Interaction Risk Calculator
- Safety Margin & toxicity assessment tools
- Natural language AI search (PharmaPendium AI)
- Regulatory data visualizations & analytics
- Supports safety, translational & regulatory research
- API access & structured data export
To know more click here.
PharmaPendium supports drug safety and efficacy decisions for better drug outcomes. PharmaPendium combines unparalleled regulatory and drug data with full-text search and predictive tools. Reduce animal testing and launch drugs faster.
MolCart Compounds
MolCart Compound
MolCart Compound Database is an up-to-date collection of vendor compound databases. This database is divided into two collections:
-
- Screening Compounds for cherry picking.
- Building blocks for combinatorial chemistry
To know more click here.
MolCart Compound Database is an up-to-date collection of vendor compound databases. This database is divided into two collections: Screening Compounds and Building blocks.
Chemical Drawing
Chemical Editors are the most basic but most essential tool in biochemical research. To facilitate the easy and efficient drawing of chemical structures and biomolecules on desktop or on the web, we offer the following editors.
Marvin
Marvin
The new Marvin is a universal chemical editor that serves the needs of any chemist involved in research and drug discovery.
- Advanced chemical structure drawing and editing

- Intuitive 2D/3D molecule sketcher
- Multi-platform support: web, desktop, mobile
- Accurate structure clean-up and standardization
- Reaction drawing and editing tools
- Stereochemistry handling and annotation
- Structure templates and fragment libraries
- Smart chemical copy/paste & drag-and-drop support
- Integration with IUPAC naming and property calculators
- Export to common chemical formats (Mol, SMILES, InChI, etc.)
- Chemical layout for publications and reports
- Embeddable in other applications via API/SDK
- Supports rapid drawing workflows for chemists and researchers
To know more click here.
The new Marvin is a web-based, feature-rich universal chemical editor that serves the needs of any chemist involved in chemical, pharmaceutical research, and drug discovery.
Marvin Sketch
MarvinSketch and Marvin JS
MarvinSketch is a fully featured chemical drawing tool built to serve any chemist’s needs running on their local computers. Marvin JS is a simplified chemical editor built to add chemical features to web applications. Both first generation software are still supported.
The next generation Marvin is a web-based application that gives you the full feature set necessary in chemical research and the flexibility to integrate with your tools. This makes Marvin the only chemical drawing tool you will ever need.
Marvin Sketch is the legacy fully loaded chemically intelligent chemical editor supporting drawing, editing, and rendering of all kinds of simple and complex chemical structures with publication-quality graphics
Store, Search, Analyse Chemical Data
The amount of chemical and biological data that gets generated in a research laboratory becomes difficult to manage over time. We offer solutions that ensure that the data is organized and stored in an efficient manner, so that retrieval of information is also easy.
Instant JChem
Instant JChem
Instant JChem is a robust desktop tool to create, manage, analyze, and search chemical structures and related non-chemical data in simple or relational databases in a user-friendly way.
- Chemical Database Management – Create, manage, and query chemical databases without extensive programming.
- Structure-Based Searching – Perform exact, substructure, similarity, and structure-based searches.
- Chemical Structure Editing – Draw and edit molecules using the integrated Marvin chemical editor.
- Chemical Data Visualization – Display structures, properties, biological data, and other chemical information in customizable views.

- Advanced Querying – Combine chemical structure searches with text, numeric, and other database fields.
- Data Import & Export – Work with common chemical and tabular data formats for easy data exchange.
- Multi-User Collaboration – Enable teams to access, manage, and share chemical information in a centralized environment.
- Database Connectivity – Connect to and work with existing relational databases and enterprise chemical data systems.
- Reporting & Data Analysis – Generate customized views and reports from chemical and associated experimental data.
- Scalable Chemical Informatics – Suitable for academic research groups as well as industrial R&D environments.
To know more visit the product documentation page here.
Instant JChem is a robust desktop tool to create, manage, analyze, and search chemical structures and related non-chemical data in simple or relational databases in a user-friendly way.
JChem for Office
JChem for Office
JChem for Office is the plugin for Microsoft Office applications that imparts chemical knowledge to office documents, allowing users to draw, edit, and analyze chemical structures in a known interface.
- Chemical Intelligence in Microsoft Office – Work with chemical structures directly in Word, Excel, and PowerPoint.
- Structure Drawing & Editing – Create and modify chemical structures using the integrated Marvin editor.
- Chemical Structure Recognition – Recognize chemical names and structures within Office documents.

- Structure-to-Name Conversion – Generate chemical names directly from molecular structures.
- Property Calculation – Calculate molecular formula, molecular weight, and key chemical properties.
- Excel Integration – Manage chemical structures alongside compound IDs, experimental data, and calculated properties.
- Structure Searching – Perform chemical structure-based searches directly within Office workflows.
- Easy Chemical Data Sharing – Insert, format, and present publication-quality chemical structures in reports, spreadsheets, and presentations.
To know more please visit the documentation page here.
JChem for Office is the plugin for Microsoft Office applications that imparts chemical knowledge to office documents, allowing users to draw, edit, and analyze chemical structures in a known interface.
JChem Engines
JChem Engines
The JChem Engines offer chemical data management, storage, and intricate chemical search technologies on various database engines for diverse chemical file types including reactions and markush structures.
- Chemical Structure Search – Supports exact, substructure, similarity, superstructure, and advanced chemical queries.
- Chemical Database Integration – Adds chemistry-aware searching and processing capabilities to enterprise databases and applications like Oracle, PostgreSQL, MySQL and other standard databases.
- Structure Standardization – Standardizes, validates, and normalizes chemical structures for consistent data handling.
- Chemical Property Calculations – Calculates molecular properties, descriptors, and other chemistry-related parameters.

- Structure & Format Conversion – Converts chemical structures between a wide range of commonly used file formats.
- Chemical Structure Handling – Supports storage, indexing, retrieval, and manipulation of molecules and chemical information.
- Developer APIs & Integration – Provides APIs and components for embedding Chemaxon chemistry functionality into custom applications and workflows.
- Scalable Chemical Informatics – Designed for efficient processing and searching of large chemical datasets in research and enterprise environments.
To know more please visit the product page here.
The JChem Engines offer chemical data management, storage, and intricate chemical search technologies on various database engines for diverse chemical file types including reactions and markush structures.
Plexus Connect
Plexus Connect
Plexus Connect provides a web-based solution for management, analysis, searching, and display of scientific data empowered by various Chemaxon technologies at the backend.
- Chemical Data Integration – Connect and integrate chemical information from multiple databases and data sources.
- Unified Data Access – Provide researchers with a centralized interface to access distributed chemical data.

- Chemical Structure Searching – Enable structure-based searching across connected chemical datasets.
- Data Standardization – Harmonize chemical structures and associated data for consistent analysis.
- Enterprise Connectivity – Connect chemical databases, applications, and R&D systems across an organization.
- Workflow Integration – Facilitate seamless movement of chemical information between different research tools and platforms.
- Scalable Architecture – Designed to support growing chemical datasets and enterprise-scale research environments.
- Improved Research Productivity – Reduce data silos and simplify access to chemical information across R&D workflows.
To know more visit the product documentation page here.
Plexus Connect provides a web-based solution for management, analysis, searching, and display of scientific data empowered by various ChemAxon technologies at the backend.
Compound Registration
Compound Registration
Compound registration uses configurable business logic to normalize, validate and quality check compounds and decide the uniqueness of the new molecules before registering them.
- Centralized Compound Registration – Register, manage, and track compounds in a single, structured repository.
- Unique Compound Identification – Automatically assign unique IDs to registered compounds and samples.
- Chemical Structure Validation – Validate structures and ensure consistent chemical representations during registration.

- Duplicate Detection – Identify duplicate or previously registered compounds using structure-based searching.
- Chemical Structure Standardization – Normalize and standardize structures for reliable data management.
- Flexible Metadata Management – Capture compound properties, project information, batch details, and other relevant metadata.
- Advanced Chemical Searching – Search registered compounds using exact, substructure, similarity, and other chemical queries.
- Integration with R&D Workflows – Connect compound registration with chemical databases, ELNs, LIMS, and other research systems.
For more details please visit the product page here.
Compound registration uses configurable business logic to normalize, validate and quality check compounds and decide the uniqueness of the new molecules before registering them.
Molcart GigaSearch
Molcart GigaSearch
The Giga-Search methods add fingerprint bit statistics to the MolCart search engine which allows an extremely fast and efficient way of filtering out molecules based on the input chemical pattern.
- Ultra-Large Chemical Searching – Search billions to hundreds of billions of compounds in seconds.
- Fast Substructure Search – Perform rapid substructure searches across massive chemical spaces using SMILES/SMARTS queries.
- Similarity & Analog Searching – Identify structurally similar compounds and analogs across giga-scale libraries.
- SMILES & SMARTS Support – Define sophisticated chemical patterns using atom, bond, ring, charge, hybridization, and connectivity properties.
- Reduced Storage Requirements – GigaSearch v2.0 avoids full enumeration of massive chemical spaces, significantly reducing storage needs.
- Major Commercial Libraries – Access ultra-large spaces such as Enamine REAL and Chemspace Freedom Space for rapid chemical exploration.
- ICM Integration – Directly integrated with MolSoft ICM-Pro/ICM-Chemist workflows for seamless chemical searching and analysis.
- Scalable High-Performance Search – Optimized for multicore systems and designed for rapid exploration of massive chemical spaces.
To know more details please visit the product page here.
The Giga-Search methods add fingerprint bit statistics to the MolCart search engine which allows an extremely fast and efficient way of filtering out molecules based on the input chemical pattern.
Chemaxon Discovery Tools
Drug discovery is challenged by uncertainty at every stage, compounded by fragmented, inconsistent, and often incomplete data.
The Discovery Toolkit delivers comprehensive chemical intelligence through an integrated suite of toolkit bundles, including calculators, property predictors, and structure preparation tools, accessible through a range of programmatic interfaces for seamless integration into existing workflows. With industry-standard scientific accuracy, it helps researchers reduce uncertainty, streamline cheminformatics workflows, and make more informed decisions across drug discovery and other chemistry-driven research applications.
Discovery Toolkit
Discovery toolkit
The Discovery toolkit is a collection of different bundle of products from Chemaxon and gives acces to Descriptor Generation Toolkit providing physiochemical properties, Structure Preparation Toolkit which helps in standardizing and checking structures, Structure Enumeration Toolkit which helps in library enumeration and the Naming toolkit which provides 2 way conversion from name to structure and vice versa.
To know more visit the product page here.
The Discovery toolkit is a collection of different bundle of products from Chemaxon and gives acces to Descriptor Generation Toolkit, Structure Preparation Toolkit , Structure Enumeration Toolkit the Naming toolkit.
Descriptor Generation Toolkit
Descriptor generation
The Descriptor Generation Toolkit provides scientifically accurate molecular property predictions and a comprehensive set of molecular descriptors to support compound profiling and prioritization. It enables researchers to characterize molecules, assess key drug-discovery properties, and generate data for building predictive models.
- Comprehensive Molecular Descriptors – Generate 2D topological, 3D geometrical, molecular surface, and electronic structure descriptors.
- Physicochemical Property Prediction – Calculate key properties including logP, logD, solubility, pKa, and HLB for compound profiling.
- ADMET & Toxicity Prediction – Support early assessment of properties such as hERG inhibition, pharmacokinetics, and cardiotoxicity risk using machine-learning models.
- Structural Analysis – Generate hydrogen-bond donor/acceptor counts, molecular surfaces, conformers, 3D alignments, and other structural descriptors.
- Isomer & Ionization Analysis – Generate tautomers and stereoisomers, predict major microspecies, and calculate pKa and pH-dependent ionization profiles.
- NMR Prediction – Predict ¹H and ¹³C NMR spectra to support structure elucidation and experimental data interpretation.
- Programmatic Integration – Integrate descriptor generation and property calculations into existing workflows through Java, Python, .NET, and Microservices APIs.
For more details please visit the product page here.
The Descriptor Generation Toolkit delivers comprehensive molecular descriptors and property predictions like pKa, LogP, LogD, LogS, NMR and many more properties for rapid compound profiling.
Structure Preparation Toolkit
Structure Preperation
The Structure Preparation Toolkit validates, standardizes, and curates chemical structures for reliable downstream use. It prepares high-quality compounds for registration, docking, screening, and accurate microspecies/isomer generation.
- Structure Standardization – Normalize chemical structures according to defined business rules for consistent database representation.
- Structure Validation & Checking – Detect and correct issues such as invalid valences, bond lengths, charges, stereochemistry, and other structural errors.
- Tautomer & Isomer Generation – Generate tautomers, stereoisomers, and resonance structures for accurate compound representation and searching.
- Protonation & Microspecies Prediction – Calculate pKa, identify major microspecies, and evaluate pH-dependent ionization profiles.
- Structure Curation – Remove unwanted fragments, counterions, and other inconsistencies while maintaining high-quality chemical data.
- Docking & Registration Preparation – Prepare clean, validated structures for compound registration, virtual screening, and molecular docking workflows.
- Programmatic Integration – Integrate structure preparation capabilities into existing workflows through Java, Python, .NET, and Microservices APIs.
To know more details please visit the product page here.
The Structure Preparation Toolkit validates, standardizes, and curates chemical structures for reliable downstream use in processes like: registration, docking, screening, and accurate microspecies/isomer generation.
Structure Enumeration Toolkit
Structure Enumeration
The Structure Enumeration Toolkit enables rapid generation of virtual and Markush libraries to explore chemical space around lead compounds. It supports reaction-based enumeration and molecular fingerprints for more comprehensive, science-driven compound design and selection.
- Virtual Library Enumeration – Generate large virtual compound libraries to systematically explore chemical space.
- Reaction-Based Enumeration – Apply user-defined reaction schemes to large reactant sets and generate chemically feasible product libraries.
- High-Performance Reactor – Rapidly enumerate synthesizable compounds at scale with flexible library-generation options.

- Markush Enumeration – Expand generic/Markush structures to explore broad combinatorial chemical spaces.
- Stereochemistry-Aware Enumeration – Account for stereochemical variations during virtual library generation.
- Chemical Fingerprints – Generate molecular fingerprints to support compound similarity analysis and chemical space exploration.
- Flexible & Programmatic Integration – Integrate enumeration workflows through Java, Python, .NET, and Microservices APIs.
For more details please visit the product page here.
The Structure Enumeration Toolkit enables rapid generation of virtual and Markush libraries to explore chemical space around lead compounds. It supports reaction as well as scaffold based enumeration.
Naming Toolkit
Naming toolkit
The Naming Toolkit enables accurate two-way conversion between chemical names and structures, individually or at scale. It simplifies chemical data standardization, registration, and workflow integration across research environments.
- Name-to-Structure Conversion – Convert chemical and biochemical names into accurate molecular structures.
- Structure-to-Name Conversion – Generate IUPAC, systematic, and common names directly from chemical structures.
- Batch Processing – Convert names and structures individually or process large compound datasets in batches.
- Broad Chemical Coverage – Support naming and conversion for radicals, natural products, peptides, and complex chemical structures.

- Multiple Naming Standards – Work with IUPAC, systematic, common, and commercial drug names.
- Custom Dictionaries & Databases – Use customizable dictionaries, databases, or web services for corporate IDs and proprietary terminology.
- Programmatic Integration – Integrate naming capabilities into existing workflows through Java, Python, .NET, and Microservices APIs.
For more details please visit the product page here.
The Descriptor Generation Toolkit delivers comprehensive molecular descriptors and property predictions like pKa, LogP, LogD, LogS, NMR and many more properties for rapid compound profiling.
Chemical Compliance & Shipping
Compliance Checker and cHemTS simplify chemical regulatory and trade compliance across the drug discovery lifecycle. Compliance Checker screens compounds against continuously updated controlled-substance regulations worldwide. cHemTS rapidly assigns HS/HTS codes to compounds with up to 99% accuracy, reducing manual effort and errors.
Compliance Checker
Compliance Checker
Compliance Checker helps researchers screen chemical compounds against continuously updated controlled-substance regulations across countries. It simplifies compliance from synthesis and storage to handling and shipping.
- Controlled Substance Screening – Identify regulated substances across individual compounds or large chemical collections.
- Up-to-Date Regulatory Coverage – Continuously updated regulatory knowledge covering multiple countries and international regulations.
- New Molecule Compliance Checks – Assess compounds before procurement, synthesis, storage, or transportation.

- Similarity-Based Regulation Checks – Identify compounds structurally similar to controlled substances using advanced fingerprint and functional-group analysis.
- Global Shipping Compliance – Check country-specific requirements for shipping controlled substances.
- Generic & Markush Definitions – Detect compounds covered by broad regulatory definitions using Markush and homology-based searches.
- Customizable Regulatory Rules – Add internal corporate policies and proprietary controlled-substance definitions to the knowledge base.
For more details please visit the product page here.
Compliance Checker helps researchers screen chemical compounds against continuously updated controlled-substance regulations across countries. It simplifies compliance from synthesis and storage to handling and shipping.
cHemTS
cHemTS
cHemTS automates the assignment of HS/HTS codes to chemical compounds directly from their structures. It delivers fast, accurate classifications, reducing manual effort and trade-compliance errors.
- Automated HS/HTS Classification – Assign Harmonized System (HS) and Harmonized Tariff Schedule (HTS) codes directly from chemical structures.
- High Classification Accuracy – Provides over 99% accuracy for supported chemical classifications.
- Multi-Country Coverage – Supports chemical classification requirements across major international markets, including India, EU, US, UK, Japan, China, Canada, Australia, and Switzerland.
- Drug & Regulatory Identification – Identifies drugs based on active ingredients and highlights relevant FDA and DEA flags.
- Organic Salt & Mixture Differentiation – Distinguishes organic salts and mixtures to enable appropriate Chapter 29 or Chapter 38 classification.

- Import & Export Support – Provides country-specific import/export codes and supports international trade classification workflows.
- Tax & Trade Optimization – Identifies potential tax-free import options by referencing applicable country-specific pharmaceutical agreements.
For more details please visit the product page here.
cHemTS automates the assignment of HS/HTS codes to chemical compounds directly from their structures. It delivers fast, accurate classifications, reducing manual effort and trade-compliance errors.
LIMS and ELN
Manage your laboratory data with ease and efficiency with the LIMS and ELN tools from our partners. We offer customizations on top of the available solutions to make it the best fit for your requirement.
GeneELN
A multifunctional tool to capture reactions and experiment details, while enabling seamless search using structure or text. GeneELN also supports Audit trails.
Know More…
GeneCIS
Chemical Inventory System enables increased inventory accuracy and operational efficiency by reducing carrying costs and optimizing inventory write-offs. GeneCIS also provides chart and reports.
GeneATS
The system enables the processing of samples by the team and allows the Analytical Team to efficiently perform tests and upload the results through online Ticket generation and report submission.
