QSAR / in silico Tools

VEGA platform 

Using the VEGA platform, you can access a series of QSAR (quantitative structure-activity relationship) models for regulatory purposes, or develop your own model for research purposes. QSAR models can be used to predict the property of a chemical compound, using information obtained from its structure.


CAESAR software (version 2) 

This is the standalone version of the CAESAR software (version 1). Most of the new features that will be present in the new CAESAR v2.0 software have been integrated in the stand-alone models for Developmental Toxicity and Mutagenicity. The stand-alone version of CAESAR can be downloaded for free and have been developed to work off-line. The CAS number input method is not available for this version of the software.


CAESAR software (version 1)  

The CAESAR Application is a JAVA™ web application that allows the access to all the toxicity predictive models developed within the CAESAR Project. CAESAR developed the algorithms, as described, and as an additional activity they have been implemented in the tool here available.



DEMETRA is an EU-funded project. This project aim has been to develop predictive models and software which give a quantitative prediction of the toxicity of a molecule, in particular molecules of pesticides, candidate pesticides, and their derivatives. The input is the chemical structure of the compound, and the software algorithms use “Quantitative Structure-Activity Relationships” (QSARs). The DEMETRA software tool can be used for toxicity prediction of molecules of pesticides and related compounds. The DEMETRA models are freely available. Five models have been developed to predict toxicity against trout, daphnia, quail (oral and dietary exposure) and bee. The software is based on the integration of the knowledge acquired in the DEMETRA EU project in a homogeneous manner using the best algorithms obtained as the basis for hybrid combinative models to be used for predictive purposes.



Toxicity Estimation Software Tool (T.E.S.T.)  will enable users to easily estimate acute toxicity using the above QSAR methodologies.



Toxtree is a full-featured and flexible user-friendly open source application, which is able to estimate toxic hazard by applying a decision tree approach. Toxtree could be applied to datasets from various compatible file types. User-defined molecular structures are also supported – they could be entered by SMILES, or by using the built-in 2D structure diagram editor.



The OCHEM is an online database of experimental measurements intergrated with the modeling environment. Submit your experimental data or use the data uploaded by other users to build predictive QSAR models for physical-chemical or biological properties.


Chemistry Development Kit (CDK)

The Chemistry Development Kit (CDK) is a Java library for structural chemo- and bioinformatics. It is now developed by more than 50 developers all over the world and used in more than 10 different academic as well as industrial projects world wide. 



R is a language and environment for statistical computing and graphics. It is a GNU project which is similar to the S language and environment which was developed at Bell Laboratories (formerly AT&T, now Lucent Technologies) by John Chambers and colleagues. R can be considered as a different implementation of S. There are some important differences, but much code written for S runs unaltered under R. R provides a wide variety of statistical (linear and nonlinear modelling, classical statistical tests, time-series analysis, classification, clustering, …) and graphical techniques, and is highly extensible. The S language is often the vehicle of choice for research in statistical methodology, and R provides an Open Source route to participation in that activity.



Weka is a collection of machine learning algorithms for data mining tasks. The algorithms can either be applied directly to a dataset or called from your own Java code. Weka contains tools for data pre-processing, classification, regression, clustering, association rules, and visualization. It is also well-suited for developing new machine learning schemes.



AMBIT is a software for chemoinformatic data management, is an outcome of the LRI project: ’Building blocks for a future (Q)SAR ((Quantitative) Structure Activity Relationship) decision support system. Since the software goal is to support decisions, including chemical grouping and QSAR applicability domain appraisal, the name AMBIT was chosen meaning ‘an area in which something acts or operates or has power or control’. The AMBIT software is available online and as a stand-alone application for beta testing. 


ChemAxon Marvin

Marvin is a collection of tools for drawing, displaying and characterizing chemical structures, queries, macromolecules and reactions.



Whether you need to find new lead candidates, optimize lead series, or perform other related life science experiments like modeling a protein structure, SYBYL®-X has solutions to move your discovery research forward.  With capabilities for small molecule modeling and simulation, macromolecular modeling and simulation, cheminformatics, lead identification, and lead optimization, all wrapped up in an easy to use, cost-effective interface, SYBYL-X has the tools and capabilities you need for molecular design.  


Discovery Studio 

Discovery Studio® is a software suite of life science molecular design solutions for computational chemists and computational biologists. Discovery Studio makes it easier to examine the properties of large and small molecules, study systems, identify leads and optimize candidates. Furthermore, built on Accelrys’ Pipeline Pilot technology, Discovery Studio enables scientists to rapidly automate routine tasks, integrate third party applications and even deploy models out to research colleagues. Together, this uniquely positions Discovery Studio as a truly comprehensive collaborative research solution for both experts and project teams alike. 


ADF: Amsterdam Density Functional software 

ADF has a 30-year track record as a premium-quality quantum chemistry software package based on Density Functional Theory (DFT). It consists of

  • the molecular DFT program ADF
  • the periodic DFT program BAND
  • the post-ADF COSMO-RS program for thermodynamics of liquids
  • The ReaxFF program for modeling chemical reactions
“Amber” refers to two things: a set of molecular mechanical force fields for the simulation of biomolecules (which are in the public domain, and are used in a variety of simulation programs); and a package of molecular simulation programs which includes source code and demos. The current version of the code is Amber version 11, which is distributed by UCSF subject to a licensing agreement described below. 
ChemDraw Ultre 12 is an outstanding package for chemical structure drawing and editing. The document settings feature gives this package an edge when preparing chemical schemes for manuscripts that will be published. the graphics prepared in ChemDraw Ultra insures a professional and neat apperance. Buy ChemDraw and start drawing today!
Gaussian 09 is the latest version of the Gaussian® series of electronic structure programs, used by chemists, chemical engineers, biochemists, physicists and other scientists worldwide. Starting from the fundamental laws of quantum mechanics, Gaussian 09 predicts the energies, molecular structures, vibrational frequencies and molecular properties of molecules and reactions in a wide variety of chemical environments. Gaussian 09’s models can be applied to both stable species and compounds which are difficult or impossible to observe experimentally (e.g., short-lived intermediates and transition structures).
MOE provides a suite of applications for manipulating and analyzing large collections of compounds, building property models, consensus models and SD pipeline command line tools.
The MolProp TK provides a customizable framework for molecular property calculation geared towards enabling rapid database filtering. Filtering attempts to eliminate inappropriate or undesirable compounds from a large set before beginning to use them in modelling studies. The goal is to remove all of the compounds that should not be suggested to a medicinal chemist as a potential hit. This exercise is obviously case dependent, depending on ease of the assay, intended target, personal bias of the modeller & medicinal chemist, strengths of the company, etc. which makes this problem one that is highly amenable to a toolkit solution.
ADMEWORKS ModelBuilder is a tool dedicated for building QSAR/QSPR models that can later be used for predicting various chemical and biological properties of compounds. A set of data on molecular structures and their respective experimental values of the property of interest is a prerequisite for every model building. Two classes of models (Qualitative and Quantitative) can be built using various algorithms. The models are based on values of physicochemical, topological, geometrical, and electronic properties derived from the molecular structure.



Bio-Rad’s award-winning KnowItAll Informatics System offers fully integrated software and/or database desktop solutions that provide scientific researchers multiple tools such as database building, management, mining/search, analysis, prediction, structure drawing, and reporting, all within a single user interface. 



MetaDrug™ is a unique systems pharmacology platform designed for evaluation of biological effects of small molecule compounds on the human body, with pathway analysis and other bioinformatics applications from toxicogenomics to translational medicine. MetaDrug™ helps to solve such problems as drug’s mechanism of action, toxicity and off-target effects, deduced from the structure and any kind of supplementary toxicogenomics data. The product is intended to be used by medicinal chemists and biologists active in pre-clinical areas of high content and high throughput screening, bioassays, hit-to-lead libraries, lead optimization, PK and toxicogenomics, with the eventual goal being practical applications in translational medicine and more. 


Noraymet ADME 

Noraymet ADME combines the functionalities of a LIMS with in vitro-in vivo extrapolation models for the prediction of in vivo pharmacokinetics of in vitro data, resulting useful software to help the researcher in the selection of the best candidate. LIMS: The software allows the user to integrate and manage in vitro ADME experiments (Caco-2, microsomes, hepatocytes, binding to plasmatic proteins, etc.), as well as automatic calculations of the in vitro results (Papp, Clint, fup, etc.). ADME predictive software: the software includes a selection of INVIVE models (in vivo-in vitro extrapolation that allows predicting the in vivo pharmacokinetics from in vitro results.



Around half of all drugs in clinical development fail to commercialize because of poor ADME and toxicity properties. There is increasing interest in the early prediction of ADME properties, in order to increase the success rate of compounds  reaching development. Using the PreADME the result of ADME prediction can be used as the most outstanding and practical guidance for the early drug discovery.



Sarchitect Designer is the model building edition of Sarchitect. The product vision is to enable building “best possible” models. Sarchitect Miner is the interface between the model builders and the model users. Miner enables the use of models by

  • medicinal chemists to profile and optimize their compounds in silico, and
  • DMPK groups to rank compounds for prioritization in their studies



The pharmacokinetic behaviour of compounds is linked to their efficacy and thus is critical for drug discovery. Understanding how to optimise compounds according to multiple simultaneous criteria is a great advantage in focusing design efforts. VolSurf+ creates 128 molecular descriptors from 3D Molecular Interaction Fields (MIFs) produced by our software GRID, which are particularly relevant to ADME prediction and are also simple to interpret. One example would be the interaction energy moment descriptor between hydrophobic and hydrophilic regions, which is important for membrane permeability prediction. These can then be used with provided chemometric tools to build statistical models.



BioByte’s new Bio-Loom program weaves several different threads of data into a cohesive whole. Of course, Bio-Loom still calculates hydrophobic and molecular refractivity parameters via CLOGP & CMR, calculations which have been the world standard for decades, but it now has the ability to access BioByte’s entire Thor Masterfile database, which includes over 60,000 measured log P and log D values (in many solvent systems), as well as 14000 pKas, including associated references.


MolCode Toolbox 

The modules of Molcode Toolbox software predict a wide range of experimentally unknown values of properties of compounds  including physicochemical, biological, ADME-Tox, ecological pathways/ecotoxicity and adverse drug  effects. The modules of Molcode ToolBox software consist of internally encoded computational models built on various datasets related to the aforementioned properties. All the models in Molcode Toolbox are specified by model’s name, CAS-number (not obligatory) and systematic name of compounds, (bio)assay, property/activity value and unit, and reference.



All TerraQSAR programs use proprietary neural networks for the computation of biological effects and physico-chemical properties of defined chemicals. The input is in the form of 2D/3D SMILES strings. For more details, see the Manuals of the individual program modules.



ADRIANA.Code comprises a unique combination of methods for calculating molecular structure descriptors on a sound geometric and physicochemical basis. These descriptors can be used for a wide range of applications in all areas of chemistry, in particular in drug design. Lead discovery and optimization, diversity assessment of compound libraries and prediction of ADME/Tox properties are some of the problems that have been addressed and successfully solved with descriptors from ADRIANA.Code. In addition, the descriptors have been used to model chemical reactivity, the scope and limitation of chemical reactions and to simulate spectra for structure elucidation.