Chemoinformatics
The computational techniques are exclusively based on the knowledge
of the chemical structures of compounds with a certain activity, and not
on the structure of a particular target:
That is, numerical values associated with the structural features of chemical compounds, so that different sets of these descriptors encode different chemical information. We can calculate more than a thousand of these indices, covering simple structural data (number of atoms, bonds, rings, etc.), topological information (shape, size, molecular branching), physicochemical properties (hydrophilicity/hydrophobicity, polarizability, etc.), or descriptors dependent on molecular conformation.
Filtering of chemical compounds according to pre-fixed rules
In the initial stages of medical chemistry projects it is common to determine certain standardized rules such as the well-known “Lipinski rules” (for the selection of drug-like compounds), “Oprea rules” (for the selection of lead-like compounds) or the “rule of three” (for the selection of fragments). In ProtoQSAR we have the means to calculate standard parameters (such as molecular weight, number of proton donors/acceptors, cLogP, number of rotatable bonds, polar surface area (PSA), etc.), which allow us to classify compounds according to these rules.
Analysis of chemical similarity and/or diversity
In ProtoQSAR we can characterize the molecules by using molecular descriptors such as the “MACCS keys” and standard algorithms such as the Tanimoto coefficient, as well as selecting subsets of compounds based on their structural similarity/diversity.
Alignment of small molecules
3D superposition of potential and known ligands -after a conformational sampling of both types of structures- in order to deduce structural requirements for a given biological activity.
QSAR
Construction of mathematical models relating the in silico structure of molecules with a biological property or activity, through the use of statistical tools. Once a correlation has been established, it can be used later to predict the property or biological effect of new structures.
Read-across (aka “neighborhood behavior”)
When there is not enough data to build QSAR models, this method is a simpler alternative based on the well-known principle of “chemical similarity”: chemicals with common structural features usually exhibit similar physico-chemical and biological properties. Therefore, compounds that share structural similarities can be grouped into a chemical category, and it is possible to use data information from members of this group to estimate properties of other members of the same group.
Try our computational prediction platform for chemical compounds
ProtoPRED uses its own QSAR (Quantitative Structure-Activity Relationships) models, widely applied in sectors such as cosmetics, pharmaceuticals and chemicals. This tool allows the prediction of a wide spectrum of properties of industrial and regulatory interest, ensuring the obtaining of valid documents in accordance with regulations such as REACH and ICH. With ProtoPRED, companies can efficiently comply with current regulations and optimize their registration processes
Frequently asked questions
What services does ProtoQSAR offer?
ProtoQSAR is a company specialized in QSAR models and in silico toxicological predictions for regulatory support (REACH, CLP, ICH, K-REACH, etc.). We offer customized studies (QSAR, SAR, read-across, compound prioritization, etc.) and ProtoPRED®, our molecular prediction platform featuring more than 60 models covering toxicity, physicochemical properties, ecotoxicity, and ADME.
We work with companies in the pharmaceutical, chemical, cosmetic, agrochemical sectors, as well as regulatory consultancies. We also provide practical training courses in QSAR and regulatory frameworks.
How long does it take to obtain results?
With ProtoPRED®, predictions are generated instantly. For tailor-made studies, timelines depend on the number of compounds and the scope of the study and typically range from a few weeks up to approximately two months. Upon completion, we deliver reports ready for submission to regulatory authorities (QPRF).
What software does ProtoQSAR use to develop its models?
We use proprietary QSAR models integrated into ProtoPRED, our molecular prediction platform with more than 60 models for toxicity, physicochemical properties, ecotoxicity, and ADME.
For customized studies, we may also use third-party tools such as QSAR Toolbox and VEGA when no equivalent internal model is available in ProtoPRED, ensuring regulatory acceptability.
Are ProtoQSAR QSAR models accepted under REACH, CLP, ICH, or other regulations?
Yes. Our models follow OECD principles and are documented with QMRF and QPRF for each prediction, facilitating regulatory acceptance and reducing the need for experimental testing.
In addition, we have examples of regulatory acceptance of our models by different authorities.
Does ProtoQSAR participate in collaborative projects?
Yes. We collaborate in European consortia (HORIZON, IHI, etc.), national programs (Torres Quevedo, NANOTECH), and regional calls (IVACE, AVI, etc.).
At ProtoQSAR, together with Moldrug and ProtoQSAR Italy (our associated companies), we are actively seeking industrial and academic partners.
Do you have a proposal? Contact us at bd@protoqsar.com.
How much does a ProtoPRED prediction or a customized study cost?
ProtoPRED® operates on a token-based system with volume discounts: the more tokens you purchase, the lower the cost per prediction. We also offer annual licenses for teams that use the platform intensively; the license becomes cost-effective from approximately 200 predictions per year.
For customized studies, pricing depends on the number of compounds, the endpoints involved, and the level of regulatory documentation required.
→ Request ProtoPRED pricing options / Request a quote for a customized study
Do you provide scientific support and regulatory guidance?
Yes. In addition to generating QSAR models and predictions, we provide scientific and regulatory support, including in silico strategy design, validation and interpretation of results, and preparation/review of QMRF and QPRF so that predictions comply with OECD guidelines and/or applicable legal frameworks, meeting regulatory authority requirements.
Our regulatory team will be pleased to assist you. Contact us at regulatory@protoqsar.com.
How are confidentiality and data protection managed?
In ProtoPRED®, privacy and data protection are built into your account. From the user page (Reports data), you can activate Data Privacy to irreversibly delete all prediction results, retaining only the model used and the date.
We also offer the possibility of signing an NDA (Non-Disclosure Agreement) to ensure information security, privacy compliance, and data protection.
Contact us and our team will advise you on everything you need
We are here to help you. Do not hesitate to contact us to receive personalized advice and resolve any questions you may have. Our team is available to offer you the best care.
Address
Technological Park of Paterna (Valencia)
Carrer de Nicolau Copèrnic 6,
1st Floor, Office 8
46980 Paterna (Valencia)
