Molecular modeling
The different computational techniques based on the knowledge of the three-dimensional structure of a therapeutic target that we apply in ProtoQSAR are:
Homology modeling
Construction of 3D models of therapeutic targets, based on their amino acid sequence and sequences of three-dimensional structures experimentally determined from one or several related homologous proteins.
Pharmacophore modeling
Pharmacophores are defined as the set of steric and electronic features of the molecules that ensure optimal supramolecular interactions with a specific biological target, thus activating (or blocking) a biological response. At ProtoQSAR we develop pharmacophore hypotheses based on the structures of ligands and/or receptors. Subsequently, with these pharmacophores we can screen our computer databases in order to find candidates with the chemical features that best fit these hypotheses.
Docking
Computational determination of the optimal conformation and orientation of a small molecule to bind to a receptor protein and generate a stable complex in which the free energy of the complete system is minimized.
Molecular dynamics
Computational simulation of molecular interactions over short periods of time. These studies allow an approximate view of the movement of proteins and biomolecules during their interaction.
Virtual screening
The application of computational models (pharmacophoric or docking) to collections of molecular structures for the identification of those that have a greater probability of being “active”. The molecular collections may be composed of client-owned compounds, commercial libraries, or even “virtual” libraries (e.g. novel structures that have not yet been synthesized). These collections can be formed by a very varying number of structures, from a few dozen to thousands or millions of them, since the rapidity of the computational analysis allow their scoring and ranking in a very short lapse of time.
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)
