Our activity consists in the development and application of computational methods for the evaluation of physicochemical, biological and/or (eco)toxicological properties of chemicals, either of natural origin or synthesized. Our computer tools allow us to work in a “virtual” environment, which has advantages over traditional laboratory tests.
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
Mission
Given the exclusively computerized nature of our methods, ProtoQSAR activity has a very positive social impact. First, through computation it is possible to reduce the number of laboratory animal tests, or even to replace them in some cases*. Approximately 12 million vertebrate animals are slaughtered annually in the EU for scientific or regulatory purposes (Taylor, K., & Rego, L. (2016). EU statistics on animal experiments for 2014. ALTEX, 33, 465-468). These tests are ethically questionable, and their preparation and execution are also expensive and time consuming.
On the other hand, our activities are also intended to contribute to environmental improvement. We have predictive models for a large number of eco-toxicological parameters (aquatic toxicity, toxicity in different species such as bees or terrestrial organisms, etc.), which allows us to guide the development of new active substances towards those that have proven effectiveness while respecting our natural environment.
*Computational approaches are part of the so-called alternative methods, whose purpose is the fulfillment of the “3 Rs”: refinement of conventional methods to reduce the potential suffering of living beings used in experimentation, reduction in the number of animals used, and finally the replacement of said tests by others in which the animal sacrifice is not necessary.
Values
At ProtoQSAR we firmly believe in the value of experience, the culture of hard work and the satisfaction for well-donework. We intend to satisfy our customers/collaborators by contributing our commitment in each of the projects in which we participate, and our high motivation to develop them and bring them to a good end.
We fully adhere to the proposals made at the 1st National Congress of Entrepreneurial Scientists (Valencia, 2012) in which a code of good practices was proposed that would make compatible the responsible use of Science with Entrepreneurship. In ProtoQSAR we subscribe completely and without exception all the points of said code. We are convinced of the importance of the good practices of entrepreneurial scientists, respect for our environment and society as a whole, and we are committed to contributing to a more fair and solidary society.
Our staff is characterized by its high academic profile and extensive scientific background. The technical team of ProtoQSAR is formed by specialists in different areas (pharmacy, chemistry, toxicology and ecotoxicology …) with extensive experience in both academic and industrial sides.
We have more than 100 publications in national and international scientific journals, eight chapters in specialized books and more than 80 participations and presentations in technical congresses.
Our Team
Since 2010: independent consultant in the area of computer science and molecular modeling for different companies and chemical-pharmaceutical groups, and since 2012 as founder and director of ProtoQSAR.
2007-2010: Scientific collaborator in the Laboratory of Structural Biochemistry, Príncipe Felipe Research Center (CIPF), Valencia. Responsible for the computational management of the database of available chemical compounds.
2001-2007: Senior scientist in the molecular modeling group of the company CEREP (Paris, France). Project Manager in different drug design projects, computational management of the company’s compound databases and the development of models for the generation of focused chemical libraries (GPCRs, CNS, kinases).
1998-2001: Postdoctoral position in the “Groupe de Chimie Informatique et Modélisation” of ITODYS – CNRS and the Faculté de Médecine (Université Paris VII). Project developed: “Computer design and experimental evaluation (in vitro and in vivo) of new active drugs against opportunistic AIDS infections”.
1998: PhD in Pharmacy (University of Valencia), title of the doctoral thesis “Application of Molecular Connectivity to the selection of new drugs with potential antiprotozoal activity”.
2021: Joined as researcher in Bioinformátics at ProtoQSAR.
2015-: Invited lecturar at the Master of Biomecial Biochemistry at the Universitat Politècnica de València.
2017-2021: Responsable of the Nuclear Magnetic Resonance Facility at the CIPF (Valencia).
2017: Research stage at King’s College of London.
2017-2019: Postdoctoral researcher at the Joint Research Unit of Metabolomics CIPF-IIES-laFe (Valencia).
2015: Research stage at KIT (Germany).
2007-2017: Postdoctoral researcher at the Structural Biochemistry group at CIPF (Valencia).
2006-2007: R&D technicien at Farmhispania R&D (Barcelona).
2005-2006: R&D technicien at Finnovequim, Fine Chemicals Process R&D.
2005: PhD in Organic Chemistry from the Universitat Autònoma de Barcelona.
2003. Master in Organic Chemistry from the Universitat Autònoma de Barcelona.
2001: Chemistry degree from the Universitat Autònoma de Barcelona.
2021: Incorporation to ProtoQSAR as a PhD student in the project: “Development of a multitask expert system based on deep neural networks for hepatotoxicity prediction”.
2021: Master’s Degree in Bioinformatics and Biostatistics, Open University of Catalonia. Final Master Project: “Research of nutraceuticals for the prrevention and treatment of Alzheimer’s disease”.
2020: Internship at ProtoQSAR as a Master’s Degree student.
2016: Bachelor’s Degree in Biotechnology, Polytechnic University of Valencia. Final Project: “Functional characterization of neonatal hepatocytes cryopreserved to be used in hepatic cell therapy.” (Health Research Institute Hospital La Fe (IIS La Fe), Valencia).
Since 2024: Professor of Technology. Department of Education, Culture, Universities, and Employment, Generalitat Valenciana.
2016: Doctor in Agronomy, Polytechnic University of Valencia. Title of Doctoral Thesis: “Analysis of the Potential of Carbonic Fertirrigation in Citrus Fruits”.
2004-2016: Technical Manager of regional, national and European projects in the private foundation “Research and Innovation for Social Development” (Valencia).
Since 2001: Professor of Secondary school, specialty Technology. Department of Education, Culture, Universities, and Employment, Generalitat Valenciana.
1995-2001: Construction manager for the company Fomento de Construcciones y Contratas S.A.
1995: Agronomist Engineer(Higher Technical School of Agricultural Engineers of the Polytechnic University of Valencia).
2021: Joined as researcher in a Marie Curie European Project: GenoQSAR – ProtoQSAR (Paterna).
2020 – 2021: Researcher/Data analyst – IIS-LaFe (València).
2018 – 2019: Data Science National Certificate- ECAM (Strasbourg, France).
2015 – 2016: Molecular modelling expert – Rolic Technologies Ltd. (Allschwil, Switzerland).
2013 – 2015: Postdoctoral Researcher – EMPA, Swiss Federal Laboratories for Materials Science and Technology. (Dübendorf, Switzerland).
2008 – 2012: PhD in Molecular Modelling – Universiteit Leiden (Leiden, The Netherlands). Thesis subject: “In-silico study of reaction mechanisms and design principles for water oxidation catalysts”.
2003-2008: University degree in Chemistry – Universitat de València.
2024: Incorporation to ProtoQSAR as a Senior Researcher.
2021-2024: Senior Researcher – Institute of Molecular Science ICMol, (Valencia, Spain).
2020-2021: Junior Researcher – University of Valencia (Valencia, Spain).
2017-2020: Research Associate – University of Bristol (Bristol, UK).
2011-2017: PhD in Theoretical Chemistry and Computational Modeling – University of Valencia. Thesis Title: “Developing Environmental Coordinates for the Study of Enzymatic Catalysis”.
2010-2012: Master’s in Theoretical Chemistry and Computational Modeling – University of Valencia (Valencia, Spain).
2005-2010: Bachelor’s Degree in Chemistry – University of Valencia (Valencia, Spain).
2024: Incoporation to ProtoQSAR as a Computer Specialist.
2024: Master’s student in Economics, Finance, and Computing, International University of Andalusia, Huelva.
2016-2018: Master’s in Computer Science, Central University “Marta Abreu” of Las Villas, Cuba.
2018-2022: Computer Specialist, Los Caneyes Hotel Complex, Villa Clara, Cuba.
2015-2018: Computer Specialist, Ministry of Tourism Delegation, Villa Clara, Cuba.
2010-2015: Bachelor’s in Computer Engineering, Central University “Marta Abreu” of Las Villas, Cuba.
2019: Incorporation to ProtoQSAR as a Chemoinformatician/ Bioinformatician.
Since 2014: Associate Professor in the Department of Biomedicine, Faculty of Medicine, University of Barcelona.
2018-2020: Master’s Degree in Bioinformatics, University of Valencia.
2013 – 2018: Postdoctoral Associate in the Immunobiology Group (Dr. Margarita Martín Andorra). Department of Biomedicine, Faculty of Medicine, University of Barcelona – Fundació Clínic per a la Recerca Biomèdica (Barcelona).
2012: Doctor in Biomedicine, Pompeu Fabra University (Barcelona).
2008: Master’s Degree in Biomedical Research, Pompeu Fabra University (Barcelona).
2006: Bachelor’s Degree in Biochemistry, University of Valencia.
2024: PhD in Chemistry with cum laude honors, industrial and international distinction. Dissertation titled: “Identification of new bioactive compounds generated by intestinal bacteria.”
2019: Incorporation to ProtoQSAR as a PhD student in the project: “Identification of new bioactive compounds generated by intestinal bacteria”.
2019: Master’s Degree in Biotechnology and Bioengineering, Miguel Hernández University, Elche. Final Master Project in the study of the interaction of Flavivirus protein E with the lipid membrane of the late endosome through computational techniques (Institute of Research, Development and Innovation in Sanitary Biotechnology of Elche).
2018: Bachelor’s Degree in Biomedical Engineering, Polytechnic University of Valencia, Valencia. Final project in Design and implementation of a software for the analysis of molecular dynamics of simulated macromolecules using Monte Carlo techniques (Center for Biomaterials and Tissue Engineering, Universitat Politècnica de València).
2023: Incorporation to ProtoQSAR as a bioinformatic researcher.
2022: Master’s Degree in Research and Development in Biotechnology and Biomedicine, University of Valencia, Valencia. Final Master Project in Coxsackievirus B3 proteases: Identification of novel cellular targets (Institute for Integrative Systems Biology).
2021: Bachelor’s Degree in Biotechnology, Miguel Hernández University, Elche. Final project in the effect of 5-Fluorouracil and Verteporfin on the infectivity and the innate immune response in viral infections of zebrafish cells (Institute of Research, Development, and Innovation in Sanitary Biotechnology of Elche).
2024 – Incorporation to ProtoQSAR as a Junior Researcher within the project: “Modeling the Toxicity of Materials Using AI-based Techniques.”
2024: Extracurricular internship at MolDrug.
2022 – 2024: Master’s in Bioinformatics, University of Valencia. Master’s Thesis: “Application of Machine Learning to Individuals with Cognitive Impairment” (Institute of Biomedicine of Valencia).
2023: Extracurricular internship at the Institute of Biomedicine of Valencia (Department of Molecular Genetics).
2018 – 2022: Bachelor’s Degree in Biotechnology, Catholic University of Valencia. Bachelor’s Thesis: “Determination of the Effects of Ectopic Expression of the NachBac Sodium Channel in Neuro-2A Cells” (Principe Felipe Research Center).
2020 – present: Business Development Manager (ProtoQSAR).
2020 – present: Associate Professor (Universitat Autònoma de Barcelona, Biological Anthropology Unit; Department of Animal Biology, Plant Biology and Ecology).
2019 – present: General Secretary of “PRISMA, Association for Afective and Sexual Diversity in Science, Technology, and Innovation” (Spain).
2018 – present: Collaborator in the citizen initiative of scientific advisory to the Spanish legislative power “Ciencia en el Parlamento” (Science in Parliament, Spain).
2015 – present: Science and culture outreach writer and professional.
2020: Research support technician (Evolutionary Biology Institute, Spanish National Research Council – Universitat Pompeu Fabra).
2019 – 2020: Coordinator (Association Bioinformatics Barcelona – BIB, Barcelona).
2018 – 2020: International relations & collaborative research projects (Association Bioinformatics Barcelona – BIB, Barcelona).
2016 – 2018: Communications Manager (Anaxomics Biotech, Barcelona).
2014 – 2018: Business Developer (Anaxomics Biotech, Barcelona).
2012 – 2014: Project Manager (Anaxomics Biotech, Barcelona).
2015: MSc Biological Anthropology (Universitat de Barcelona & Universitat Autònoma de Barcelona).
2013: BSc & MSc Biotechnology, Universitat Autònoma de Barcelona.
2023: Joined ProtoQSAR as Chemoinformatics Specialist.
2012-2023: Founder of Kode srl and (from 2019) of the subsidiary company Kode Chemoinformatics srl.
Since 2008: Scientific collaborator in the Laboratory of Environmental Chemistry and Toxicology led by prof. Emilio Benfenati at Istituto di Ricerche Farmacologiche “Mario Negri”.
2006-2012: Scientific collaborator in the Milano Chemometrics and QSAR Research Group led by prof. Roberto Todeschini, at University of Milano – Bicocca.
2006: University degree in Computer Science – University of Milano Statale.
2023: Incorporation to ProtoQSAR as a bioinformatician.
2023: Internship at MolDrug as a master’s student.
2023: Master in Applied and Pharmacological Chemistry, Jaume I University, Castellón. Final Master Project on “Theoretical study of the first stage of the reaction mechanism catalyzed by CD38” (Biocomp research group, Castellón).
2023: Research grant in “Initiation to research in the study of the mechanism of reactions catalyzed by CD38 glycoprotein and design of new inhibitors”. (Biocomp research group, Castellón).
2022: Degree in Biotechnology, University of Girona, Girona. Final Degree Project on “Structural and dynamic study of the RNA recognition process in the CRISPR/Cas9 system” (Institut de Química Computacional i Catàlisi, Girona).
2024: Incorporation to ProtoQSAR as a Junior Researcher.
2024: Extracurricular internship at ProtoQSAR.
2024: Graduated in Chemistry from the University of Valencia. Final degree project “Síntesis de óxidos metálicos transparentes como transportadores de cargas selectivos para dispositivos fotovoltaicos y fotodetectores” at the Institute of Materials Science of the University of Valencia.
2021-2023: Creator and Administrator of Websites.
2024: Joining ProtoQSAR as Project Manager.
2021-2024: Management Assistant (Economic Management, PRL, HR, Logistics) in ITENE.
Higher Degree in Administration and Finance.
Diploma in Tourism.
2024: Incorporation to ProtoQSAR as a junior researcher
2023: Internship at the In Silico Discovery department of Johnson & Johnson Innovative Medicine as a postgraduate student, Toledo.
2023: Citius Program (Postgraduate Training Program), Autonomous University of Madrid.
2022: Master’s in Bioinformatics, Autonomous University of Barcelona, Barcelona. Master’s Thesis on Comparative Analysis and Optimization of a New Computational Protein-Peptide Docking Protocol (Zymvol Biomodeling SL, Barcelona).
2021: Bachelor’s in Biotechnology, Pablo de Olavide University, Seville. Bachelor’s Thesis on New Tools for Spatiotemporal Control of Gene Expression (Andalusian Center for Developmental Biology (CABD), Seville). Work focused on the utilization of Flipasa for gene expression regulation in different cellular types of Caenorhabditis elegans.
2024: Incorporation to ProtoQSAR as Communication Specialist
2024: Training Internship at ProtoQSAR S.L. as a Research Assistant in Data Science and Toxicology through the University-Business Foundation of the University of Valencia (ADEIT)
2023: Bachelor’s Degree in Chemistry from the University of Valencia. Final Degree Project, “Theoretical Exploration of Diels-Alder Reactions Guided by Non-Covalent Interactions” at the Institute of Molecular Science (ICMol) under the supervision of Dr. Joaquín Calbo.2022: Intern at Polymer Solutions S.L. in the distribution of industrial chemical additives for sectors such as plastics, rubber, and paints. Also handled document management, sales support, and chemical product regulation.
2019: Internship at the Institute for Molecular Recognition and Technological Development (IDM) under the supervision of Dr. Margarita Parra in the development of sensors and molecular probes.
2024: Incorporation to ProtoQSAR as Junior Researcher.
2024 – Extracurricular internship at Mendel’s Brain.
2022-2024 – Chromatographic laboratory analyst. Analysis of antibiotics and mycotoxins using HPLC-MS/MS techniques.
2022-2024 – Interuniversity Master’s at UOC-UB in Bioinformatics and Biostatistics. Master’s thesis: “Implementation of information systems for the detection of genomic variants” (Institute of Molecular and Cellular Biology of Plants).
2020 – Extracurricular internship at the Valencian Institute of Agricultural Research.
2017-2021 – Bachelor’s degree in Biotechnology from the Catholic University of Valencia. Bachelor’s thesis: “Identification of potential regulators in the secondary growth of Arabidopsis thaliana.”
2017 – Internship at Laboratorios Tecnológicos de Levante in the analysis and detection of pesticides and mycotoxins using HPLC-MS/MS techniques.
2015-2017 – Advanced specific vocational training in Environmental Health.
Do you want to work with us?
At ProtoQSAR we are an innovative company and we are interested in finding
motivated people to join our team. Even if there are no vacancies open, you can
send us your CV and we can explore opportunities.
Fill out our form and
send us your resume to rrhh@protoqsar.com
Frequently asked questions
Is ProtoQSAR a consultancy company or a vendor of specialized software on molecular modeling and chemoinformatics?
ProtoQSAR is a company that conducts studies for its clients and collaborators, currently we do not sell molecular simulation programs, nor our QSAR models. We provide our services to groups and entities that for the most part do not have specific training in chemistry-computing and molecular modeling -or it is very limited- and therefore our expertise can represent a greater added value for them.
How long does it take for a client to get the results of their project?
The projects in which we work are very different from each other, and prior to their execution we make an evaluation of the time necessary. The great advantage of computer studies compared to experimental tests is that we can obtain results in a much shorter time. For example, the prediction of the profile of a compound by QSAR methods is very fast (few days), since we already have models for this kind of evaluation. The virtual screening of a database to search for a candidate interacting with a particular target can represent 1 week to 2 months, depending on the number of chemicals filtered (a few thousands or hundreds of thousands).
Can I propose a collaborative project to ProtoQSAR? How?
At ProtoQSAR we are very interested in the development of new collaborative projects in which chemoinformatics and molecular modeling can provide an added value to our collaborators. If you have any idea to raise, please contact us explaining your proposal, and in a very short time we will give you an answer.
How much do ProtoQSAR services cost? How are the costs estimated?
Costs vary depending on the type of service we provide and the time we spend on a project. Since computing allows results to be obtained in a much shorter time than experimental tests, our services are also much cheaper.
What software does ProtoQSAR use to develop its models?
In ProtoQSAR we work with the whole palette of molecular modeling and chemoinformatics techniques, and therefore we have all the necessary programs for the execution of our projects. We systematically use standardized programs that are well referenced in the scientific literature, and sometimes we carry out our own software developments for specific needs. In any case, these developments remain the property of ProtoQSAR, and are not for sale.
What degree of confidence do the computer models have?
Computational studies are not an “exact science” and a certain degree of uncertainty is expected, as is the case with experimental tests (both in vitro and in vivo) to a certain extent. We conduct our studies according to scientifically recognized quality guidelines, and our extensive experience (demonstrable through our scientific and technical publications) makes our studies as accurate as possible. Before conducting a study, we inform our clients about the reasonable results’ expectations. At the time of providing the results, we also contribute our expert evaluation and inform the customer of the potential limitations of the obtained models.
How much time is needed to do a virtual screening? And how many compounds can be filtered?
Both questions are linked: the execution time of a virtual screening depends essentially on the number of compounds that are screened. To give a general idea, an already developed QSAR model allows the user to evaluate tens of thousands of compounds in a single day. Screening by docking (in a therapeutic target with known 3D structure) requires a longer period of time, but we can also evaluate thousands of compounds in a few days.
Can computational models be applied at the regulatory level?
Chemoinformatic models are recognized as a valid alternative at a the regulatory level, and the international regulations themselves increasingly encourage their use. For example, in the case of REACH, ECHA systematically requests companies to demonstrate that they have fully considered the use of alternative methods before concluding that a new test with vertebrates is necessary.
Can computer models replace the experimental tests required by legislation (e.g. REACH)?
Yes, in a lot of cases our models make it unnecessary to perform additional assays. This is particularly common when there is already some bibliographic information on the studied compounds, or when the products are of natural origin. In other cases the computational studies do not completely replace the experimental tests, but it is usually possible to reduce them (and therefore reduce time and costs). Another factor to consider is the credibility of the company in front of the authorities, which is clearly favored when presenting a complete dossier including the evaluation by alternative methods.
What type of model do I need for the registration/authorization of my substance: QSAR or read-across?
The type of model depends on the baseline information and on the substance to be evaluated. In principle, QSAR models are technically more robust and reliable, but they cannot always be used (for example, if the compound to be evaluated does not fall within the domain of applicability of the compounds that have been used to generate the models). In that case read-across is a good alternative, since this technique has the same validity at the regulatory level when properly executed by an experienced professional.
What is the “Applicability Domain”? How does it affect the prediction of my substance at the regulatory level?
Applicability domain is the “chemical space” to which a specific compound belongs in relation to the compounds that have served as the basis for developing a QSAR model. One of the parameters required by the OECD (and therefore necessary from a regulatory point of view) when determining whether a QSAR is valid on a given compound is the characterization of that space.
How are QSAR models validated?
All our models are subjected to a double validation, internal and external, and when possible we perform an experimental validation with independent structures belonging to the same chemical space or “domain of applicability”.
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
ProtoQSAR SL - CEEI Valencia
Technological Park of Paterna (Valencia)
Avda. Benjamin Franklin 12, Desp. 28
46980 Paterna (Valencia)
