🔬Research

đź“Ś The Structural Bioinformatics, Modelling and Biological Mechanisms Group (Model3DBio) is part of the Institute of Grapevine and Wine Sciences (ICVV), a joint research center governed by the Spanish National Research Council (CSIC), the Government of La Rioja, and the University of La Rioja. Our multidisciplinary team includes experts in Bioinformatics, Biochemistry, Physics, and Computer Science, specializing in statistical, mathematical, engineering, and biological modeling.

The main objective of the group is the development and application of computational methods for the structural modeling of biomolecules and biological mechanisms relevant to viticulture and oenology. We aim to understand and rationally manipulate biomolecular processes related to wine, covering everything from metabolite biosynthesis in grapevines and their transformation in fermentation microorganisms to their effects on human health.

Our work is organized into three main research lines:

1. Development of Multiscale Computational Methods

  • 1.1 Modeling of Biomolecular Interactions:
    • Development of energy functions and artificial intelligence techniques to study complexes such as antibody-antigen, multiprotein assemblies, and association dynamics.
  • 1.2 Impact of Mutations on Protein Binding:
    • Evaluation of changes in affinity and stability of protein-protein complexes using energy potentials combined with machine learning.
  • 1.3 Analysis of Biological Data and Probabilistic Modeling:
    • Modeling of dynamics at the cellular and population levels through statistical and probabilistic approaches.
  • 1.4 Validation and Implementation:
    • Rigorous testing of developed methods, with deployment of web servers for use by the scientific community.

2. Applications in Wine Sciences

  • 2.1 Molecular Targets Related to Wine Polyphenols:
    • Identification and structural modeling of potential biomolecular targets with protective or therapeutic activity.
  • 2.2 Quality Determinants and Sensory Perception Mechanisms:
    • Analysis of molecular bases of wine compounds and simulation of interactions explaining taste and aroma sensations.
  • 2.3 Enzymes and Biomolecules in Yeasts and Winemaking Processes:
    • Design and stabilization of key enzymes in fermentation and oenological processes to optimize performance and quality.
  • 2.4 Modeling of Grapevine Proteins and Genetic Variants:
    • Computational structuring of Vitis vinifera proteins and molecular-level study of genetic polymorphisms linked to agronomic or quality traits.

3. Experimental Validation and Search for New Compounds

  • 3.1 In Vitro Validation of Anthocyanins and Dietary Polyphenols:
    • Biochemical and cellular assays to verify the biological activity of grape-derived compounds.
  • 3.2 Structural and Biochemical Analysis of Molecular Mechanisms:
    • In-depth investigations of how polyphenols and other compounds interact with their targets, using crystallography, NMR, or molecular dynamics simulations.

⚙️ Infrastructure and Computational Resources

We have powerful computing resources to support the development of our models:

  • ICVV-CSIC Bullx R423E4 Local Server: In-house HPC resources at ICVV.
  • Beronia HPC Cluster (University of La Rioja): Provided by the University of La Rioja for intensive workloads.
  • Cluster Drago (CSIC): Up to 5 Petaflops of theoretical performance for large-scale simulations.
  • CESGA (Finis Terrae III): Access to national/government-level supercomputing.

We also coordinate the Structural Bioinformatics and Modelling Platform within the ICVV’s Molecular, Cellular and Bioinformatics Biology Service, hosting:

  • Web Servers and Computational Tools developed by the group (e.g., pyDockDNA, LightDock).
  • Omics Analysis Technologies (genomics, transcriptomics, metabolomics).
  • Databases specific to viticulture and oenology research.

đź”— Useful Links

🚀 Mission and Vision

Our mission is to advance wine and grapevine research through cutting-edge computational methods, integrating artificial intelligence and multiscale modeling to:

  • Discover new bioactive compounds derived from wine.
  • Optimize oenological processes (enzymes, yeasts, biotechnology).
  • Understand the molecular impact of grapevine varieties and their genetic polymorphisms.
  • Promote interdisciplinary collaboration between bioinformaticians, biologists, chemists, and engineers.

In the long term, we aim to be an international reference in structural bioinformatics applied to grapevine and wine sciences, providing open tools and accessible data to the scientific community and production sector.