Strategic Research

Molecular Modelling and Bioinformatics (MMB)

This group focuses on the study of molecular recognition processes of biological significance from a methodological and an application point of view. The main subjects addressed are the structure of non-standard nucleic acids, the dynamic properties of macromolecules, and protein-ligand and protein-protein recognition. The long-term objective is to understand the behavior of living organisms from the basic rules of physics; in other words, to represent life by means of theoretical calculations. The main topics we concentrate our efforts on are the study of protein dynamics and the analysis of unusual or stressed DNAs of biological importance, with particular emphasis in chromatin-stressed DNAs.

The group devotes a large effort in the development of new methodologies, but also in the study of especially relevant biological systems.

Main projects

  • 1.

    Multiscale Complex Genomics (MuG)

    Multi-Scale Complex Genomics will provide tools to integrate the navigation in genomics data from sequence to 3D/4D chromatin dynamics data. 3D/4D genomics represents one of the biggest challenges for biology and biomedicine in the next decade. The MuG project will provide tools to integrate the navigation in genomics data from sequence to 3D/4D chromatin dynamics data. Research efforts in 3D and 4D genomics are experiencing exponential growth. However, the current lack of standardization in analysis and simulation tools is threatening to become a bottleneck. MuG responds to the latest computational challenges of 3d/4D genomics by bringing this community closer to the HPC world and providing a suitable set of tools and infrastructure. H2020-EINFRA-9-2015; Project no. 676556

  • 2.

    Elixir-Excelerate: Fast-track ELIXIR implementation and drive early user exploitation across the life sciences

    Building a sustainable European infrastructure for biological information, supporting life science research and its translation to medicine, agriculture, bioindustries and society. ELIXIR unites Europe’s leading life science organisations in managing and safeguarding the massive amounts of data being generated every day by publicly funded research. It is a pan-European research infrastructure for biological information. H2020-INFRADEV-1-2015-1, Project no. 676559.

  • 3.

    Bioexcel : Centre of excellence for biomolecular research

    BioExcel is a newly launched Centre of Excellence for provision of support to academic and industrial researchers in the use ofhigh-performance computing (HPC) and high-throughput computing (HTC) in biomolecular research. Centre activities are on i) improvement of the performance and efficiency of software for biomolecular modelling (in particular GROMACS, HADDOCK and CPMD) to allow optimal usage and scaling of large supercomputer systems; ii) improvement of the usability and accessibility of tools based on workflow systems such as KNIME, Galaxy, Apache Taverna or COMPSs and iii) providing training and consultancy on the best practices in the field. H2020-EINFRA-5-2015, Project No. 675728.



Bioinformatics expertise:

Group Leader:

Modesto Orozco

Bioinformatics services offered

  • Protein Data Bank Local Repository

    Protein Data Bank. Mirror to the central repository for experimental 3D structures.

  • MDWeb & MDMoby

    A comprehensive set of tools to allow automated setup and analysis of molecular dynamics trajectories.

  • MoDEL: Molecular Dynamics Extended Library

    Database holding over 1,800 trajectories ranging from 10 ns to 1ms in length, from a representative set of protein structures.

  • NAFlex: Nucleic Acid Flexibility

    Web tool to study the flexibility of nucleic acids, either isolated or bound to other molecules.

  • BIGNASim

    a NoSQL database structure and analysis portal for nucleic acids simulation data. A novel database system to store MD trajectories and analyses of nucleic acids.