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Molecular Modeling Platform

Objective. The platform for molecular modeling and virtual screening arises as a unit that brings the capabilities of groups in bioinformatics methods based on biomolecular structures. Its mission is to integrate efforts to the use (databases) or the construction of macromolecular structures (homology modeling) to be used for rational protein modification (computer design), to determine protein interaction maps (protein-protein interactions), or to identify novel active compounds (molecular docking and virtual screening) from libraries of compounds (chemical libraries). Additionally, simulation (Molecular Dynamics) recreates the macromolecules in their native environment, including lipids, water and ions.

Theoretical basis. The high resolution (3D) structural data are used to extract useful information about protein-protein interactions to elucidate protein interaction networks, and to understand the formation of the macromolecular complex. The modeling of macromolecular structures, in which the target is treated as a single molecule or a ligand-receptor complex, allows the determination of structure-function relationships of the soluble and membrane proteins, mechanical molecular simulations of complex systems, the binding ligand, or even enzyme mechanism.

Facilities. For this purpose there is dedicated room endowed with an air-conditioned machine and a proper electrical installation to house two high performance servers and two "cluster" of computers with 182 processors, as well as the programs needed to address the management, editing and modification of macromolecules. Clusters: and

Synergy and complementarity. The combination of the experimental techniques of high throughput screening (HTS) with computational techniques and virtual screening bioinformatics open ways for high performance research, because the computational in silico calculations determine quickly and economically those families of compounds capable of exerting a biological effect with the chosen targets, whereas with experimental screening techniques the parameters of interaction between ligands and receptors are quantified. Once certain lead compounds, and again using computational techniques, the ligands can be redesigned to increase the specificity of action, the affinity, or both.

Services offered. From Molecular Modeling Platform we offer a variety of services aimed to developing bioactive molecules using computational strategies. The services are offered to research groups or companies interested in using in silico approaches in their research.

List of services on offer.

1.- Homology modeling.

  • Modeling of soluble proteins (by homology).
  • Modeling of membrane protein (by homology).
  • Modeling of peptides.
  • Check structures and problem solving.
  • Matching of structures and density maps obtained by cryo-electron microscopy.

2.- Protein design.

  • Virtual mutagenesis.
  • Alanine scanning.
  • Prediction of stability energy.
  • Increased thermal stability.
  • Increased solubility.
  • Modeling of mini-proteins.

3.- Protein-protein interaction.

  • Modeling ligand-receptor type.
  • Predicting interactions. Sequence space scanning.
  • Genomic screening.
  • Improved affinity and stability.
  • Specificity changes.
  • Second site suppressor designs (compensatory mutagenesis).
  • Targeted molecular design.
  • Building of peptide ligands in the binding site.
  • Design of peptide inhibitors of interactions.

4.- Molecular dynamics.

  • Molecular dynamics from crystallographic structures.
  • Steered Molecular Dynamics.
  • Simulation of real conditions: membranes, ion, solvent, pH, etc.
  • Simulation of protonation / deprotonation states.

5.- Molecular docking.

  • Location of the interaction sites of a given protein structure.
  • Protein-protein docking (-lípids, -nucleotides, -carbohydrates, etc).
  • Protein-drug (nucleotide-drug) docking.

6.- Virtual screening.

  • Based on structure (necessary 3D).
  • Based on the flexibility of the ligand.
  • Based on pharmacophore (3D necessary).
  • Based on molecular assemblies.
  • Ligand-based (3D not necessary).
  • Ligand-based pharmacophore search.
  • Structure similarity ligand search.
  • Ligands overlap.
  • Protein-drug from a database of any size.

7.- Chemical Libraries.

  • General. Derived from databases.
  • Directed. Own construction.
  • Markush enumeration (base molecule with variable positions).
  • Peptide library (peptides with a length of 3 to 7 aa) N- and C- free or protected.

Contact with us.

Dr. Gregorio Fernández-Ballester (IBMC-UMH).

Dr. José Antonio Encinar (IBMC-UMH).

Dr. Vicente Galiano Ibarra (Departamento de Física y Arquitectura de Computadores, UMH).