Molecular Modelling and Bioinformatics

Methodologic aspects

• Analysis of the influence of solvent in molecular recognition. Continuum methods are being compared to analysis of explicit solvent simulations.
• Fine tuning of the parametrization of molecular dynamics simulations.

Studies on Small Models

• Theoretical studies of small model systems of large biological impact . This includes among others tautomeric and isomerism processes, stacking interactions, salt bridges, hydrogen bonding, cation-ð interactions, and general mechanisms of molecular recognition.

Studies on Proteins

• We are interested in the understanding of the basis of protein interactions, including those of pharmacological importance. Methods are being developed to understand both protein-protein and protein-ligand recognition.
• Protein flexibility is being analysed using massive molecular dynamics simulations

Studies on Nucleic Acids

• Molecular dynamics and statistical mechanics to study anomalous forms of nucleic acids. Particular attention is paid to the study of conformational transitions in DNA, drug-DNA interactions, and the analysis of triple helices and other structures of potential impact in antigene or antisense therapies.

Massive Genomic Analysis

• Datamining of genomic DNA to find regions with inusual structures or unusual mechanical properties
• Development of algorithms for the prediction of the pathological character of single nucleotide polymorphisms.
• Structural study of alternative splicing in proteins.