Alfredo Di Nola

Learn More
In this article we use the recently developed perturbed matrix method (PMM) to investigate the effect of conformational fluctuations on the electronic properties of heme in Myoglobin. This widely studied biomolecule has been chosen as a benchmark for evaluating the accuracy of PMM in a large and complex system. Using a long, 80-ns, molecular dynamics(More)
The calculation of free energies by computer simulation represents one of the most promising areas in molecular modeling. While the computational methods developed so far give reliable results for liquids or solutions, they are not satisfactory for globular proteins. The reproducibility of the data is poor due to several sources of error. The most important(More)
In recent years several implementations of molecular dynamics Ž. Ž. MD codes have been reported on multiple instruction multiple data MIMD machines. However, very few implementations of MD codes on single instruction Ž. multiple data SIMD machines have been reported. The difficulty in using pair lists of nonbonded interactions is the major problem with MD(More)
Human neutrophil collagenase (HNC, MMP-8) is one of the target enzymes for drug treatment of pathologic extracellular matrix degradation. Peptidomimetic inhibitors bind in the S'-side of the enzyme active site occupying the S'1 primary specificity pocket by their large hydrophobic side-chains. The crystal structure of the complex between the catalytic(More)
  • 1