Laboratory of Molecular Modeling and Dynamics

The computer simulation is emerging as a powerful tool to support research and industrial development. Considered as silicon experience in this technique lies in the interface between theory and experiment will often act as a liaison between them. A huge saving of resources, time and environmental damage have been achieved with their jobs in different sectors of human activity. In Biology, Medicine and Pharmacy this technique has been useful for understanding biological processes of drug action and disease in atomic-molecular scale.

Molecular Complexes

    We applied the simulation in research of structures molecularers, complex protein-protein and protein binders, biological membranes and protein folding. We have studied complexes involving enzyme inhibitors of HIV-1 protease, T. cruzi, P falciparum and Y pestis by Molecular Modeling and Molecular Dynamics Simulation. In studies of HIV-1 protease have focused virus subtypes that have emerged in Latin America, Africa and Asia, since antiretroviral drugs available against AIOS were not developed specifically for these subtypes. Our interest in this area is contributing to the development of protease inhibitors against infectious diseases.

Biological Membranes

    The molecular dynamics simulation of biological membranes and proteins and peptides in the membrane environment has become low. From a simple model for a dielectric biomembrane in recent years simulate the dynamics of peptides, hormones, and fragments of the sodium channel, important in opening and closing the channel at the interface membrane ¬ water. Since the computational processing power continues to increase, we have worked on a model atom-by-atom to a biological membrane composed of lipid molecules and water. Our interest is to simulate the dynamics of proteins, peptides anesthetics and antibiotics that environment to contribute to the understanding of the mechanism of action of these molecules in biomembranes.

Protein folding

    Theoretically, proteins have an astronomical number of possible conformations, considered that the folded structure occurs in a native conformation with the lowest energy. Techniques "Simulated Annealing" have been applied in search of stable conformations in polypeptide chains by using methods of statistical mechanics and molecular dynamics.

    A more general formulation for Statistical Physics was proposed in the last two decades, in which the Boltzmann statistic is only a particular case. We suggest that the folding process of proteins was described by this generalized formulation. Subsequently, we optimized peptide chains and found the lowest energy conformation using the "Simulated Annialing" widespread, which is based on this new formulation of Statistical Physics. Our interest in this area is to implement this new formalism in studies of protein folding ab initio modeling and refinement of proteins obtained by comparative molecular modeling, optimizing dissimilar regions.


Pedro Geraldo Pascutti - Head of the Laboratory

Post-doctoral fellows

Pedro Alexandre Lapido Loureiro

Diego Enry Barreto Gomes

ucas Villas Bôas Hoeltz

Carla Maria de Souza  Menezes

PhD students

Reinaldo Souza de Oliveira Júnior

Rosemberg de Oliveira Soares

Tacio Vinício Amorim Fernandes

Pedro Henrique Monteiro Torres

Priscila da Silva Figueiredo Celestino Gomes

Laura Machado de Faria

Raísa da Rocha Reis

Master students

Raquel Gama Gomes Leite

Undergraduate students

Cristóvão Freitas Iglesias Jr.

Wesley Junio Alves da Conceição

Structural and Molecular Biology
Chefe do laboratório: