Martínez Molecular Modeling Group

Institute of Chemistry and Center for Computing in Engineering and Science

University of Campinas

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Home Computer simulations and computer modeling are fundamental tools for the understanding the relationships between structure and function of biomolecules. In our group, we aim to develop new computational tools and simulation strategies to study the structure and dynamics of biological macromolecules in solution. We stimulate students to develop computer programming skills in order to develop novel modeling or data-analysis methods. Computational tools developed in our group include the widely used `Packmol` package for building initial configurations for molecular dynamics simulations, and the `TopoLink` program for the analysis of chemical-crosslinking distance constraints. Fast and versatile packages for structural alignment and analysis of MD simulations are also available as free software. Currently, we focus in two major research topics: 1) Modeling the tertiary structure of proteins using distance constraints, particularly those derived from chemical-crosslinking mass-spectrometry, and 2) the understanding of the solvation structure of solutes of complex structure. On-demand application of molecular modeling and simulations to the understanding of specific bimolecular systems is also recurrent. We have tight interaction with experimental groups, and we hope to suggest from the computational models new hypothesis that should be testable by experiments. The group is also experienced in the application of large-scale optimization techniques to problems arising in computational chemistry and biochemistry.
We thank the financial support of Grants: FAPESP 2010/16947-9 (Taz), 2018/24293-0 (Otimização), 2013/08293-7 (CCES), 2018/14274-9 (XL) and CNPq (302332/2016-2 - Produtividade Fluorescência)