Projects

Scientific software development

In-house and public tools to set up systems, run protocols and analyse trajectories, kept open.

2 projects

OCDocker - open consensus docker

OCDocker - open consensus docker

Artur Duque RossiPhD.

This project proposes the development, improvement, and validation of a molecular docking system that employs consensus scoring to assist in identifying compounds with therapeutic potential. To this end, a machine learning model was trained using molecular descriptors of ligands and receptors from specialized databases, alongside data derived from docking simulations performed with various molecular docking programs. The consensus approach demonstrated a competitive-and often superior-ability to distinguish active compounds from inactive ones, based on classifications from the DUDEz and PDBbind databases.

Team: Artur Duque Rossi, Guilherme Ian Spelta, Maria Clara Monachesi

TARDIS: A genome-scale metabolic network tool to identify new targets for computer-aided antimicrobial design

TARDIS: A genome-scale metabolic network tool to identify new targets for computer-aided antimicrobial design

Camila Rodrigues ChavesMSc.

Throughout history, many alternatives for tackling epidemics have been adopted, and yet we still observe outbreaks of infectious diseases taking on devastating proportions. With the advancement of bioinformatics, computer-aided drug design (CADD) methodologies have emerged to reduce the time and cost required for the development of new drugs. However, this field suffers from a scarcity of new targets for pharmacological intervention, making it necessary to develop new methodologies to meet this demand. Therefore, this project aims to develop TARDIS: TARgets DIScoverer, a program for identifying molecular targets in bacterial genomes in an automated and user-friendly way.

Team: Camila Rodrigues Chaves, Artur Duque Rossi, Guilherme Ian Spelta, Pedro Torres

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