Rita Magalhães

Rita Magalhães
University of Porto | UP · BioSIM (UCIBIO@REQUIMTE) Faculdade de Medicina

BSc in Biochemistry | MSc in Chemistry

About

16
Publications
1,128
Reads
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70
Citations
Citations since 2016
16 Research Items
70 Citations
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2016201720182019202020212022010203040
2016201720182019202020212022010203040
2016201720182019202020212022010203040
Introduction
Skills and Expertise

Publications

Publications (16)
Article
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the infectious agent that has caused the current coronavirus disease (COVID) pandemic. Viral infection relies on the viral S (spike) protein/cellular receptor ACE2 interaction. Disrupting this interaction would lead to early blockage of viral replication. To identify chemical tools to...
Article
The emergence of multi-drug resistant bacteria in the past decades has become one of the major public health issues of our time. One of the main mechanisms of resistance and persistence of bacteria is their ability to form biofilms. Quorum-sensing (QS) is one of the main mechanisms of biofilm formation. Interfering with the QS cascade constitutes a...
Article
Full-text available
Pseudomonas aeruginosa is an opportunistic Gram-negative bacterium responsible for acute and chronic infections in planktonic state or in biofilms. The sessile structures are known to confer physical stability, increase virulence, and work as a protective armor against antimicrobial compounds. P. aeruginosa can control the expression of genes, popu...
Article
Plastic accumulation is one of the main environmental issues of our time. In 2016, two enzymes capable of degrading polyethylene terephthalate (PET), one of the most common plastic polymers, were discovered. PETase and MHETase from Ideonella sakaiensis (IsPETase and IsMHETase, respectively) work sequentially to degrade PET to its constituent monome...
Article
Resistance to antibiotics is an increasing threat in global health and strategies to develop or find new drugs are of the utmost importance. Pseudomonas aeruginosa is a Gram-negative pathogen that...
Poster
Full-text available
Optimization of Classification Models for the Identification of Ligand-Target Inhibition Pairs in Biofilm Formation in P.aeruginosa
Article
Full-text available
Plastics are highly durable and widely used materials. Current methodologies of plastic degradation, elimination, and recycling are flawed. In recent years, biodegradation (the usage of microorganisms for material recycling) has grown as a valid alternative to previously used methods. The evolution of bioengineering techniques and the discovery of...
Poster
The work, entitled “Development of a Classification Model for the Identification of Targets to Known P.aeruginosa Biofilm Formation Inhibitors”, constitutes an example of how machine learning algorithms can be employed to improve the drug design pipeline and fight biofilm infections more efficiently.
Article
The Biofilms Structural Database (BSD) is a collection of structural, mutagenesis, kinetics, and inhibition data to understand the processes involved in biofilm formation. Presently, it includes curated information on 425 structures of proteins and enzymes involved in biofilm formation and development for 42 different bacteria. It is available at w...
Article
Full-text available
Quantum mechanics/molecular mechanics (QM/MM) methods are presently a well‐established alternative for the study of enzymatic reaction mechanisms. They enable the description of a small part of the enzyme, where reactions take place through QM, while the majority of the thousands of atoms that comprise these biomolecules are handled through MM. Whi...
Chapter
Biofilms are a growing concern to human health, particularly due to the increased drug resistance associated with them. One way to inhibit biofilm formation is through interfering with the process of quorum sensing, a cell-to-cell communication mechanism in bacteria. Computational methods can be used to evaluate “in silico” a variety of aspects rel...

Questions

Question (1)
Question
Hello, I am trying to use mdpocket (from fpocket 3.0) to analyze pockets in a MD trajectory. I am in the Pocket Exploration stage. I have a .nc trajectory file, and am trying to run fpocket on it. However, in the output, the trajectory is not aligned with my structures, even though they are centered. I think this might be because I am indicating the initial MD structure as the pdb topology file, a required parameter. I thought the point of using fpocket 3.0 was that we no longer needed pdb files, only trajectory files. What should the input pdb topology for the -f flag file be?

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