Personne

Marta Andreia Da Silva Perez

Cette personne n’est plus à l’EPFL

Publications associées (11)

Machine learning predictions of MHC-II specificities reveal alternative binding mode of class II epitopes

Florence Pojer, George Coukos, Kelvin Ka Ching Lau, Amédé Noredine Larabi, Julien Racle, David Gfeller, Marta Andreia Da Silva Perez, Alexandre Harari

CD4+T cells orchestrate the adaptive immune response against pathogens and cancer by recognizing epitopes presented on class II major histocompatibility complex (MHC-II) molecules. The high polymorphism of MHC-II genes represents an important hurdle toward ...

CELL PRESS2023

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The amino acid serine has long been known to form a protonated “magic-number” cluster containing eight monomer units that shows an unusually high abundance in mass spectra and has a remarkable homochiral preference. Despite many experimental and theoretica ...

2018

A genetic algorithm based design and experimental characterization of a highly thermostable metalloprotein

Ursula Röthlisberger, Rudolf Hovius, Marta Andreia Da Silva Perez, Esra Bozkurt, Nicholas John Browning

The development of thermostable and solvent-tolerant metalloproteins is a long-sought goal for many applica- tions in synthetic biology and biotechnology. In this work, we were able to engineer a highly thermo- and organic solvent- stable metallo variant o ...

2018

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Biomimicry is a strategy that makes practical use of evolution to find efficient and sustainable ways to produce chemical compounds or engineer products. Exploring the natural machinery of enzymes for the production of desired compounds is a highly profita ...

2016

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We report the first results from a new instrument capable of acquiring infrared spectra of mobility-selected ions. This demonstration involves using ion mobility to first separate the protonated peptide Gly-Pro-Gly-Gly (GPGG) into two conformational famili ...

2015

Cryogenic Spectroscopy and Quantum Molecular Dynamics Determine the Structure of Cyclic Intermediates Involved in Peptide Sequence Scrambling

Ursula Röthlisberger, Thomas Rizzo, Marta Andreia Da Silva Perez, Oleg Aseev

Collision-induced dissociation (CID) is a key technique used in mass spectrometry-based peptide sequencing. Collisionally activated peptides undergo statistical dissociation, forming a series of backbone fragment ions that reflect their amino acid (AA) seq ...

2015

Establishing the Catalytic Mechanism of Human Pancreatic α-Amylase with QM/MM Methods

Marta Andreia Da Silva Perez

In this work, we studied the catalytic mechanism of human pancreatic α-amylase (HPA). Our goal was to determine the catalytic mechanism of HPA with atomic detail using computational methods. We demonstrated that the HPA catalytic mechanism consists of two ...

2015

Lessons from Nature: Computational Design of Biomimetic Compounds and Processes

Ursula Röthlisberger, Pablo Campomanes Ramos, Elizabeth Claire Brunk, Negar Ashari Astani, Marta Andreia Da Silva Perez, Esra Bozkurt, Nicholas John Browning

Through millions of years of evolution, Nature has accomplished the development of highly efficient and sustainable processes and the idea to understand and copy natural strategies is therefore very appealing. However, in spite of intense experimental and ...

2014

Computational Alanine Scanning Mutagenesis: MM-PBSA vs TI

Marta Andreia Da Silva Perez

Understanding protein-protein association and being able to determine the crucial residues responsible for their association (hot-spots) is a key issue with huge practical applications such as rational drug design and protein engineering. A variety of comp ...

2013

We have studied the influence of implicit solvent models, inclusion of explicit water molecules, inclusion of vibrational effects, and density functionals on the quality of the predicted pK a of small amino acid side chain models. We found that the inclusi ...

2012

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