Author

Marta A. S. Perez

Observed names: M. A. S. Perez, M.A.S. Perez, Marta A S Perez, Marta A.S. Perez, Marta AS Perez, Marta A S Perez, Perez, Marta A. S., Perez, Marta A.S.

Institutions: SIB Swiss Institute of Bioinformatics, University of Lausanne

Observed institutions: SIB Swiss Institute of Bioinformatics, Universidade do Porto, Ludwig Cancer Research, Centre Hospitalier Universitaire Vaudois, Ludwig Cancer Research, Rede de Química e Tecnologia, Swiss Cancer Center Léman, École Polytechnique Fédérale de Lausanne, University of Coimbra, University of Lausanne

ORCID: 0000-0002-3963-5965

Observed ORCID: 0000-0002-3963-5965

OpenAlex ID: A5111961845

SwissDock 2024: major enhancements for small-molecule docking with Attracting Cavities and AutoDock Vina

2024 · Marine Bugnon, Ute F Röhrig, et al. · Nucleic Acids Research · 659

SwissParam 2023: A Modern Web-Based Tool for Efficient Small Molecule Parametrization

2023 · Marine Bugnon, Mathilde Goullieux, et al. · Journal of Chemical Information and Modeling · 367

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T-cell repertoire analysis and metrics of diversity and clonality

2020 · Johanna Chiffelle, Raphael Genolet, et al. · Current Opinion in Biotechnology · 225

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2022 · Maiia E. Bragina, Antoine Daina, et al. · International Journal of Molecular Sciences · 160

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

2023 · Julien Racle, Philippe Guillaume, et al. · Immunity · 146

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Sensitive identification of neoantigens and cognate TCRs in human solid tumors

2021 · Marion Arnaud, Johanna Chiffelle, et al. · Nature Biotechnology · 104

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The Structure of the Protonated Serine Octamer

2018 · Valeriu Scutelnic, Marta A. S. Perez, et al. · Journal of the American Chemical Society · 84

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Neoantigen-specific CD8 T cells with high structural avidity preferentially reside in and eliminate tumors

2023 · Julien Schmidt, Johanna Chiffelle, et al. · Nature Communications · 78

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Infrared Spectroscopy of Mobility-Selected H + -Gly-Pro-Gly-Gly (GPGG)

2015 · Antoine Masson, Michael Z. Kamrath, et al. · Journal of the American Society for Mass Spectrometry · 74

Computational Alanine Scanning Mutagenesis: MM-PBSA vs TI

2013 · Sílvia A. Martins, Marta A. S. Perez, et al. · Journal of Chemical Theory and Computation · 74

SwissBioisostere 2021: updated structural, bioactivity and physicochemical data delivered by a reshaped web interface

2021 · Alessandro Cuozzo, Antoine Daina, et al. · Nucleic Acids Research · 56

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Accuracy of Density Functionals in the Prediction of Electronic Proton Affinities of Amino Acid Side Chains

2011 · Natércia F. Brás, Marta A. S. Perez, et al. · Journal of Chemical Theory and Computation · 46

Identification of clinically relevant T cell receptors for personalized T cell therapy using combinatorial algorithms

2024 · Rémy Pétremand, Johanna Chiffelle, et al. · Nature Biotechnology · 42

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

2015 · Gaspar P. Pinto, Natércia F. Brás, et al. · Journal of Chemical Theory and Computation · 41

Structural Prediction of Peptide–MHC Binding Modes

2022 · Marta A. S. Perez, Michel A. Cuendet, et al. · Methods in molecular biology · 27

Phage display enables machine learning discovery of cancer antigen–specific TCRs

2025 · Giancarlo Croce, Rachid Lani, et al. · Science Advances · 26

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Substrate Recognition in HIV-1 Protease: A Computational Study

2010 · M. A. S. Perez, P. A. Fernandes, et al. · The Journal of Physical Chemistry B · 22

Genetic Algorithm Based Design and Experimental Characterization of a Highly Thermostable Metalloprotein

2018 · Esra Bozkurt, Marta A. S. Perez, et al. · Journal of the American Chemical Society · 21

Deciphering the Mechanisms of Improved Immunogenicity of Hypochlorous Acid-Treated Antigens in Anti-Cancer Dendritic Cell-Based Vaccines

2020 · Michele Graciotti, Fabio Marino, et al. · Vaccines · 18

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Predicting Antigen‐Specificities of Orphan T Cell Receptors from Cancer Patients with TCRpcDist

2024 · Marta A. S. Perez, Johanna Chiffelle, et al. · Advanced Science · 16

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Ribonucleotide Reductase: A Mechanistic Portrait of Substrate Analogues Inhibitors

2010 · M.A.S. Perez, N.M.F.S.A. Cerqueira, et al. · Current Medicinal Chemistry · 16

Drug design: New inhibitors for HIV-1 protease based on Nelfinavir as lead

2007 · M.A.S. Perez, P.A. Fernandes, et al. · Journal of Molecular Graphics and Modelling · 16

Analysis of Secondary Structure Biases in Naturally Presented HLA-I Ligands

2019 · Marta A. S. Perez, Michal Bassani-Sternberg, et al. · Frontiers in Immunology · 12

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Improving the study of proton transfers between amino acid side chains in solution: choosing appropriate DFT functionals and avoiding hidden pitfalls

2012 · Pedro J. Silva, Marta A. S. Perez, et al. · Theoretical Chemistry Accounts · 9

Understanding the Mechanism for Ribonucleotide Reductase Inactivation by 2′- Deoxy-2′-methylenecytidine-5′-diphosphate

2010 · M. A. S. Perez, P. A. Fernandes, et al. · Journal of Chemical Theory and Computation · 9

Works count: 45

Citation count: 2,402

H-index: 18

I10-index: 23