Marta A. S. Perez

SIB Swiss Institute of Bioinformatics — Switzerland

Biochemistry, Genetics and Molecular Biology · Life Sciences

18h-index1.8kcitations47works46.22yr avg
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Research Topics

Protein Structure and Dynamics(9), Monoclonal and Polyclonal Antibodies Research(9), vaccines and immunoinformatics approaches(9), Computational Drug Discovery Methods(7), Immunotherapy and Immune Responses(7)

Publications47 total

Universal paratope–epitope interaction patterns in antibody–antigen structures
Protein Science·2025Open Access
Rapid and Reliable Structural Modeling of Adaptive Immune Receptors Using an Optimized AlphaFold3 workflow
2025
A fingerprint approach to pioneer structure-based T cell receptor repertoire analysis and specificity prediction
Frontiers in Immunology·2025· 1 citedOpen Access
Phage display enables machine learning discovery of cancer antigen–specific TCRs
Science Advances·2025· 8 citedOpen Access
Predicting Antigen‐Specificities of Orphan T Cell Receptors from Cancer Patients with TCRpcDist
Advanced Science·2024· 6 citedOpen Access
Phage display enables machine learning discovery of cancer antigen specific TCRs
2024· 1 citedOpen Access
Author Correction: Identification of clinically relevant T cell receptors for personalized T cell therapy using combinatorial algorithms
Nature Biotechnology·2024· 4 citedOpen Access
Identification of clinically relevant T cell receptors for personalized T cell therapy using combinatorial algorithms
Nature Biotechnology·2024· 28 citedOpen Access
SwissDock 2024: major enhancements for small-molecule docking with Attracting Cavities and AutoDock Vina
Nucleic Acids Research·2024· 368 citedOpen Access
Open Access Databases and Datasets for Computer‐Aided Drug Design. A Short List Used in the Molecular Modelling Group of the <scp>SIB</scp>
Methods and principles in medicinal chemistry·2023Open Access
Bioisosteric Replacement for Drug Discovery Supported by the SwissBioisostere Database
Methods and principles in medicinal chemistry·2023· 1 cited
SwissParam 2023: A Modern Web-Based Tool for Efficient Small Molecule Parametrization
Journal of Chemical Information and Modeling·2023· 223 citedOpen Access
Mol2 files used to test SwissParam 2023
2023Open Access
Mol2 files used to test SwissParam 2023
Zenodo (CERN European Organization for Nuclear Research)·2023Open Access
TCRpcDist: Estimating TCR physico-chemical similarity to analyze repertoires and predict specificities
2023· 4 citedOpen Access
Neoantigen-specific CD8 T cells with high structural avidity preferentially reside in and eliminate tumors
Nature Communications·2023· 63 citedOpen Access
EVOLVE: An Evolutionary Toolbox for the Design of Peptides and Proteins
2023· 1 citedOpen Access
Machine learning predictions of MHC-II specificities reveal alternative binding mode of class II epitopes
Immunity·2023· 112 citedOpen Access
Machine learning predictions of MHC-II specificities reveal alternative binding mode of class II epitopes
2022· 13 citedOpen Access
The SwissSimilarity 2021 Web Tool: Novel Chemical Libraries and Additional Methods for an Enhanced Ligand-Based Virtual Screening Experience
International Journal of Molecular Sciences·2022· 137 citedOpen Access
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Frequent Co-authors

Vincent Zoete(25), Pedro Alexandrino Fernandes(15), Maria J. Ramos(13), Alexandre Harari(12), George Coukos(10), Michal Bassani‐Sternberg(10), Antoine Daina(8), Olivier Michielin(8), Johanna Chiffelle(8), Julien Schmidt(8), Sara Bobisse(8), Raphaël Genolet(7), David Gfeller(7), Ursula Röthlisberger(7), Marine Bugnon(6), Ute F. Röhrig(6), Marion Arnaud(6), Natércia F. Brás(6), Maiia E. Bragina(5), Lana E. Kandalaft(5)