João M. C. Teixeira

Current Position

Senior Research Software Engineer at Zymvol Biomodeling.

Scientific Workflows: Leading the development of Zymvol’s core research software suites, ensuring they meet the stringent reliability standards of a production-grade scientific environment.
Scientific Strategy & Advisory: Serving as the critical bridge between domain science and software engineering. Advising the company on data architecture, data structuring, and core biophysical concepts, translating complex scientific requirements into actionable computational strategies to drive product design.
Cloud Architecture & FinOps: Architecting and scaling scientific workflows to run seamlessly across HPC clusters and Google Cloud. Deeply integrating FinOps strategies to optimize cloud infrastructure, ensuring maximum cost efficiency and resource utilization without compromising computational power.
DevOps Vision & Engineering Excellence: Guiding the overarching DevOps strategy. Fostering Test-Driven Development (TDD), clean code principles, and robust CI/CD pipelines to ensure the continuous delivery of highly stable, deployable software for multidisciplinary research teams.
Technical Leadership & Mentorship: Directing strategic technical decision-making while promoting a blameless, growth-oriented team culture.

Specialized in computational structural biology, holding a Licentiate in Biochemistry (2008) and a Ph.D. in Biophysics (2014). My academic research focused on the structural dynamics of proteins using NMR spectroscopy, bridging wet-lab execution with advanced computational modeling. From 2015 to 2024, I expanded my expertise into software engineering in Python, delivering critical open-source suites including the NIH-funded IDPConformerGenerator and the BioExcel-funded HADDOCK3. I have consistently served as a scientific advisor across numerous collaborations.

In 2024, I transitioned to the private sector to supervise, develop and optimize scalable scientific pipelines, applying my expertise to architect robust software solutions that run seamlessly across HPC clusters and cloud infrastructure.

Throughout my career, I have secured participation in over a dozen funded projects and grants, authored 34 scientific publications and one book chapter, presented 26 posters at international conferences, and dedicated myself to mentoring over 15 students and junior researchers.

Education

Ph.D in Biochemistry with specialization in Biophysics January 9th, 2014

CNC (University of Coimbra, Portugal) and CERM (University of Florence, Italy).

Title awarded by the University of Coimbra, Portugal.

Approved Unanimously with Distinction and Honours.

Grant: FCT Doctoral Research Grant for International Training (4 years)

Thesis title: "Paramagnetic NMR of Proteins to Study the Collagenolytic Mechanism of MMP-1."

Supervisors: Carlos F.G.C. Geraldes and Claudio Luchinat.

Thesis PDF | Slides

Licentiate in Biochemistry September 9th, 2008

University of Coimbra, Portugal.

Thesis title: "Study of the interaction of Ln3+ complexes of targeted contrast agents to HSA and RCA120 binding models using high resolution Saturation Transfer Difference (STD) NMR techniques."

Supervisor: Carlos F.G.C. Geraldes

Thesis PDF

Research

I am passionate about understanding the role of protein's flexibility in life and disease: Protein flexibility includes structural adaptation, coordinated multi-domain motions, flexible linkers, disordered regions, and fully disordered proteins. On the other hand, the processes of life and disease include: cell signaling, catalysis, inhibition, activation, coordination, condensation, and many others. Therefore, structural dynamics is intrinsic and necessary to all biomolecules.

Below is a short description of my main research topics. Here, the most relevant articles are highlighted but all my papers are listed in the publications section.

Protein fuzzy binding in aberrant protein condensates in disease

Structural dynamics is vital for cellular processes; hence, protein flexibility governs cell homeostasis in health and disease. In the last two decades, researchers built the basis for understanding intrinsically disordered proteins and we are now able to investigate protein condensation through the lens of structural biology. Specifically, my research focused on understanding how fuzzy binding networks control and describe protein-protein interactions [1, 2], protein liquid-liquid phase separation [3], and how single or multiple mutations result in aberrant condensation in disease.

Modeling Intrinsically Disordered Proteins

Working with Dr. Julie Forman-Kay and Dr. Teresa Head-Gordon, we developed a comprehensive software framework to model proteins with high conformational heterogeneity. Our approach integrated experimental data (NMR, SAXS, FRET, etc.), Bayesian inference, machine learning, and statistical sampling incorporating state-of-the-art knowledge of intrinsically disordered proteins (IDPs).

IDPConformerGenerator: I developed the core engine for this modular, open-source suite [1, 2, 3]. By integrating PDB-derived fragment sampling, Monte Carlo algorithms, and machine learning, it rapidly generates physically realistic ensembles of large disordered proteins—achieving experimental agreement comparable to molecular dynamics simulations, but at a fraction of the computational cost.
Bayesian Ensemble Selection: We proposed and implemented a framework that rigorously accounts for uncertainties in experimental data during ensemble selection [4].
Machine Learning Integration: Leveraged ML methods to generate highly data-accurate ensembles of IDPs and refined conformer models [5, 6, 7].

This robust framework paved the way for numerous research projects that continued long after my tenure in Toronto.

Fuzzy interactions regulating Src Family Kinases

At the BioNMR group in Barcelona, we described a new regulatory mechanism for Src Family Kinases (SFK), whose activity is governed by the contraction and expansion of domains via localized phosphorylations on the unstructured domains.

Novel Signaling Pathway: Using advanced NMR techniques, we discovered that the N-terminal disordered Unique Domain transfers signals from the cell membrane to the SFK receptor via a network of fuzzy interactions with the folded SH3 domain.
Structural Fine-Tuning: Demonstrated that the structural details of the unstructured Unique Domain (UD) dictate SFK activity. For example, a mere 21-residue deletion in the UD of SFK Lyn isoform B completely alters the regulatory behavior of this 512-residue protein.
Universal Mechanism: Proposed that this membrane-UD-SH3 mechanism is common across the entire SFK family.

Find here my publications on how flexible linkers and fuzzy binding networks regulate SFK’s activity.

Role of MMP linkers in collagenolysis

During my Ph.D., we described how the MMP's flexible linker orchestrates the relative movements of MMP's catalytic and hemopexin folded domains by poising them favorably to cleave the triple helical collagen—a process necessary for the metastatic progression of tumor cells [1, 2].

My work was one of the first to combine several NMR techniques, crystallography, and software from the We-NMR consortium to solve a large biochemical unknown and provide models for MMP-1 free, and collagen-bound, in solution. This research was highlighted in the first issue of the paraNMR FP-7 letters, and you can download my Ph.D. thesis from ResearchGate where the MMP-1:Collagen models are presented. I am also the author of the MMP-1 dedicated chapter in the Handbook of Proteolytic Enzymes, 2024.

New mechanisms to combat antibiotic resistance

Antibiotic resistance by pathogenic bacteria is likely today’s top concern in health security. Therefore, identifying alternative routes to destroy infectious bacteria is crucial to develop future disease-control strategies. We demonstrated that TomB antitoxin activity is oxygen dependent, and it actively oxidizes the Hha toxin to reduce the latter’s activity through the oxidation of a conserved cysteine residue [1].

Software engineering for biophysical sciences

Because of my continuous interest in software architecture and in sharpening best practices in open-source software, I have led the development of (or significantly contributed to) several software suites applied to biophysical sciences.

I highlight my contribution to the HADDOCK3 project as a lead developer from July 2021 to August 2022, when I brought the project from a proof-of-concept to a fully-featured beta version. HADDOCK is the largest biomolecular docking software in academia with thousands of active users worldwide and is part of the three-times European-funded BioExcel project. Plus, to engage and share with the community, I imparted talks on developing open-source software, DevOps best practices, and software architecture.

Understanding COVID-19 infection through computational modeling

In the absence of experimental data, computational modeling allows us to have prior knowledge of protein systems and complexes that can guide experimental analysis and project design. Early on during the devastating COVID-19 pandemic, together with colleagues worldwide, we investigated the cross-species transmission capacity of SARS-CoV-2 [1] by modeling the ACE2 receptors of different domestic animal species with the virus’ RBD protein, thus shedding light on the infections reported in farms and zoos and helping predict possible cross-species transmission.

Also, we generated a data set of 242 modeled ACE2 human variants bound to the RBD protein [2]. This data set can boost the design of therapies against SARS-CoV-2 and coronaviruses in general by considering different world populations, and is available openly online.

Scientific Articles

Publications listed by inverse chronological order.
#: equal contribution | @: corresponding author | 🔓: open-access
See publications also at Google Scholar and PubMed.

🔓 HADDOCK3: A Modular and Versatile Platform for Integrative Modeling of Biomolecular Complexes

Journal of Chemical Information and Modeling, 2025, Volume 65, issue 13. DOI

Marco Giulini, Victor Reys, João M. C. Teixeira, Brian Jiménez-García, Rodrigo V Honorato, Anna Kravchenko, Xiaotong Xu, Raphaëlle Versini, Anna Engel, Stefan Verhoeven, Alexandre M J J Bonvin

🔓 Integrative Modeling in the Age of Machine Learning: A Summary of HADDOCK Strategies in CAPRI Rounds 47–55

Proteins: Structure, Function, and Bioinformatics, 2025. DOI

Victor Reys, Marco Giulini, Vlad Cojocaru, Anna Engel, Xiaotong Xu, Jorge Roel-Touris, Cunliang Geng, Francesco Ambrosetti, Brian Jiménez-García, Zuzana Jandova, Panagiotis I. Koukos, Charlotte van Noort, João M. C. Teixeira, Siri C. van Keulen, Manon Réau, Rodrigo V. Honorato, Alexandre M. J. J. Bonvin

🔓 DeepRank2: Mining 3D Protein Structures with Geometric Deep Learning

Journal of Open Source Software (JOSS), 2024, volume 9, issue 94, 5983. DOI

Giulia Crocioni, Dani L. Bodor, Coos Baakman, Farzaneh M. Parizi, Daniel T. Rademaker, Gayatri Ramakrishnan, Sven van der Burg, Dario F. Marzella, João M.C. Teixeira, Li C. Xue

🔓 PED in 2024: improving the community deposition of structural ensembles for intrinsically disordered proteins

Nucleic Acids Research, 2024, volume 52, issue D1, D536-544. DOI

Hamidreza Ghafouri, Tamas Lazar, Alessio Del Conte, Luiggi G Tenorio Ku, PED Consortium (incl. João M.C. Teixeira), Peter Tompa, Silvio C. E. Tosatto, Alexander Miguel Monzon

🔓 Local Disordered Region Sampling (LDRS) for Ensemble Modeling of Proteins with Experimentally Undetermined or Low Confidence Prediction Segments

Bioinformatics, 2023, volume 39, issue 12, btad739. DOI | [Preprint]

Zi Hao Liu, João M.C. Teixeira, Oufan Zhang, Thomas E. Tsangaris, Jie Li, Claudiu C. Gradinaru, Teresa Head-Gordon, Julie D. Forman-Kay

🔓 Impact of AlphaFold on Structure Prediction of Protein Complexes: The CASP15-CAPRI Experiment.

Proteins: Structure, Function, and Bioinformatics, 2023, volume 91, issue 12, 1658-1683. DOI

Marc Lensink, Guillaume Brysbaert, Nessim Raouraoua, Paul A. Bates, Marco Giulini, Rodrigo V. Honorato, Charlotte van Noort, João M.C. Teixeira, Alexandre M. J. J. Bonvin, et. al.

🔓 Alternatively spliced exon regulates context-dependent MEF2D higher-order assembly during myogenesis

Nature Communications, 2023, 14, 1329. DOI

Mónika Gönczi, João M.C. Teixeira, Susana Barrera-Vilarmau, Laura Mediani, Francesco Antoniani, Tamás Milán Nagy, Zsolt Ráduly, Viktor Ambrus, József Tőzsér, Endre Barta, Katalin E. Kövér, László Csernoch, Serena Carra, Monika Fuxreiter

🔓 FuzPred: A Web Server for the Sequence-Based Prediction of the Context-Dependent Binding Modes of Proteins

Nucleic Acids Research, 2023, gkad214. DOI

Andras Hatos#, João M.C. Teixeira#, Susana Barrera-Vilarmau, Attila Horvath, Silvio CE Tosatto, Michele Vendruscolo, Monika Fuxreiter

Learning to Evolve Structural Ensembles of Unfolded and Disordered Proteins Using Experimental Solution Data

Journal of Chemical Physics, 2023, 158, 174113. DOI | 🔓 Preprint

Oufan Zhang, Mojtaba Haghighatlari, Jie Li, Zi Hao Liu, Ashley Namini, João M.C. Teixeira, Julie D. Forman-Kay, Teresa Head-Gordon

Learning Correlations between Internal Coordinates to improve 3D Cartesian Coordinates for Proteins

Journal of Chemical Theory and Computation, 2023, 19, 14, 4689-4700. DOI | 🔓 [Preprint]

Jie Li, Oufan Zhang, Seokyoung Lee, Ashley Namini, Zi Hao Liu, João M.C. Teixeira, Julie D. Forman-Kay, Teresa Head-Gordon

🔓 SPyCi-PDB: A modular command-line interface for back-calculating experimental datatypes of protein structures

The Journal of Open Source Software, 2023, 8(85), 4861. DOI

Zi Hao Liu, Oufan Zhang, João M.C. Teixeira, Jie Li, Teresa Head-Gordon, Julie D. Forman-Kay

🔓 Protein interactions: anything new?

Essays in Biochemistry, 2022, 66, 7, 821-830. DOI

Susana Barrera-Vilarmau#; João M.C. Teixeira#; Monika Fuxreiter

🔓 IDPConformerGenerator: A Flexible Software Suite for Sampling Conformational Space of Disordered Protein States

Journal of Physical Chemistry A, 2022, 126, 5985–6003. DOI | [Preprint]

João M.C. Teixeira@, Zi Hao Liu, Ashley Namini, Jie Li, Robert M. Vernon, Mickaël Krzeminski, Alaa A. Shamandy, Oufan Zhang, Mojtaba Haghighatlari, Lei Yu, Teresa Head-Gordon, Julie D. Forman-Kay@

🔓 BioExcel Whitepaper on Scientific Software Development

Zenodo, 2022. DOI

Abraham, Mark J.; Melquiond, Adrien S.J.; Ippoliti, Emiliano; Gapsys, Vytautas; Hess, Berk; Trellet, Mikael; Rodrigues, João P.G.L.M.; Laure, Erwin; Apostolov, Rossen; de Groot, Bert L.; Bonvin, Alexandre M.J.J.; Lindahl, Erik; Bauer, Paul; João M.C. Teixeira; Groenhof, Gerrit; Morozov, Dmitry; Honorato, Rodriga; Jimenez, Brian

Protein Dynamics to Define and Refine Protein Ensembles

Journal of Physical Chemistry B, 2022, 126, 9, 1885-1894. DOI

Pavithra M. Naullage, Mojtaba Haghighatlari, Ashley Namini, João M.C. Teixeira, Jie Li, Oufan Zhang, Claudiu C. Gradinaru, Julie D. Forman-Kay, Teresa Head-Gordon

A Methionine Chemical Shift Based Order Parameter Characterizing Global Protein Dynamics

ChemBioChem, 2021, 22, 1001–1004. DOI

Saeed Chashmniam#, João M.C. Teixeira#, Juan Carlos Paniagua, Miquel Pons

🔓 PDB-Tools Web: A User-Friendly Interface for the Manipulation of PDB Files

Proteins: Structure, Function, and Bioinformatics, 2021, 89 (3), 330–335. DOI

Brian Jiménez-García, João M.C. Teixeira, Mikael Trellet, João P.G.L.M. Rodrigues, Alexandre M.J.J. Bonvin

🔓 Taurenmd: A Command-Line Interface for Analysis of Molecular Dynamics Simulations

Journal of Open Source Software, 2020, 5 (50), 2175. DOI

João M.C. Teixeira@

🔓 Insights on Cross-Species Transmission of SARS-CoV-2 from Structural Modeling

PLOS Computational Biology, 2020, 16, e1008449. DOI | [Preprint]

João P.G.L.M. Rodrigues, Susana Barrera-Vilarmau#, João M.C. Teixeira#, Marija Sorokina, Elizabeth Seckel, Panagiotis L. Kastritis, Michael Levitt

🔓 Structural Models of Human ACE2 Variants with SARS-CoV-2 Spike Protein for Structure-Based Drug Design

Scientific Data, 2020, 7 (1), 309. DOI

Marija Sorokina#, João M.C. Teixeira#, Susana Barrera-Vilarmau#, Reinhard Paschke#, Ioannis Papasotiriou#, João P.G.L.M. Rodrigues#, Panagiotis L. Kastritis#

🔓 Extended Experimental Inferential Structure Determination Method in Determining the Structural Ensembles of Disordered Protein States

Communications Chemistry, 2020, 3 (74), 1–12. DOI | [Preprint]

James Lincoff, Mojtaba Haghighatlari, Mickael Krzeminski, João M.C. Teixeira, Gregory-Neal W. Gomes, Claudiu C. Gradinaru, Julie D. Forman-Kay, Teresa Head-Gordon

🔓 Cis-Trans Proline Isomers in the Catalytic Domain of Calcineurin

The FEBS Journal, 2019, 286 (6), 1230–1239. DOI

João M.C. Teixeira, Alicia Guasch, Atilla Biçer, Álvaro Aranguren-Ibáñez, Saeed Chashmniam, Juan Carlos Paniagua, Mercè Pérez-Riba, Ignacio Fita, Miquel Pons

🔓 A Myristoyl-Binding Site in the SH3 Domain Modulates c-Src Membrane Anchoring

iScience, 2019, 12, 194–203. DOI

Anabel-Lise Le Roux, Irrem-Laareb Mohammad, Borja Mateos, Miguel Arbesú, Margarida Gairí, Farman Ali Khan, João M.C. Teixeira, Miquel Pons

🔓 Pdb-Tools: A Swiss Army Knife for Molecular Structures

F1000Res, 2018, 7, 1961. DOI

João P. G. L. M. Rodrigues, João M.C. Teixeira, Mikaël Trellet, Alexandre M.J.J. Bonvin

🔓 The Two Isoforms of Lyn Display Different Intramolecular Fuzzy Complexes with the SH3 Domain

Molecules, 2018, 23 (11), 2731. DOI

João M.C. Teixeira, Héctor Fuentes, Stasė Bielskutė, Margarida Gairi, Szymon Żerko, Wiktor Koźmiński, Miquel Pons

🔓 Farseer-NMR: Automatic Treatment, Analysis and Plotting of Large, Multi-Variable NMR Data

Journal Biomolecular NMR, 2018, 71 (1), 1–9. DOI

João M.C. Teixeira@, Simon P. Skinner, Miguel Arbesú, Alexander L. Breeze, Miquel Pons

🔓 Intramolecular Fuzzy Interactions Involving Intrinsically Disordered Domains

Frontiers Molecular Biosciences, 2018, 5. DOI

Miguel Arbesú, Guillermo Iruela, Héctor Fuentes, João M.C. Teixeira, Miquel Pons

🔓 The Unique Domain Forms a Fuzzy Intramolecular Complex in Src Family Kinases

Structure, 2017, 25 (4), 630-640.e4. DOI

Miguel Arbesú, Mariano Maffei, Tiago N. Cordeiro, João M.C. Teixeira, Yolanda Pérez, Pau Bernadó, Serge Roche, Miquel Pons

🔓 An Oxygen-Sensitive Toxin-Antitoxin System

Nature Communications, 2016, 7, 13634. DOI

Oriol Marimon, João M.C. Teixeira, Tiago N. Cordeiro, Valerie W. C. Soo, Thammajun L. Wood, Maxim Mayzel, Irene Amata, Jesús García, Ainara Morera, Marina Gay, Marta Vilaseca, Vladislav Yu Orekhov, Thomas K. Wood, Miquel Pons

🔓 A C2HC Zinc Finger Is Essential for the RING-E2 Interaction of the Ubiquitin Ligase RNF12

Scientific Reports, 2016, 6 (1), 29232. DOI

Marie-José Bijlmakers, João M.C. Teixeira, Roeland Boer, Maxim Mayzel, Pilar Puig-Sàrries, Göran Karlsson, Miquel Coll, Miquel Pons, Bernat Crosas

A Bis(Pyridine N-Oxide) Analogue of DOTA: Relaxometric Properties of the Gd(III) Complex and Efficient Sensitization of Visible and NIR-Emitting Lanthanide(III) Cations Including Pr(III) and Ho(III)

Chemistry, 2014, 20 (45), 14834–14845. DOI

André F. Martins, Svetlana V. Eliseeva, Henrique F. Carvalho, João M.C. Teixeira, Carlos T.B. Paula, Petr Hermann, Carlos Platas-Iglesias, Stephane Petoud, Éva Tóth, Carlos F.G.C. Geraldes

🔓 Examination of Matrix Metalloproteinase-1 in Solution A PREFERENCE FOR THE PRE-COLLAGENOLYSIS STATE

Journal of Biological Chemistry, 2013, 288 (42), 30659–30671. DOI

Linda Cerofolini, Gregg B. Fields, Marco Fragai, Carlos F.G.C. Geraldes, Claudio Luchinat, Giacomo Parigi, Enrico Ravera, Dmitri I. Svergun, João M.C. Teixeira

🔓 The Catalytic Domain of MMP-1 Studied through Tagged Lanthanides

FEBS Letters, 2012, 586 (5), 557–567. DOI

Ivano Bertini, Vito Calderone, Linda Cerofolini, Marco Fragai, Carlos F.G.C. Geraldes, Petr Hermann, Claudio Luchinat, Giacomo Parigi, João M.C. Teixeira

The Interaction of La3+ Complexes of DOTA/DTPA Glycoconjugates with the RCA120 Lectin: A Saturation Transfer Difference NMR Spectroscopic Study

Journal of Biological Inorganic Chemistry, 2011, 16 (5), 725. DOI

João M.C. Teixeira, David M. Dias, F. Javier Cañada, José A. Martins, João P. André, Jesús Jiménez-Barbero, Carlos F.G.C. Geraldes

Enantioselective Binding of a Lanthanide(III) Complex to Human Serum Albumin Studied by 1H STD NMR Techniques

Organic & Biomolecular Chemistry, 2011, 9 (14), 5047–5050. DOI

David M. Dias, João M.C. Teixeira, Ilya Kuprov, Elizabeth J. New, David Parker, Carlos F.G.C. Geraldes

Peer-review

Reviewer for the following editorials:

Newspaper Highlights

"Entre cães e gatos, galinhas e chimpanzés há animais imunes e susceptíveis ao SARS-CoV-2". Publico.pt, 2020
"Así es el coronavirus que ha mutado en Dinamarca". El País, 2020
"Why some animals don't get COVID". inverse
"Matrix Metalloproteinases: proteins in action". pNMR news, Paramagnetic NMR Newsletters of the FP7-PEOPLE-2012-ITN “PNMR”. PDF, 2012

Book Chapters

Chapter 89: Matrix Metallopeptidase-1/Interstitial Collagenase

Handbook of Proteolytic Enzymes, 4th Edition, Volume 1: Metallopeptidases, August 5, 2025, Elsevier. [Link]

Editors: Neil D. Rawlings, David S. Auld.
Invited by Dr Neil D. Rawlings. EMBL-European Bioinformatics Institute alumnus.

Talks, Teaching, and Workshops

Finding enzymes: horizontal scaling on Google Cloud 2025

Google Cloud Summit Madrid 2025. Invited Talk.

Post on LinkedIn

From modeling multidomain proteins with HADDOCK2 to building HADDOCK3. 2023

20 Years of HADDOCK, Huizen, The Netherlands.

X.com | LinkedIn | Slides

Modular code for a modular software: developing HADDOCK3. 2022

INSTRUCT-ERIC Software Developers Exchange Webinar 5. Invited Talk.

Website | X.com | LinkedIn | Youtube | Slides

Introducing HADDOCK3: Enabling modular integrative modelling pipelines. 2022

BioExcel Webinar. Invited Talk.

Website | X.com | LinkedIn | Youtube | Slides

Introducing HADDOCK3, Enabling modular integrative modelling pipelines. 2022

NMR Meeting at Utrecht University.

Slides

Effective open-science practices for organizing a scientific software repository - extended. 2022

International Symposium on Grids & Clouds (ISGC). Talk, Virtual Conference.

Abstract | Slides

Effective open-science practices for organizing a scientific software repository - short. 2021

OSCU Open Science Symposium - Faculty of Science, Utrecht University, Netherlands. Talk.

Slides on OSF | Slides on GDrive

Protein docking. 2021

EMBL-EBI Structural Bioinformatics virtual course. Hands-on Session tutor.

Modelling Intrinsically Disorder Proteins by experimental data. 2021

SickKids Postdoctoral Seminar Series. Invited Talk.

Slides

A summary of the Farseer-NMR project and its current state. 2019

Invited Researcher at SickKids, Toronto, Canada. Talk. Hosted by: Dr Julie Forman-Kay.

Slides

Lyn's natural isoforms display different fuzzy complexes in UD-SH3 interaction. 2019

Invited Researcher at SickKids, Toronto, Canada. Talk. Hosted by: Dr Julie Forman-Kay.

Slides

Farseer-NMR: automatic treatment, analysis and plotting of large scale, multi-variable BioNMR data – knowledge exchange within the community. 2018

NMR Groups at Utrecht University and Leiden, The Netherlands. Organizer and lecturer. Hosted by: Dr Hugo van Ingen.

Slides | DOI

Farseer-NMR: automatic treatment, analysis and plotting of large scale, multi-variable BioNMR data. 2018

Parc Cientific de Barcelona, CCiTUB, University of Barcelona, Spain. Organizer and lecturer. Hosted by: NMR Facility of the University of Barcelona.

Slides | DOI

Cis-trans proline isomers and ligand binding in the catalytic domain of Calcineurin. 2018

Open seminar, RMBLab, Protein Biophysical Chemistry Group, University of Coimbra, Portugal. Invited Talk.

Slides

Farseer-NMR: automatic treatment, analysis and plotting of large scale, multi-variable BioNMR data 2018

Nuclear Magnetic Resonance Spectroscopy Facility, Faculdade de Ciências e Tecnologia, Universidade Nova de Lisboa, Portugal. Organizer and lecturer. Hosted by: Dr Eurico J Cabrita.

Slides

Farseer-NMR: automatic treatment, analysis and plotting of large scale, multi-variable BioNMR data 2018

Seminar and Hands-on Session at the Workshop NMR FOCUS, PTNMR, University of Coimbra, Portugal. Organizer and lecturer. Hosted by: Dr Rui Brito.

Slides

2D- and 3D-NMR Processing and Analysis with introduction to CCPNMR Analysis Suite v2.4. 2018

Hands-on Session at the Workshop NMR FOCUS, PTNMR, University of Coimbra, Portugal. Lecture at workshop. Hosted by: Dr Rui Brito.

Chemical Shift Perturbation – Protein Based Studies 2018

Workshop NMR FOCUS, PTNMR, University of Coimbra, Portugal. Lecture at workshop. Hosted by: Dr Rui Brito.

Automated NMR data treatment of simple and complex experimental datasets. 2017

1 minute flash-presentation at CECAM Workshop, Paris, France. Talk.

Slides

The concept of Farseer-NMR: automatic treatment and plotting of lage-scale NMR titration data. 2017

Barcelona Biomed Seminars, Parc Scientific de la Universitat de Barcelona, Spain. Organizer and Speaker.

Introductory workshops on Farseer-NMR Software. 2017

CIC bioGUNE Institute, Spain. Organizer and Speaker. Hosted by: Jesús Jiménez-Barbero.

Slides

Analysis of Calcineurin’s structure and conformational changes via methionine labelling NMR spectroscopy. 2016

Barcelona Biomed Seminars, Parc Scientific de la Universitat de Barcelona, Spain. Talk.

Slides

On the ‘tectonics’ of MMP-1 catalyzed collagenolysis: joint use of paramagnetic NMR and computational tools. 2014

Barcelona Biomed Seminars, Parc Scientific de la Universitat de Barcelona, Spain. Talk.

Slides

Joint use of NMR and bioinformatic tools to unveil the dynamics and the ‘tectonic’ enzymatic mechanism of MMP-1 2013

EJIBCE, Oporto, Portugal. Talk.

Slides

MMP-1: intradomain mobility and substract interaction. 2013

Visiting researcher at the NMR Spectroscopy Research Group, Utrech University, The Netherlands. Talk.

Molecular Biology preparation of paramagnetic equipped MMP-1. 2012

Ph.D. Day 3, University of Florence, Italy. Talk.

Characterizing MMP-1 Internal Dynamics. 2011

IX Annual Meeting of CNC – Center for Neuroscience and Cell Biology, Coimbra, Portugal. Talk.

Posters

Presented and as co-author.

IDPConformerGenerator: A Flexible Software Suite for Sampling the Conformational Space of Disordered Protein States 2023

67th Biophysical Society Annual Meeting, San Diego CA USA. Poster

Effectively developing, distributing, and managing a Python package with a large community 2022

ISMB/BOSC, virtual. Abstract | Poster | LinkedIn

Introducing HADDOCK v3: A rebuilt, renewed, modern, extensible, and modular version 2022

Bijvoet Symposium, Utrecht, The Netherlands. Poster

Introducing HADDOCK v3: A rebuilt, renewed, modern, extensible, and modular version 2021

EMBO-Workshop: Advances and challenges in biomolecular simulations. Poster

pdb-tools: a swiss army knife for molecular structures 2019

ISMB/ECCB, Basel, Switzerland. Best poster prize. F1000 poster publication

Automated NMR Data treatment of simple and complex experimental datasets 2017

CECAM Workshop: “Disordered protein segments: revisiting the structure-function paradigm”, Paris, France. Poster

Fuzzy intramolecular interactions in Src family kinases 2017

EUROMAR, Warsaw, Poland.

Farseer - Automatic treatment, calculation and plotting of NMR data. Reducing weeks to seconds 2016

First All Hands Meeting of iNEXT (iNEXT AHM), Alcalá de Henares, Spain. Poster

A python tool to automatically treat, calculate and plot NMR-derived peaklists data 2016

16th CCPN / CCPBioSim joint conference, Buxton, United Kingdom.

A python tool to instantly treat, calculate and plot NMR-derived peaklists data 2016

8th GERMN/5th Iberian NMR Meeting, Valencia, Spain. Awarded Travel Fellowship from GERMN (RSEQ).

A conserved aromatic-residue code shapes the intrinsically disordered Unique domain of c-Src 2016

16th CCPN / CCPBioSim joint conference, Buxton, United Kingdom.

A conserved aromatic-residue code shapes the intrinsically disordered Unique domain of c-Src 2016

EUROMAR, Aarhus, Denmark.

Transient contacts in the instrinsically Disordered Unique Domain of c-Src 2015

Chemical Complexity & Biology, Strasbourg, France.

A C2HC zinc finger is essential for the activity of the RING ubiquitin ligase RNG125 2015

EMBO Conference “Ubiquitin and ubiquitin-like modifiers: from molecular mechanisms to human diseases”, Cavtat, Croatia.

Transient contacts in the instrinsically Disordered Unique Domain of c-Src 2015

VII GERMN Biennal Meeting / IV Iberian NMR Meeting / VI Iberoamerican NMR Meeting, Alcalá de Henares, Spain.

Paramagnetic analysis of collagenolysis by matrix metalloproteinase-1 (MMP-1) 2014

EMBO Workshop – Magnetic Resonance for cellular structural biology, Grosseto, Italy.

Interactions of an essential Zn-finger in the ubiquitin ligase RNF125 2014

4th Annual User group Meeting of BioNMR, Warsaw, Poland.

The interdomain mobility of MMP-1 and its mechanism of interaction with a collagen analogue explored by paramagnetic NMR 2013

5th CAPRI Evaluation Meeting, Utrecht, The Netherlands.

Analysis of conformational heterogeneity in multidomain enzymes: the prologue of the collagenolysis mechanism 2012

IV Ibero-American NMR Meeting – VI GERMN Bienal Meeting – III Iberian NMR Meeting, Aveiro, Portugal.

3D-view of MMP-1 conformational heterogeneity in solution: the prologue of the collagenolysis mechanism 2012

12th Chianti/INSTRUCT Workshop on BioNMR. Electron and Nuclear Relaxation for Structural Biology, Montecatini Terme, Italy.

3D-view of MMP-1 conformational heterogeneity in solution: the prologue of the collagenolysis mechanism 2012

Breakthroughs in NMR of Structural Biology - 2nd BioNMR Annual User Meeting, Portoroz, Slovenia.

3D-view of MMP-1 conformational heterogeneity in solution: the prologue to the collagenolysis mechanism 2012

XXVth International Conference on Mangetic Resonance in Biological Systems, Lyon, France.

Lanthanide binding CLaNP-5.2 for NMR of proteins: exploring PCS and RDCs in MMP-1 internal dynamics 2011

BioNMR and EAST-NMR Annual User Meeting, Brno, Czech Republic.

Interaction of Ln3+-based MRI contrast agents with HSA using Saturation Transfer Difference NMR Techniques 2010

Joint EUROMAR and 17th ISMAR conference / Worldwide Magnetic Resonance conference, Florence, Italy.

Study of the interaction of La3+ complexes of DOTA/DTPA-glycoconjugates with RCA120 using the High Resolution Saturation Transfer Difference (STD) NMR technique 2009

COST Chemistry D38 “Metal Based Systems for Molecular Imaging Applications”, Warsaw, Poland.

Study of the interaction of Ln3+ complexes of BOPTA or DTPA-cholate with HSA and of DOTA/DTPA-glycoconjugates with RCA120 using the High Resolution Saturation Transfer Difference (STD) NMR technique 2008

IV Reunión Bienal del GERM-I Reunión Iberica de RMN, Sevilla, Spain.

Previous Positions

AIRC-funded Research Software Engineer / Data Analyst 2022 - 2023

Monika Fuxreiter Lab

Department of Biomedical Sciences, University of Padua, Italy.

BioExcel-funded Research Software Engineer 2021 - 2022

Alexandre Bonvin lab, Computational Structural Biology Group

Bijvoet Center for Biomolecular Research, Utrecht University. Utrecht, Holland.

NIH-funded Research Software Engineer 2019 - 2021

Julie Forman-Kay lab

Program in Molecular Medicine, Hospital for Sick Children. Toronto, Canada.

Postdoctoral Researcher / Research Software Engineer 2014 - 2018

Miquel Pons lab, BioNMR Group

Department of Inorganic and Organic Chemistry, University of Barcelona. Barcelona, Spain.

FCT-funded Doctorate International Training 2009 - 2013

Claudio Luchinat lab

Centro Risonanze Magnetiche (CERM), University of Florence. Florence, Italy.

FCT-funded Ph.D. candidate 2009 - 2014

Carlos F.G.C. Geraldes lab, Inorganic Biochemistry and Molecular Imaging Group

CNC – Center for Neuroscience and Cell Biology, University of Coimbra. Coimbra, Portugal.

Research Assistant in Nuclear Magnetic Resonance (NMR) 2007 - 2009

Carlos F.G.C. Geraldes lab, Inorganic Biochemistry and Molecular Imaging Group

CNC – Center for Neuroscience and Cell Biology, University of Coimbra. Coimbra, Portugal.

Research Missions

Visiting Collaborator 2018

Group of Structural Biology, School of Medicine Stanford University.

Aim: Simulation of a multicomponent system using OpenMM.

Collaborators: João P.G.L.M. Rodrigues, Susana Barrera-Vilarmau

Group leader: Michael Levitt (2013 Nobel Prize in Chemistry)

Palo Alto, The United States of America.

Visiting Collaborator 2017

Alexander L. Breeze Lab

Astbury Centre for Structural Molecular Biology, University of Leeds

Aim: Development of the Farseer-NMR Software user interface.

Collaborators: Simon P. Skinner and Alexander L. Breeze

Leeds, United Kingdom.

Transnational Knowledge Transfer 2013

Miquel Pons Lab, BioNMR Group, University of Barcelona

Aim: Protocols to purify multidomain proteins for paramagnetic NMR strategies.

Barcelona, Spain.

Visiting PhD. Student 2013

Alexandre Bonvin Lab, Computational Structural Biology Group

Bijvoet Center for Biomolecular Research, Utrecht University

Aim: Protein-protein docking calculations and analysis using HADDOCK Web Server.

Collaborators: João P.G.L.M. Rodrigues

Utrecht, Holland.

Short Term Scientific Mission 2009

Petr Hermann

Charles University, Prague, Czech Republic

Aim: Chemical Synthesis of Metal-based systems for Molecular Imaging Applications and Paramagnetic Solution NMR Probes.

Prague, Czech Republic.

Short Term Scientific Mission 2009

Jesús Jiménez-Barbero Lab

NMR Group, Centro de Investigaciones Biológicas (CIB), CSIC, Spain.

Aim: Protein-ligand interaction studies using Autodock 4.

Madrid, Spain.

Funding & Awards

Aberrant condensates as drug targets for cancer

Fondazione AIRC per la Ricerca sul Cancro ETS, AIRC IG id. 26229

PI: Monika Fuxreiter, University of Padua, Italy.

Virtual Research Environment for Integrative Modelling of Biomolecular Complexes

i-VRESSE, The Netherlands eScience Center, eTEC 2020

PI: Alexandre MJJ Bonvin, Utrecht University, Holland.

EGI Advanced Computing for EOSC

EGI-ACE, EU Horizon 2020, Contract 101017567

PI: EGI Foundation

Calculating Dynamic Ensembles of Intrinsically Disordered Proteins

National Institute of Health (NIH) - R01 GM127627-01

PI: Julie Forman-Kay, SickKids Research Institute, Toronto, Canada.

BioExcel Centre of Excellence for Computational Biomolecular Research: BioExcel-2

BioExcel, EU Horizon 2020, Contract 823830

PI: Alexandre MJJ Bonvin, Utrecht University, Holland.

El elemento regulador N-terminal de Src: métodos y estrategia hacia una nueva generación de fármacos contra el cáncer

MINECO-FEDER, Contract BIO2016-78006-R

PR: Miquel Pons, University of Barcelona, Spain.

Src unique domain signalling in colorectal cancer

Maratò 2012 cancer-20132830

PI: Miquel Pons, University of Barcelona, Spain.

The Unique Domain of c-Src: disordered protein domains at the cellular membrane surface

MINECO-FEDER, Contract BIO2013-45793-R

PI: Miquel Pons, University of Barcelona, Spain.

New methods and new concepts for the study of biomolecules with dynamic interactions involved in cell signalling

MICINN, Contract BIO2010-15683

PI: Miquel Pons, University of Barcelona, Spain.

Transnational Activity Fellowship. Scientific Knowledge Transfer to and within BioNMR

BIO-NMR: NMR for structural Biology. Task 3.4, EU-FP7 Contract no. 261863

PI: Miquel Pons and João M.C. Teixeira, University of Barcelona, Spain.

Chemical Synthesis of Metal-based systems for Molecular Imaging Applications and Paramagnetic Solution NMR Probes

Short Term Scientific Mission. COST Action D38, COST-STSM-D38-05161

PI: João M.C. Teixeira and Carlos FGC Geraldes, Charles University, Czech Republic.

Paramagnetic NMR of Proteins to study the collagenolytic mechanism of MMP-1

Foundation of Science and Technology (FCT), Doctoral Fellowship. Contract: SRFH/BD/45928/2008

PI: João M.C. Teixeira and Carlos FGC Geraldes, University of Coimbra, Portugal.

Nanostructures addressed to Multimodal Medical Molecular Imaging

COMPETE, Contract PTDC/QUI/70063/2006

PI: Carlos FGC Geraldes, University of Coimbra, Portugal.

Development of new lanthanide–based compounds as MRI Molecular Imaging agents

Network of Excellence (NoE) “European Molecular Imaging Laboratory” (EMIL), LSCH-2004-503569

PI: Carlos FGC Geraldes, University of Coimbra, Portugal.

Award of “Best Student” ROTARY Club 1998

Secondary School “Escola E.B. 2-3 D. José de Vila Real de Santo António, Portugal.

Continuous Learning

Preparing for Google Cloud Certification: Cloud Architect 2025

Coursera Course Certificate.

Preparing for your Professional Cloud Architect Journey 2025

Coursera Course Certificate.

Architecting with Google Kubernetes Engine: Foundations 2025

Coursera Course Certificate.

Reliable Google Cloud Infrastructure: Design and Process 2025

Coursera Course Certificate.

Elastic Google Cloud Infrastructure: Scaling and Automation 2025

Coursera Course Certificate.

Essential Google Cloud Infrastructure: Core Services 2025

Coursera Course Certificate.

Essential Google Cloud Infrastructure: Foundation 2025

Coursera Course Certificate.

Google Cloud Fundamentals: Core Infrastructure 2025

Coursera Course Certificate.

Inferential Statistical Analysis with Python 2021

Coursera Course Certificate.

Academic Writing in English 2019

Series of workshops and classes, School of Graduate Studies, University of Toronto, Canada.

Environmental Omics Integration & Modelling, International Workshop 2017

Cosmo Caixa, Barcelona, Spain.

CECAM Workshop: "Disordered protein segments: revisiting the structure-function paradigm" 2017

Paris, France.

Python for Scientists 2015

University of Barcelona, Spain.

Advanced Isotopic Labelling Methods for Integrated Structural Biology, AILM2015, International Workshop 2015

IBS-Grenoble, France.

Communication and Scientific Culture 2014

Campus Gutenberg, Universitat Pompeu Fabra, Spain.

Iniciació a la utilizació dels equips de RMN, Varian en mode automàtic 2014

University of Barcelona, Spain.

Advanced methods for the investigation of other structural data with NMR data 2013

CERM, University of Florence, Italy.

Principles and rules for security and accident prevention in CERM’s laboratories 2012

CERM, University of Florence, Italy.

Learn to Program: The Fundamentals 2012

Cousera.org, University of Toronto, Canada.

Introduction to the Python Programming language, V Edition 2012

CEV – University of Granada, Spain.

Writing in Sciences 2012

Cousera.org – Stanford University, USA.

Biomedical Magnetic Resonance: Molecular Imaging and Metabolism 2009

Center for Neuroscience and Cell Biology PDBEB Program, Portugal.

7th Short Course of the Portuguese Biophysical Society – Biospectroscopy and Imaging 2007

Portuguese Biophysical Society, Portugal.

Mentoring Experience

Technical Leadership & Mentorship @Zymvol: Directing strategic technical decision-making while promoting a blameless, growth-oriented team culture.

Students I have mentored and dedicated throughout the years. Thanks to all of them for the fantastic moments and the two-way learning.

Zi Hao Liu 2023

Ph.D. student, SikKids, Toronto, Canada.

Zi Hao Liu 2022

MSc graduate student, SikKids, Toronto, Canada.

Ashley Nanimi 2021

Summer Student, SickKids, Toronto, Canada.

Serene Rodrigues 2020

COOP Student SickKids-University of Waterloo, Toronto, Canada.

Alaa Shamandy 2020

Research student SickKids-University of Toronto, Toronto, Canada.

Héctor Fuentes de la Osa 2018