João Miguel Correia Teixeira Email & Phone Number

Salamanca, Castilla And Leon, Spain

Padua, Veneto, Italy

AIRC (Fondazione AIRC per la Ricerca sul Cancro) fellow.During this period, I analyzed a panoply of data available on Intrinsically Disordered Proteins (IDPs) to understand how intra- and intermolecular interactions in IDP/IDRs and with folded domains break conventional paradigms to adopt conformational binding ensembles (fuzzy binding) that describe rigid and dynamic interactions that ultimately govern the formation of biomolecular condensates. The data analyzed englobes structural data from the RCSB database and molecular dynamics simulations.

Utrecht, Utrecht, Netherlands

Lead software engineer and structural biologist for HADDOCK 3. BioExcel-2 fellow.Within the BioExcel-2 project (E.U. https://doi.org/10.3030/823830), I was responsible for designing and implementing the architecture of the HADDOCK-3 infrastructure for macromolecular docking. HADDOCK is the world's most used academic software for modeling macromolecular interactions, where version 2 has +40.000 users in over 144 countries in 2023. I designed HADDOCK3 to allow users to build custom pipelines from modular execution units, a paradigm change from version 2, which had a rigid protocol. During this period, I presented two main talks explaining best practices and strategies to develop maintainable and documented software for large codebases (available on YouTube, see below).The project continued to grow after my departure - demonstrating my commitment and capacity to creating sustainable, readable, and well-documented software - and now sustains new research in the group.

Toronto, Canada Area

NIH Postdoctoral Fellow.I conceptualized and developed a software suite to model highly flexible proteins (a.k.a. intrinsically disordered proteins - IDPs) - named IDPConformerGenerator. This software is an ecosystem of coherent CLIs that mines, filters, catalogs, and finally samples structural data from the RCSB PDB database to generate physically meaningful computational models of IDPs and IDRs.IDPs (highly flexible protein regions) represent 30% of the cellular proteome. They are involved in all sorts of biochemical processes that govern health and disease. Therefore, IDPs are now considered pharmaceutical targets of the future. IDPConformerGenerator is unique for its flexibility, modularity, openness, and quality of the output models. For this, it plays a crucial role in describing IDPs computationally - a much-needed step to develop new therapeutic drugs.The project continued to evolve seamlessly after my departure, and I continued mentoring students working on this project.

Salamanca, Spain

During this period, I was an active, independent, and ad-honorem scientific researcher in computational structural biology. During this period, I developed and contributed to open-source scientific software to treat structural data (protein structures) and analyze molecular dynamics trajectories.

Barcelona Area, Spain

I leveraged and improved my skills in Nuclear Magnetic Resonance (data acquisition and computational analysis) and molecular biology (cloning, expression, purification, etc.) to study flexible protein systems and fuzzy biomolecular complexes between intrinsically disordered proteins and folded domains to describe innovative biochemical targets for pharmaceutical research.During this period, I developed an intense interest in developing software that could solve our research bottlenecks. I conceptualized and developed a whole software program to streamline the analysis and plotting of large datasets of multi-variable NMR data, automatizing tedious and error-prone operations (if performed by humans). I published this software in a high-impact journal in the field and performed several workshops at different institutions to explain and disseminate FarSeer-NMR.

Coimbra Area, Portugal

Project funded by PhD Scholarship from Fundação para a Ciência e a Tecnologia (FCT), entitled: "Paramagnetic NMR of Proteins to study the Collagenolytic Mechanism of MMP-1". Supervisor: Prof. Dr. Carlos F. G. C. Geraldes (CNC, Coimbra) and Co-supervisor: Prof. Claudio Luchinat (CERM, Florence).I used paramagnetic NMR to investigate how the movements of the MMP-1 domains govern the cleavage of the triple helical collagen - a process needed for tumors to metastasize. We concluded the flexible linker tethering the two MMP-1 domains orchestrates the domain's movements toward a collagenolytic-prone state. We presented also the first in-solution model of MMP-1 bound to a collagen triple helix analog which agrees with a multitude of experimental data.

Florence Area, Italy

I perform the experiments needed for my thesis project at CERM. These englobe prepare samples of large multi-domain proteins functionalized with paramagnetic lanthanides and acquire and analyze NMR data of such samples.

Prague, The Capital, Czech Republic

Work co-financed by COST D38 Actions. Supervised by Prof. Dr. Petr Hermann, Charles University, Prague.Chemical synthesis of Metal-based systems for Molecular Imaging Applications and Paramagnetic Solution NMR Probes; namely, synthesis of CLaNP-5.2 tag and its precursors.

Coimbra Area, Portugal

Describing the interaction mode between novel MRI contrast agents and their protein receptors. I was responsible for developing, maintaining, acquiring, and analyzing nuclear magnetic resonance (NMR) experiments.

Coimbra Area, Portugal

Thesis title: "Study of the interaction of Ln(III) complexes of targeted contrast agents to HSA and RCA120 binding models using High-Resolution Saturation Transfer Difference (STD) NMR techniques". Supervisor: Dr. Carlos F.G.C. GeraldesI studied new lanthanide-based contrast-agents for MRI applications using Nuclear Magnetic Resonance (NMR) by investigating the molecular interactions with their protein receptors.

Doctor Of Philosophy (Ph.D.), Biochemistry, Biophysics And Molecular Biology, Approved Unanimously With Distinction And Honours

Paramagnetic NMR of Proteins to Study the Collagenolitic Mechanism of MMP-1.

Licentiate Degree, Biochemistry

Study of the interaction of Ln3+ complexes of targeted contrast agents to HSA and RCA120 binding models using high resolution Saturation.