Nuno (F. B.) Oliveira
Computational Biochemist
Experience
Author
Journal of Chemical Information and Modeling
CpHMD Container - a stochastic constant-pH Molecular dynamics container available to all. (Manuscript in preparation)
Author
Journal of Chemical Information and Modeling
Improving the Estimation of pKa Values for All Titrable Amino Acids at the Water/Membrane Interface (In Review process)
Author
Journal of Chemical Theory and Computation
Toward Accurate pH-Dependent Binding Constant Predictions Using Molecular Docking and Constant-pH MD Calculations.
Author
Biophys. J.
Constant-pH MD Simulations of the Protonation-Triggered Conformational Switching in Diphtheria Toxin Translocation Domain
Author
Pharmacol. Res.
A novel combinatory treatment against a CDDP-resistant non-small cell lung cancer based on a Ruthenium(II) cyclopentadienyl compound
Author
Journal of Chemical Information and Modeling
Interfacial Dynamics and Growth Modes of B2-Microglobulin Dimers
Author
Journal of Medicinal Chemistry
Fighting Multidrug Resistance with Ruthenium-Cyclopentadienyl Compounds: Unveiling the Mechanism of P-gp Inhibition
Author
Toxins
Histidine Protonation and Conformational Switching in Diphtheria Toxin Translocation Domain
Author
J. Chem. Inf. Model.
MembIT - a tool to calculate solute membrane insertions and deformations in molecular dynamics simulations
Author
Journal of Chemical Information and Modeling
Novel US-CpHMD Protocol to Study the Protonation-Dependent Mechanism of the ATP/ADP Carrier
Author
Computational and Structural Biotechnology Journal
Predicting stable binding modes from simulated dimers of the D76N mutant of B2-microglobulin
Author
Springer US
pKa Calculations in Membrane Proteins in Methods in Molecular Biology: Computational Design of Membrane Proteins, Volume 2315, Editors: Irina Moreira, Joana Mourão, Miguel Machuqueiro. In Press.
Author
Journal of Chemical Theory and Computation
Improved GROMOS 54A7 Charge Sets for Phosphorylated Tyr, Ser, and Thr to Deal with pH-Dependent Binding Phenomena
Industry Experience
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Experienced in Biotechnology, Chemical, and Pharmaceutical.
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Experienced in Research and Development.
Summary
Computational biochemist currently integrated in the Machuqueiro Computational Biophysics Lab, specializing in constant-pH MD, enhanced sampling methods, membrane biophysics, and Al-driven peptide/drug design.
Experienced in computational technique application to health related problems, force field development, and inter-disciplinary collaboration across computational and wet-lab groups.
Skills
Programming & Tools
- Python, Bash, Awk, Sed
- Docker & Singularity Containerization
- Git, Linux/unix Environments
- Ai/ml Model Integration For Drug/peptide Design
Modeling & Simulation Tools
- Md, Enhanced Sampling (Us, Reus), Stochastic Cphmd
- Gromacs, Amber, Charmm, Gromos Force-fields
- Docking (Autodock, Haddock)
- Continuum Electrostatics, Membrane Systems Modelling
Domain Expertise
- Ph-dependent Protein/drug Behavior
- Biological Membrane Biophysics
- Peptide Binder Design
- Protein Conformational Dynamics
Languages
Education
University of Lisbon
Ph.D. in Biochemistry · Biochemistry · Lisbon, Portugal
University of Lisbon
MSc in Biochemistry · Biochemistry · Lisbon, Portugal
University of Lisbon
BSc in Biochemistry · Biochemistry · Lisbon, Portugal
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Experience
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