???global.info.a_carregar???
Identification

Personal identification

Full name
Pedro Rafael da Silva Álvaro Magalhães

Citation names

  • Magalhães, Pedro R.

Author identifiers

Ciência ID
4817-573A-D201
ORCID iD
0000-0003-4118-2800
Google Scholar ID
gf0_kX0AAAAJ

Email addresses

  • prmagalhaes@fc.ul.pt (Professional)

Addresses

  • Instituto de Biosistemas e Ciências Integrativas. Faculdade de Ciências da Universidade de Lisboa, Edifício C8, Campo Grande, 1749-016, Lisboa, Lisboa, Portugal (Professional)

Knowledge fields

  • Natural sciences - Biological Sciences - Biophysics

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1) Advanced (C1)
Spanish; Castilian Beginner (A1) Intermediate (B1) Beginner (A1) Beginner (A1)
French Beginner (A1) Beginner (A1) Beginner (A1) Beginner (A1)
Education
Degree Classification
2017/11/23
Concluded
 Bioquímica (Doutoramento)
Major in Simulação Biomolecular
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
"Inclusion of Protonation Effects in Simulation of Proteins in Membrane Environments" (THESIS/DISSERTATION)
 Unanimously approved
2008 - 2009
Concluded
 Bioquímica (Mestrado)
Universidade de Lisboa Faculdade de Ciências, Portugal
"Interaction between the neuropeptide kyotorphin and a lipid bilayer: a constant-pH molecular dynamics study" (THESIS/DISSERTATION)
 18
2004 - 2007
Concluded
 Bioquímica (Licenciatura)
Universidade de Lisboa Faculdade de Ciências, Portugal
 17
Affiliation

Science

Category
Host institution 		Employer
2021/11/10 - Current Contracted Researcher (Research) Universidade de Coimbra Centro de Neurociências e Biologia Celular, Portugal
2019/01/01 - 2020/12/31 Contracted Researcher (Research) FCiênciasID Associação para a Investigação e Desenvolvimento de Ciências, Portugal
Universidade de Lisboa Instituto de Biossistemas e Ciências Integrativas, Portugal
2018/03/16 - 2018/12/01 Postdoc (Research) Fundação da Faculdade de Ciências da Universidade de Lisboa, Portugal

Others

Category
Host institution 		Employer
2010/02/15 - 2010/10/31 Bolseiro de Investigação Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
Outputs

Publications

Book chapter
  1. "Identification of Pan-Assay INterference compoundS (PAINS) Using an MD-Based Protocol". 263-271. Springer {US, 2021.
    10.1007/978-1-0716-1468-6_15
Conference poster
  1. Magalhães, Pedro R.; Reis, Pedro B P S (BA1A-8F17-5F20); Vila-Viçosa, Diogo; Machuqueiro, Miguel; Victor, Bruno (5A17-09B5-48A5). Corresponding author: Magalhães, Pedro R.. "Identification of membrane PAINS via an optimized computational protocol". Paper presented in 8th EJIBCE, Coimbra, Portugal, 2021.
  2. Magalhães, Pedro R.; Reis, Pedro B P S (BA1A-8F17-5F20); Vila-Viçosa, Diogo; Machuqueiro, Miguel; Victor, Bruno (5A17-09B5-48A5). Corresponding author: Magalhães, Pedro R.. "Development of a Novel Computational Protocol for the Identification of Membrane PAINS". Paper presented in Computer Simulation and Theory of Macromolecules, Hunfeld Online Workshop, 2021.
  3. Magalhães, Pedro R.; Reis, Pedro B P S (BA1A-8F17-5F20); Vila-Viçosa, Diogo; Machuqueiro, Miguel; Victor, Bruno (5A17-09B5-48A5). "Speeding-up the identification of membrane PAINS with a new computational approach". Paper presented in Ciências Research Day, 2020.
  4. Magalhães, Pedro R.; Reis, Pedro B P S; Vila-Viçosa, Diogo; Machuqueiro, Miguel; Victor, Bruno. "Refining an umbrella-sampling protocol to describe membrane PAINS". Paper presented in EJIBCE 2019 (7th Encontro de Jovens Investigadores de Biologia Computacional Estrutural), Lisboa, Portugal, 2019.
  5. Magalhães, Pedro R.; Vila-Viçosa, Diogo; Machuqueiro, Miguel; Victor, Bruno. "Structural characterization of Aquaporin-1 and evaluation of a PMF based protocol to determine water permeability rates". Paper presented in EJIBCE 2019 (7th Encontro de Jovens Investigadores de Biologia Estrutural Compucacional), Lisboa, Portugal, 2019.
  6. Magalhães, Pedro R.; Reis, Pedro B P S; Vila-Viçosa, Diogo; Machuqueiro, Miguel; Victor, Bruno. "Computational Characterization of Membrane PAINS". Paper presented in Joint 12th EBSA 10th ICBP-IUPAP Biophysics Congress, Madrid, Spain, 2019.
  7. Magalhães, Pedro R.; Vila-Viçosa, Diogo; Machuqueiro, Miguel; Victor, Bruno. "Computational prediction of water permeability rates in Aquaporin-1". Paper presented in Joint 12th EBSA congress 10th ICBP-IUPAP Congress, Madrid, Spain, 2019.
  8. Magalhães, Pedro R.; Reis, Pedro B P S; Vila-Viçosa, Diogo; Machuqueiro, Miguel; Victor, Bruno. "Optimization of a computational protocol to characterize membrane PAINS". Paper presented in Workshop on Integrative Approaches to Protein Folding & Aggregation, Lisboa, Portugal, 2019.
  9. Magalhães, Pedro R.; Vila-Viçosa, Diogo; Silva, Tomás; Machuqueiro, Miguel. "pH effects on PG/PC and PS/PC lipid binary mixtures". Paper presented in EJIBCE 2018 (6th Encontro de Jovens Investigadores de Biologia Computacional Estrutural), Porto, Portugal, 2018.
    10.3390/mol2net-04-05922
  10. Magalhães, Pedro R.; Vila-Viçosa, Diogo; Silva, Tomás; Machuqueiro, Miguel. "pH effects on PG/PC and PS/PC lipid binary mixtures: a CpHMD study". Paper presented in Protein Electrostatics Conference, Serbia, Belgrade, 2018.
  11. Magalhães, Pedro R.; Campos, Sara R. R.; Oliveira, A. Sofia. F.; Soares, Cláudio M.; Baptista, António M.. "pH gradients in continuum electrostatics calculations of Ccox". Paper presented in EJIBCE 2014 (2nd Encontro de Jovens Investigadores de Biologia Estrutural Computacional), Coimbra, Portugal, 2014.
  12. Magalhães, Pedro R.; Campos, Sara R. R.; Oliveira, A. Sofia. F.; Soares, Cláudio M.; Baptista, António M.. "Continuum electrostatics calculations of Ccox in the presence of a pH gradient". Paper presented in Protein Electrostatics Satellite Meeting of EBEC 2014, Lisboa, Portugal, 2014.
  13. Magalhães, Pedro R.; Campos, Sara R. R.; Oliveira, A. Sofia. F.; Soares, Cláudio M.; Baptista, António M.. "Titration of key sites in bacteriorhodopsin in the presence of a pH gradient". Paper presented in Frontiers in dynamics simulations of biological molecules, Barcelona, Spain, 2013.
  14. Magalhães, Pedro R.; Campos, Sara R. R.; Oliveira, A. Sofia. F.; Soares, Cláudio M.; Baptista, António M.. "Probing energy transduction mechanisms in bacteriorhodopsin using electrostatic calculations". Paper presented in EBSA 2013 (9th European Biophysics Congress), Lisboa, Portugal, 2013.
  15. Magalhães, Pedro R.; Campos, Sara R. R.; Oliveira, A. Sofia. F.; Soares, Cláudio M.; Baptista, António M.. "Continuum electrostatics study of energy transduction mechanisms in bacteriorhodopsin". Paper presented in COST Action CM0902 Training School on Molecular machineries for ion translocation across membranes, Lisboa, Portugal, 2013.
  16. Magalhães, Pedro R.; Campos, Sara R. R.; Oliveira, A. Sofia F.; Baptista, António M... "Study of energy transduction in bacteriorhodopsin using continuum electrostatics methods". Paper presented in 3rd ITQB PhD Students' Meeting, Oeiras, Portugal, 2012.
  17. Magalhães, Pedro R.; Machuqueiro, Miguel; Baptista, António M.. "The effect of pH on the interaction between the neuropeptide kyotorphin and a lipid bilayer: a molecular simulation study". Paper presented in X Girona Seminar on Theoretical and Computational Chemistry for the Modeling of Biochemical Systems: From Theory to Applications, Girona, Spain, 2012.
  18. Baptista, António M.; Magalhães, Pedro R.; Campos, Sara R. R.; Machuqueiro, Miguel. "Ionization of a neuropeptide unaffected by the membrane environment: simulations of kyotorphin using constant-pH MD and linear response approximation". Paper presented in Gordon Research Conference on Protons & Membrane Reactions, San Francisco, USA, 2012.
  19. Magalhães, Pedro R.; Machuqueiro, Miguel; Baptista, António M.. "Simulation of explicit bilayers with constant-pH molecular dynamics". Paper presented in 5th Theoretical Biophysics International Symposium, Madeira, Portugal, 2011.
  20. Magalhães, Pedro R.; Machuqueiro, Miguel; Baptista, António M.. "Constant-pH molecular dynamics simulations of the neuropeptide kyotorphin in a lipid bilayer". Paper presented in Frontiers in Protein Research Interbio Symposium, Oeiras, Portugal, 2011.
  21. Magalhães, Pedro R.; Machuqueiro, Miguel; Baptista, António M.. "Constant-pH molecular dynamics simulations of explicit membranes: study of peptide-bilayer interactions". Paper presented in V Spanish-Portuguese Biophysics Congress, Zaragoza, Spain, 2010.
  22. Magalhães, Pedro R.; Machuqueiro, Miguel; Baptista, António M.. "Interaction between kyotorphin and biological membranes: a constant-pH MD study". Paper presented in Expanding the Frontiers of Molecular Dynamics Simulations in Biology Conference, Barcelona, Spain, 2009.
Journal article
  1. Enrico Cadoni; Pedro R. Magalhães; Rita M. Emídio; Eduarda Mendes; Jorge Vítor; Josué Carvalho; Carla Cruz; Bruno L. Victor; Alexandra Paulo. "New (Iso)quinolinyl-pyridine-2,6-dicarboxamide G-Quadruplex Stabilizers. A Structure-Activity Relationship Study". Pharmaceuticals (2021): https://doi.org/10.3390/ph14070669.
    10.3390/ph14070669
  2. Magalhães; Machuqueiro; Almeida; Melo; D. S. Cordeiro; Verde; Gümüs; Moreira; D. G. Correia. "Dynamical Rearrangement of Human Epidermal Growth Factor Receptor 2 upon Antibody Binding: Effects on the Dimerization". Biomolecules 9 11 (2019): 706. http://dx.doi.org/10.3390/biom9110706.
    10.3390/biom9110706
  3. Magalhães, Pedro R.; Oliveira, A. Sofia F.; Campos, Sara R. R.; Soares, Cláudio M.; Baptista, António M.. "Effect of a pH Gradient on the Protonation States of Cytochrome c Oxidase: A Continuum Electrostatics Study". Journal of Chemical Information and Modeling 57 2 (2017): 256-266. http://dx.doi.org/10.1021/acs.jcim.6b00575.
    Published • 10.1021/acs.jcim.6b00575
  4. Conceição, Katia; Magalhães, Pedro R.; Campos, Sara R. R.; Domingues, Marco M.; Ramu, Vasanthakumar G.; Michalek, Matthias; Bertani, Philippe; et al. "The anti-inflammatory action of the analgesic kyotorphin neuropeptide derivatives: insights of a lipid-mediated mechanism". Amino Acids 48 1 (2015): 307-318. http://dx.doi.org/10.1007/s00726-015-2088-9.
    Published • 10.1007/s00726-015-2088-9
  5. Magalhães, Pedro R.; Machuqueiro, Miguel; Baptista, António M.. "Constant-pH Molecular Dynamics Study of Kyotorphin in an Explicit Bilayer". Biophysical Journal 108 9 (2015): 2282-2290. http://dx.doi.org/10.1016/j.bpj.2015.03.052.
    Published • 10.1016/j.bpj.2015.03.052
Thesis / Dissertation
  1. Magalhães, Pedro R.. "Inclusion of protonation effects in the simulation of proteins in membrane environments". PhD, Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, 2017. https://run.unl.pt/handle/10362/78959.
  2. Magalhães, Pedro R.. "Interaction between the neuropeptide kyotorphin and a lipid bilayer: a constant-ph molecular dynamics study". Master, Universidade de Lisboa Departamento de Química e Bioquímica, 2009. http://repositorio.ul.pt/handle/10451/3498.
Activities

Oral presentation

Presentation title Event name
Host (Event location)
2014/11/06 pH gradients in continuum electrostatics calculations of Ccox 5th ITQB PhD Students' Meeting
ITQB NOVA (Oeiras, Portugal)
2013/05/15 Continuum electrostatics study of energy transduction mechanisms in bacteriorhodopsin COST Action CM0902 Training School on Molecular machineries for ion translocation across membrane
(Lisboa, Portugal)
2013/04/04 Inclusion of pH gradients in membrane calculations 2nd Portuguese Biomolecular Modelling Meeting
(Foz do Arelho, Portugal)
2012/06/24 Interaction between the neuropeptide kyotorphin and lipid membranes using constant-pH molecular dynamics methods 2nd EBSA Course on: Membrane Biophysics & Lipid/Protein Interaction
(Lacanau, France)
2011/05/12 Lys/Arg Interactions in G53A6 1st Portuguese Biomolecular Modelling Meeting
(Tavira, Portugal)

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2020/10 - 2021/07 Identification of new inhibitors of the p53-MDM2 complex as potentially novel anticancer therapies
Co-supervisor
 Projeto (Degree)
Universidade de Lisboa Departamento de Química e Bioquímica, Portugal
2020/10 - 2021/06 Computer-assisted interaction studies of DNA-G4 with newly identified stabilizers
Co-supervisor
 Projeto (Degree)
Universidade de Lisboa Departamento de Química e Bioquímica, Portugal

Event organisation

Event name
Type of event (Role) 		Institution / Organization
2019/01/01 - 2019/12/20 EJIBCE 2019 (7th Encontro de Jovens Investigadores de Biologia Computacional Estrutural). Main duties: website design, updates and support; graphic materials editing and design. (2019/12/20 - 2019/12/20)
Conference (Member of the Organising Committee)
 Universidade de Lisboa Faculdade de Ciências, Portugal
2016 - 2016 EJIBCE 2016 (4th Encontro de Jovens Investigadores de Biologia Computacional Estrutural). Main duties: website design, updates and support; graphic materials editing and design. (2016/12/21 - 2016/12/21)
Conference (Member of the Organising Committee)
 Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
2014 - 2014 PROTELEC 2014 (Protein Electrostatics Meeting) Main duties: website design, updates and support; graphic materials editing and design (2014/07/08 - 2014/07/11)
Conference (Member of the Organising Committee)
 Universidade de Lisboa Faculdade de Ciências, Portugal

Course / Discipline taught

Academic session Degree Subject (Type) Institution / Organization
2019/07/10 - 2019/07/11 Como se organizam e constroem as moléculas? Estruturas (bio)químicas em 3 dimensões - Workshop VI Encontro Internacional da Casa das Ciências (Ensino de Professores de Física e Química do Ensino Secundário) (Outros) Universidade de Lisboa Faculdade de Ciências, Portugal