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Membrane proteins – development of new computational approaches and its application to G-Protein Coupled Receptors

Total Cost €


EC-Contrib. €






Project "MEMBRANEPROT" data sheet

The following table provides information about the project.


Organization address
postcode: 3584 CS

contact info
title: n.a.
name: n.a.
surname: n.a.
function: n.a.
email: n.a.
telephone: n.a.
fax: n.a.

 Coordinator Country Netherlands [NL]
 Project website
 Total cost 177˙598 €
 EC max contribution 177˙598 € (100%)
 Programme 1. H2020-EU.1.3.2. (Nurturing excellence by means of cross-border and cross-sector mobility)
 Code Call H2020-MSCA-IF-2014
 Funding Scheme MSCA-IF-EF-ST
 Starting year 2016
 Duration (year-month-day) from 2016-03-01   to  2018-02-28


Take a look of project's partnership.

# participants  country  role  EC contrib. [€] 
1    UNIVERSITEIT UTRECHT NL (UTRECHT) coordinator 177˙598.00


 Project objective

Protein-protein tridimensional (3D) structures are fundamental for structural biology and drug discovery. Many docking algorithms were developed for that purpose, but they have limited accuracy in generating native-like structures and identifying the most correct one, particularly in the case of membrane proteins such as G-protein Coupled Receptors (GPCRs). In order to deal with these complex systems and overcome the limitations of existing software, we will develop and optimize computational approaches and construct novel combinations of mature methodologies, to serve in the study of membrane proteins in general. In particularly, we will focus in: i) improving the search and scoring algorithms for the docking process of membrane proteins, ii) developing software to accurately predict the high-order oligomers interfacial residues, and iii) constructing a docking algorithm able to predict their 3D oligomeric structure. Our new approaches will be applied to a relevant biological system: the dopamine receptor type 2 (D2R), a typical member of Class A GPCRs involved in many cognitive, emotional and motor functions. D2R acts by ligand-dependent signalling through two major systems: the G-proteins, and the Arrestin proteins (Arr-s). How ligands determine the preference for one or the other is not yet understood at the molecular level, and this precludes both the characterization of pathway selectivity and the design of biased ligands. More importantly, the physiological relevance of oligomerization for this process is still topic of vigorous debate. Therefore, building on both my unique expertise and Prof. Bonvin well-known impact in methodological development, this project will yield novel methods and approaches to serve in the study of membrane protein systems and their functional mechanisms, benefiting the entire research field. It will also provide truly new fundamental knowledge and insights into the selectivity of D2R signalling.


year authors and title journal last update
List of publications.
2017 Irina S. Moreira, Panos Koukos, Rita Melo, Jose G. Almeida, Antonio J. Preto, Jorg Schaarschmidt, Mikael Trellet, Zeynep H. Gumus, Joaquim Costa, Alexandre M.J.J. Bonvin
Spoton: A Machine-Learning Approach for Hot-Spot Determination
published pages: 45a, ISSN: 0006-3495, DOI: 10.1016/j.bpj.2016.11.284
Biophysical Journal 112/3 2019-06-18
2018 Zeynep Kurkcuoglu, Panagiotis I. Koukos, Nevia Citro, Mikael E. Trellet, J. P. G. L. M. Rodrigues, Irina S. Moreira, Jorge Roel-Touris, Adrien S. J. Melquiond, Cunliang Geng, Jörg Schaarschmidt, Li C. Xue, Anna Vangone, A. M. J. J. Bonvin
Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2
published pages: 175-185, ISSN: 0920-654X, DOI: 10.1007/s10822-017-0049-y
Journal of Computer-Aided Molecular Design 32/1 2019-06-18
2017 Jose G. Almeida, Antonio J. Preto, Panagiotis I. Koukos, Alexandre M.J.J. Bonvin, Irina S. Moreira
Membrane proteins structures: A review on computational modeling tools
published pages: 2021-2039, ISSN: 0005-2736, DOI: 10.1016/j.bbamem.2017.07.008
Biochimica et Biophysica Acta (BBA) - Biomembranes 1859/10 2019-06-18
2018 Agostinho Lemos, Rita Melo, Irina S. Moreira, M. Natália D. S. Cordeiro
Computer-Aided Drug Design Approaches to Study Key Therapeutic Targets in Alzheimer’s Disease
published pages: 61-106, ISSN: , DOI: 10.1007/978-1-4939-7404-7_3
Neuromethods 2019-06-18
2018 Agostinho Lemos, Rita Meloc, Antonio J. Preto, Jose G. Almeida, Irina S. Moreira, M. Natalia D. S. Cordeiro
In silico studies targeting G-protein coupled receptors for drug research against Parkinson’s disease
published pages: , ISSN: 1570-159X, DOI: 10.2174/1570159X16666180308161642
Current Neuropharmacology 16 2019-06-18
2016 Ozge Sensoy, Irina S. Moreira, Giulia Morra
Understanding the Differential Selectivity of Arrestins toward the Phosphorylation State of the Receptor
published pages: 1212-1224, ISSN: 1948-7193, DOI: 10.1021/acschemneuro.6b00073
ACS Chemical Neuroscience 7/9 2019-06-18
2018 Pedro Filipe, António Preto, Panos Koukos, Alexandre Bonvin, Irina Moreira
Alpha-helical and beta-sheet membrane- membrane protein dimers: centralizing information
published pages: 5107, ISSN: , DOI: 10.3390/mol2net-03-05107
Proceedings of MOL2NET 2017, International Conference on Multidisciplinary Sciences, 3rd edition 2019-06-18
2017 Rita Melo, Jose Almeida, Sandra Cabo Verde, Zeynep Gumus, I. Moreira, J. Correia
Structural mechanism of HER2-antibodies complexes by molecular dynamics studies
published pages: 5084, ISSN: , DOI: 10.3390/mol2net-03-05084
Proceedings of MOL2NET 2017, International Conference on Multidisciplinary Sciences, 3rd edition 2019-06-18
2017 Beatriz Bueschbell, António Preto, Carlos Barreto, Anke Schiedel, Irina Moreira
Creating a valid in silico Dopamine D2-receptor model for small molecular docking studies
published pages: 5088, ISSN: , DOI: 10.3390/mol2net-03-05088
Proceedings of MOL2NET 2017, International Conference on Multidisciplinary Sciences, 3rd edition 2019-06-18
2017 José Almeida, Alexandre Bonvin, Irina Moreira
Using big-data to understand the protein interface landscape
published pages: 5087, ISSN: , DOI: 10.3390/mol2net-03-05087
Proceedings of MOL2NET 2017, International Conference on Multidisciplinary Sciences, 3rd edition 2019-06-18
2017 Irina S. Moreira, Panagiotis I. Koukos, Rita Melo, Jose G. Almeida, Antonio J. Preto, Joerg Schaarschmidt, Mikael Trellet, Zeynep H. Gümüş, Joaquim Costa, Alexandre M. J. J. Bonvin
SpotOn: High Accuracy Identification of Protein-Protein Interface Hot-Spots
published pages: , ISSN: 2045-2322, DOI: 10.1038/s41598-017-08321-2
Scientific Reports 7/1 2019-06-18
2017 Carlos Barreto, Miguel Machuqueiro, Alexandre Bonvin, Irina Moreira
Structural and dynamic understanding of the ghrelin receptor high constitutive activity
published pages: 5089, ISSN: , DOI: 10.3390/mol2net-03-05089
Proceedings of MOL2NET 2017, International Conference on Multidisciplinary Sciences, 3rd edition 2019-06-18
2016 Rita Melo, Robert Fieldhouse, André Melo, João Correia, Maria Cordeiro, Zeynep Gümüş, Joaquim Costa, Alexandre Bonvin, Irina Moreira
A Machine Learning Approach for Hot-Spot Detection at Protein-Protein Interfaces
published pages: 1215, ISSN: 1422-0067, DOI: 10.3390/ijms17081215
International Journal of Molecular Sciences 17/8 2019-06-18
2017 Irina Moreira, José Almeida, António Preto, Rita Melo, Zeynep Gümüş, Joaquim Costa, Alexandre Bonvin
Co-evolution importance on binding Hot-Spot prediction methods
published pages: 3889, ISSN: , DOI: 10.3390/mol2net-02-03889
Proceedings of MOL2NET 2016, International Conference on Multidisciplinary Sciences, 2nd edition 2019-06-18

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