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

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Publications

Performance of HADDOCK and a simple contact-based protein–ligand binding affinity predictor in the D3R Grand Challenge 2

Author(s): 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
Published in: Journal of Computer-Aided Molecular Design, Issue 32/1, 2018, Page(s) 175-185, ISSN 0920-654X
DOI: 10.1007/s10822-017-0049-y

A Machine Learning Approach for Hot-Spot Detection at Protein-Protein Interfaces

Author(s): Rita Melo, Robert Fieldhouse, André Melo, João Correia, Maria Cordeiro, Zeynep Gümüş, Joaquim Costa, Alexandre Bonvin, Irina Moreira
Published in: International Journal of Molecular Sciences, Issue 17/8, 2016, Page(s) 1215, ISSN 1422-0067
DOI: 10.3390/ijms17081215

SpotOn: High Accuracy Identification of Protein-Protein Interface Hot-Spots

Author(s): 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
Published in: Scientific Reports, Issue 7/1, 2017, ISSN 2045-2322
DOI: 10.1038/s41598-017-08321-2

Membrane proteins structures: A review on computational modeling tools

Author(s): Jose G. Almeida, Antonio J. Preto, Panagiotis I. Koukos, Alexandre M.J.J. Bonvin, Irina S. Moreira
Published in: Biochimica et Biophysica Acta (BBA) - Biomembranes, Issue 1859/10, 2017, Page(s) 2021-2039, ISSN 0005-2736
DOI: 10.1016/j.bbamem.2017.07.008

Understanding the Differential Selectivity of Arrestins toward the Phosphorylation State of the Receptor

Author(s): Ozge Sensoy, Irina S. Moreira, Giulia Morra
Published in: ACS Chemical Neuroscience, Issue 7/9, 2016, Page(s) 1212-1224, ISSN 1948-7193
DOI: 10.1021/acschemneuro.6b00073

In silico studies targeting G-protein coupled receptors for drug research against Parkinson’s disease

Author(s): Agostinho Lemos, Rita Meloc, Antonio J. Preto, Jose G. Almeida, Irina S. Moreira, M. Natalia D. S. Cordeiro
Published in: Current Neuropharmacology, Issue 16, 2018, ISSN 1570-159X
DOI: 10.2174/1570159X16666180308161642

Spoton: A Machine-Learning Approach for Hot-Spot Determination

Author(s): 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
Published in: Biophysical Journal, Issue 112/3, 2017, Page(s) 45a, ISSN 0006-3495
DOI: 10.1016/j.bpj.2016.11.284

Alpha-helical and beta-sheet membrane- membrane protein dimers: centralizing information

Author(s): Pedro Filipe, António Preto, Panos Koukos, Alexandre Bonvin, Irina Moreira
Published in: Proceedings of MOL2NET 2017, International Conference on Multidisciplinary Sciences, 3rd edition, 2018, Page(s) 5107
DOI: 10.3390/mol2net-03-05107

Co-evolution importance on binding Hot-Spot prediction methods

Author(s): Irina Moreira, José Almeida, António Preto, Rita Melo, Zeynep Gümüş, Joaquim Costa, Alexandre Bonvin
Published in: Proceedings of MOL2NET 2016, International Conference on Multidisciplinary Sciences, 2nd edition, 2017, Page(s) 3889
DOI: 10.3390/mol2net-02-03889

<strong>Creating a valid <em>in silico</em> Dopamine D2-receptor model for small molecular docking studies</strong>

Author(s): Beatriz Bueschbell, António Preto, Carlos Barreto, Anke Schiedel, Irina Moreira
Published in: Proceedings of MOL2NET 2017, International Conference on Multidisciplinary Sciences, 3rd edition, 2017, Page(s) 5088
DOI: 10.3390/mol2net-03-05088

Structural mechanism of HER2-antibodies complexes by molecular dynamics studies

Author(s): Rita Melo, Jose Almeida, Sandra Cabo Verde, Zeynep Gumus, I. Moreira, J. Correia
Published in: Proceedings of MOL2NET 2017, International Conference on Multidisciplinary Sciences, 3rd edition, 2017, Page(s) 5084
DOI: 10.3390/mol2net-03-05084

Using big-data to understand the protein interface landscape

Author(s): José Almeida, Alexandre Bonvin, Irina Moreira
Published in: Proceedings of MOL2NET 2017, International Conference on Multidisciplinary Sciences, 3rd edition, 2017, Page(s) 5087
DOI: 10.3390/mol2net-03-05087

<strong>Structural and dynamic understanding of the ghrelin receptor high constitutive activity </strong>

Author(s): Carlos Barreto, Miguel Machuqueiro, Alexandre Bonvin, Irina Moreira
Published in: Proceedings of MOL2NET 2017, International Conference on Multidisciplinary Sciences, 3rd edition, 2017, Page(s) 5089
DOI: 10.3390/mol2net-03-05089

Computer-Aided Drug Design Approaches to Study Key Therapeutic Targets in Alzheimer’s Disease

Author(s): Agostinho Lemos, Rita Melo, Irina S. Moreira, M. Natália D. S. Cordeiro
Published in: Neuromethods, 2018, Page(s) 61-106
DOI: 10.1007/978-1-4939-7404-7_3