Publications

SCI – INDEXED PUBLICATIONS

1. Melo R, Lemos A, Preto AJ, Bueschbell B, Matos-Filipe P, Barreto C, Almeida JG, Silba RDM, Correia JDG, Moreira IS, An overview of antiretroviral agents for treating HIV infection in paediatric population, Curr Med Chem, 2018 – Submitted.

2. Schiedel AC, Kose M, Barreto C, Bueschbell B, Morra G, Sensoy O, Moreira IS, Prediction and targeting of interaction interfaces in G-protein coupled receptor oligomers, Curr Topics Med Chem, 2018 – Submitted.

3. Melo R, Lemos A, Preto AJ, Almeida JG, Correia JDG, Sensoy O, Moreira IS, Computational approaches in antibody-drug conjugate optimization for targeted cancer therapy, 2018 – Submitted.

4. Lemos A, Melo R, Preto AJ, Almeida JG, Moreira IS, Cordeiro MNDS, In silico studies in the drug research against Parkinson’s disease, 2017, Curr Neuropharmacology, In press.

5. Kurkcuoglu Z, Koukos PI, Citro N, Trellet ME, Rodrigues JPGLM, Moreira IS, Roel-Touris J, Melquiond ASJ, Geng C, Schaarschmidt J, Xue LC, Vangone A, Bonvin AMJJ, Performance of HADDOCK and a simple contact-based protein-ligand binding affinity predictor in the D3R Grand Challenge 2, 2018, J Comput Aided Mol Des, 32(1): 175-185.

6. Moreira IS, Koukos P, Melo R, Almeida JG, Preto AJ, Schaarschmidt J, Trellet M, Gumus ZH, Costa J, Bonvin, AMJJ, SpotOn: a web server for prediction of protein-protein binding hot-spots, Sci Rep, 7(1):8007.

7. Almeida JG, Preto AJ, Kuokos P, Bonvin AMJJ, Moreira IS, Membrane proteins structure: a review on the major computational tools, Biochim Biophys Acta, 1859(10), 2021-2039.

8. Torsello M, Pimenta AC, Wolters LP, Moreira IS, Orian L, Polimero A, General amber force field parameters for diphenyldiselenides and diphenylditellurides, 2016, J Chem Phys A, 120, 4389-400.

9. Melo R, Fieldhouse R, Melo A, Correia JDG, Cordeiro MNDS, Gümüş ZG, Costa J, Bonvin AMJJ, Moreira IS, A Machine-Learning Approach for Hot-Spot Detection at Protein-Protein Interfaces, 2016, Int J Mol Sci., 2016, 17(8). Pii: E1215.

10. Sensoy O, Moreira IS, Morra G, Understanding the differential selectivity of arrestins toward the phosphorylation state of the receptor, 2016, ACS Chem. Neurosci., 2016, 7, 1212-24.

11. Moreira IS, The role of water occlusion for the definition of a protein binding Hot-spot, Curr. Top. Med. Chem., 2015, 20, 2068-79.

12. Oliveira BL, Morais M, Mendes F, Moreira IS, Cordeiro C, Fernandes PA, Ramos MJ, Alberto R, Santos I, Correia JDG, Re(i) and Tc(i) Complexes for Targeting Nitric Oxide Synthase: Influence of the chelator in the affinity for the enzyme, Chem. Biol. Drug Design, 2015, 86, 1072-86.

13. Munteanu CR, Pimenta AC, Fernandez-Lozano C, Melo A, Cordeiro MNDS, Moreira IS. SASA-Based Hot-Spot Detection 2 (SBHD) method for protein-protein and protein-nucleic acid interfaces, J. Chem. Info. Model., 2015, 55, 1077-86.

14. Moreira IS, Martins JM, Coimbra JTS, Ramos MJ, Fernandes PA. A new scoring function for protein-protein docking that identifies native structures with unprecedented accuracy, Phys Chem. Chem. Phys., 2015, 17, 2378-87.

15. Pimenta AC, Dourado DFAR, Martins JM, Melo A, Cordeiro MNDS, Almeida RD, Morra G, Moreira IS, Dynamic structure of NGF and proNGF complexed with p75NTR: pro-peptide effect. J. Chem. Info. Model., 2014, 54, 2051-67.

16. Martins JM, Ramos RM, Pimenta AC, Moreira IS, Solvent-accessible surface area: how well can be applied to hot-spot detection? Proteins, 2014, 82, 479-90.

17. Pimenta, AC, Fernandes R, Moreira IS, Evolution of drug resistance: insight on TEM beta-lactamases structure and activity and beta-lactam antibiotics pharmacodynamics, Mini Rev. Med. Chem., 2014, 14, 111-12.

18. Moreira IS, Structural features of the G-protein/GPCR interactions, Biochim. Biophys. Acta, 2014, 1840, 16-33.

19. Pimenta AC, Martins JM, Fernandes R, Moreira IS, Ligand-induced structural changes in TEM-1 probed by molecular dynamics and relative free binding energy calculations, J. Chem. Info. Model., 2013, 53, 2648-58.

20. Ramos RM, Moreira IS, Computational alanine scanning mutagenesis – an improved methodological approach for protein-DNA complexes, J. Chem. Theor. Comput. 2013, 9, 4243–4256.

21. Oliveira BL, Moreira IS, Fernandes PA, Ramos MJ, Santos I, Correia JDG, Binding of Re(I) complexes inhibitors to inducible nitric oxide synthase: insight through molecular dynamics and free energy calculations, J. Mol. Graph. Model., 2013, 45, 13-25.

22. Carneiro J, Duarte-Pereira S, Azevedo L, Castro FC, Aguiar P, Moreira IS, Amorim A, Silva RM., The evolution portrait of metazoan NAD salvage pathways, Plos One, 2013, 8, 64674.

23. Ramos RM, Fernandes LM, Moreira IS, Extending the applicability of the O-ring theory to protein-DNA complexes, Comput. Biol. and Chem., 2013, 44, 31-39.

24. Martins S, Perez M, Moreira IS, Sousa, SF, Fernandes PA, Ramos MJ, Computational alanine scanning mutagenesis: ASM vs TI, J. Chem. Theor. Comput., 2013,9, 1311-1319.

25. Oliveira BL, Moreira IS, Santos I, Fernandes PA, Ramos MJ, Correia JDG, Insights into the structural determinants for selective inhibition of nitric oxide synthase isoforms, J. Mol. Mod. 2013, 19,1537-1551.

26. Moreira IS, Ramos RM, Martins JM, Fernandes PA, Ramos MJ, Are hot-spots occluded from water?, J. Biomol. Struct. Dyn., 2014, 32:186-197.

27. Martins JM, Ramos RM, Moreira IS, Structural determinants of a typical leucine-rich repeat protein, Commun. Comput. Phys., 2013, 13, 238-255.

28. Moreira IS, Martins JM, Ramos RM, Fernandes PA, Ramos MJ, Understanding the importance of the aromatic amino-acid residues as hot-spots, Biochim. Biophys. Acta, 2013, 1834: 404-414.

29. Ribeiro J, Cerqueira NMFSA, Moreira IS, Fernandes PA, Ramos MJ, CompASM: an Amber-VMD Alanine Scanning Mutagenesis plug-in, Theor. Che, Acc. 2012, 131, 1271-1278.

30. Bach A, Thorsen TS, Stuhr-Hansen N, Padrah S, Moreira IS, Madsen KL, Weinstein HA, Gether U, Strømgaard K, Structure-Activity relationships for a small-molecules inhibitor of the PDZ domain of PICK1, Org Biomol Chem. 2010, 8: 4281-4288.

31. Thorsen TS, Madsen KL, Rebola N, Rathje M, Anggono V, Bach A, Moreira IS, Stuhr-Hansen N, Dyhring T, Peters D, Beuming T, Huganir R, Weinstein HA, Mulle C, Strømgaard K, Ron LC, Gether U, Identification of a small molecule inhibitor of the PICK1 PDZ domain that inhibits hippocampal LTP and LTD – Proc. Nat. Acad.Sci. USA, 2010, 107: 413-418.

32. Moreira IS, Fernandes PA, Ramos MJ, Reviewing protein-protein docking. Dealing with the unknown, J. Comput. Chem., 2010, 31: 317-342.

33. Han Y., Moreira IS, Urizar E., Weinstein H, Javitch J, Allosteric communication between protomers of dopamine class A GPCR dimers modulates activation, Nature Chem. Biol., 2009, 5: 688-695.

34. Moreira IS, Fernandes PA, Ramos MJ, Protein-protein recognition: a computational mutagenesis study of the MDM2-P53 complex, Theor. Chem. Acc., 2008, 120: 533-542.

35. Moreira IS, Fernandes PA, Ramos MJ, The backbone importance for protein-protein binding, J Chem Theory Comput, 2007, 3: 885-893.

36. Moreira IS, Fernandes PA, Ramos MJ, Hot spots occlusion from bulk water – a comprehensive study of the complex between the lysozyme HEL and the antibody FvD1.3, J. Phys. Chem. B, 2007, 111: 2697-2706.

37. Moreira IS, Fernandes PA, Ramos MJ, Hot spots – a detailed review of protein-protein interface determinant amino acid residues, Proteins, 2007, 68: 803-812.

38. Moreira IS, Fernandes PA, Ramos MJ, Vascular endothelial growth factor (VEGF) inhibitiona critical review, AntiCancer Agents Med. Chem., 2007, 7: 223-245.

39. Moreira IS, Fernandes PA, Ramos MJ, Unravelling Hot Spots: a comprehensive computational mutagenesis study, Theor. Chem. Acc., 2007, 117: 99-113.

40. Moreira IS, Fernandes PA, Ramos MJ, Hot spots computational identification- application to the complex formed between the hen egg-white lysozyme (HEL) and the antibody HyHEL-10, Int. J. Quantum Chem., 2007, 107: 299-310.

41. Moreira IS, Fernandes PA, Ramos MJ, Computational Alanine Scanning Mutagenesis – an improved methodological approach, J. Comput. Chem., 2007, 28:644-654.

42. Moreira IS, Fernandes PA, Ramos MJ, Unravelling the importance of protein-protein interaction: application of a computational alanine scanning mutagenesis to the study of the IgG1: Streptococcal Protein G (C2 Fragment) complex, J. Phys. Chem. B, 2006, 110: 10962-10969.

43. Moreira IS, Fernandes PA, Ramos MJ, Detailed microscopic study of the full ZipA:FtsZ interface, Proteins, 2006, 63: 811-821.

44. Moreira IS, Fernandes PA, Ramos MJ, Accuracy of the numerical solution of the Poisson-Boltzmann equation, J. Mol. Struct, 2005, 729: 11-18.

45. Fernandes PA, Carvalho ATP, Marques AT, Pereira ALF, Madeira APS, Ribeiro ASP, Carvalho AFR, Ricardo ETA, Pinto FJV, Santos HÁ, Mangericao HDG, Martins HM, Santos HRR, Moreira IS, Azeredo MJV, Abreu RPS, Oliveira RMS, Sousa SFM, Silva RJAM, Mourão ZS, Ramos MJ, New designs for MRI contrast agents, J. Comp. Aided Mol. Design, 2003, 17: 463-473.

BOOK CHAPTERS

1. A.J. Preto, J.G. Almeida, J. Schaarschmidt, L.C. Xue, I.S. Moreira and A.M.J.J. Bonvin. Computational tools for the structural characterization of proteins and their complexes from sequence-evolutionary data. Encyclopedia of Analytical Chemistry, 2018 – In press.

2. Lemos A, Melo R, Moreira IS, Cordeiro MNDS, Computational approaches to target key therapeutical targets in Alzheimer disease, in Neuromethods, ed. Kunal Roy, Springer, 2017, 61-106.

3. Sensoy O, Almeida JG, Moreira IS, Morra G, Computational modeling – a way to understand GPCR structure, function and mechanism, in Methods in Cell Biology, 2017, 205-245.

4. Moreira IS, Bras NB, Carvalho A, Cerqueira NMFSA, Dourado DF, Perez MAS, Ribeiro AJM, Sousa SF, Fernandes PA, Ramos MJ, Computational proteomics – from methodological developments to biological applications, Academia Ciências de Coimbra, 2012.

5. Moreira IS, Shi L, Freyberg Z., Eriksen S. S., Weinstein H, Javitch J, Structural Basis of Dopamine Receptor Activation and Function in The Dopamine Receptors, ed Kim Neve, Humana/Springer, 2010, 47-73.

6. Moreira IS, Fernandes PA, Computational Alanine Scanning Mutagenesis in Computational Proteomics, ed Maria J. Ramos, Transworld Research Network, 2008, 81-100.

7. Moreira IS, Fernandes PA, Ramos MJ, Computational Determination of the Relative Free Energy of Binding – Application to Alanine Scanning Mutagenesis in Molecular Materials with Specific Interactions: Modeling and Design, ed W.Andrzej Sokalski, Springer, 2007, 305-340.

 

 

 

 

CONFERENCE PROCEEDINGS

1. Filipe P, Preto A, Koukos P, Bonvin A, Moreira IS, Alpha-helical and beta-sheet membrane- membrane protein dimers: centralizing information. In Proceedings of the MOL2NET 2017, International Conference on Multidisciplinary Sciences, 3rd edition.

2. Barreto C, Machuqueiro M, Bonvin AMJJ, Moreira IS, Structural and dynamic understanding of the ghrelin receptor high constitutive activity. In Proceedings of the MOL2NET 2017, International Conference on Multidisciplinary Sciences, 3rd edition.

3. Bueschbell B, Preto AJ, Barreto C, Schiedel A, Moreira IS, Creating a valid in silico Dopamine D2-receptor model for small molecular docking studies. In Proceedings of the MOL2NET 2017, International Conference on Multidisciplinary Sciences, 3rd edition.

4. Almeida J, Bonvin AMJJ, Moreira IS, Using big-data to understand the protein interface landscape. In Proceedings of the MOL2NET 2017, International Conference on Multidisciplinary Sciences, 3rd edition.

5. Melo R, Almeida J, Cabo Verde S, Gumus Z, Moreira IS, Correia J, Structural mechanism of HER2-antibodies complexes by molecular dynamics studies. In Proceedings of the MOL2NET 2017, International Conference on Multidisciplinary Sciences, 3rd edition.

6. Moreira IS, Koukos P, Melo R, Almeida JG, Gomes A, Schaarschmidt J, Trellet M, Gumus ZH, Costa J, Bonvin, AMJJ, Spoton: a Machine-learning approach for hot-spot determination, Biophys J, 2017.

7. Almeida JG, Preto AJ, Melo R, Gumus ZH, Costa J, Bonvin AMJJ, Moreira IS, Coevolution importance on binding hot-spots prediction methods, In Proceedings of the MOL2NET 2016, International Conference on Multidisciplinary Sciences, 2nd edition, doi:10.3390/mol2net-02-03889.

8. Munteanu CR, Pimenta AC, Fernandez-Lozano C, Melo A, Cordeiro MNL, Moreira IS, Solvent Accessible Surface Area Hot-Spot Detection Method, In Proceedings of the MOL2NET 2015, International Conference on Multidisciplinary Sciences, 1st edition, doi: 10.13140/RG.2.1.3605.4487

9. Ramos RM, Martins JM, Pimenta AC, Moreira IS, Hot-spots detection – application to a variety of different protein-based systems, Biophys. J. 2014.

10. Moreira IS, Martins JM, Ramos RM, Fernandes PA, Ramos MJ, Are hot-spots occluded from water?, Biophys. J. 2013, 104: 505a.

11. Moreira IS, Ge X, Madsen KL, Gether U, Weinstein H. Design and characterization of small molecule inhibitors of PICK1 PDZ domain with binding free energy calculations, Biophys. K. 2010, 98: 428a.