Publications in ISI Web of Science
OVERVIEW
- 62 Papers Published
-
2 Articles Submitted for Publication
- 7 Book Chapters
- 3 Proceedings in International Meetings
- h-index: 19 (ISI Web of Science / Scopus)
- Sum of Times Cited: 2003
- Average Citations per item: 33.38
- Number of Highly Cited Papers (According to the ISI Web of
Science criteria):
2018
64.
Mechanistic
studies on Flavin-monoxygenases: the sulfur oxidation of
dibenzothiophenes by DszC
Ana C. C. Barbosa, Rui. P.P Neves, Sergio F. Sousa,
Maria Joao Ramos, Pedro A. Fernandes
(Submitted for publication)
63.
Analyzing
PEGylation through Molecular Dynamics Simulations
Claudia T. Vieira, Sergio F. Sousa,
Joana Peres, Manuel Coelho
(Submitted for publication)
62.
Transport
Properties of Gases in Nanochannels of L-Leu-L-Ser Dipeptide
Crystals: a Comparative Study by Molecular Dynamics
Simulations
Krzysztof Biernacki, Sergio F. Sousa,
Luis Gales, Maria Joao Ramos, Alexandre L. Magalhaes
ChemistrySelect,
(2018) in press
61.
Understanding
the Catalytic Machinery and the Reaction Pathway of the
Malonyl-Acetyl Transferase domain of human Fatty Acid
Synthase
Pedro Paiva, Sergio F. Sousa, Maria Joao Ramos, Pedro A. Fernandes
ACS Catalysis, Vol. 8, 4860-4872, (2018)
60. Study of Human Salivary Proline-Rich Proteins Interactions with Food Tannins
Susana Soares, I. Garcia-Estevez, R. Ferrer-Galego, Natercia F.
Bras, E. Brandao, N. Teixeira, F. Fonseca, Sergio F. Sousa,
F. Ferreira-da-Silva, Nuno Mateus, Vitor de Freitas
Food Chemistry, Vol. 243, 175-185, (2018)
2017
59.
Improving
the Catalytic Power of the DszD Enzyme for the
Biodesulfurization of Crude Oil and Derivatives
Pedro Ferreira, Sergio F. Sousa, Maria Joao Ramos, Pedro A. Fernandes
Chemistry - A European Journal, Vol. 23, 17231-17241, (2017)
58.
Application
of Quantum Mechanics/Molecular Mechanics Methods in the
Study of Enzymatic Reaction Mechanisms
Sergio F. Sousa, Antonio J. M. Ribeiro, Natercia F. Bras, Nuno M. F. S. A. Cerqueira, Pedro A. Fernandes, Maria Joao Ramos
Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 7, e1281, (2017)
2016
57.
Molecular
Dynamics Simulations and Structure-based Pharmacophore
Development for Farnesyltransferase Inhibitors Discovery
N.S.H.N. Moorthy, Sergio F. Sousa, Pedro A. Fernandes, Maria Joao Ramos
Journal of Enzyme Inhibition and Medicinal Chemistry, Vol. 31, 1428-1442, (2016)
56.
HMG-CoA
Reductase Inhibitors: An Updated Review of Patents of
Novel Compounds and Formulations (2011-2015)
Eduardo F. Oliveira, Diogo Santos-Martins, Antonio M. Ribeiro, Natercia F. Bras, Nuno S. Cerqueira, Sergio F. Sousa, Maria J. Ramos, Pedro A. Fernandes
Expert Opinion on Therapeutic Patents, Vol. 26, 1257-1272, (2016)
55.
A
Flow Cytometric and Computational Approaches to
Carbapenems Affinity to the Different Types of
Carbapenemases
Cidalia
Pina-Vaz, A. P. Silva, I. Faria-Ramos, R. Teixeira-Santos, D.
Moura, T. F. Vieira, Sergio F. Sousa,
S. Costa-de-Oliveira, R. Canton, A. G. Rodrigues
Frontiers in Microbiology, Vol. 7, 1259, (2016)
54.
Improving
the Biodesulfurization of Crude Oil and Derivatives: A
QM/MM Investigation of the Catalytic Mechanism of NADH-FMN
Oxidoreductase (DszD)
Sergio
F. Sousa, Joana F. M. Sousa, Ana C.
C. Barbosa, Cleide E. Ferreira, Rui P. P. Neves, Antonio J. M.
Ribeiro, Pedro A. Fernandes, Maria J. Ramos
Journal of Physical Chemistry A, Vol. 120, 5300-5306, (2016)
53.
Binding
Mode of Conformations and Structure-based Pharmacophore
Development for Farnesyltransferase Inhibitors
N.S.H.N. Moorthy, Sergio F. Sousa, Maria J. Ramos, Pedro A. Fernandes
Medicinal Chemistry Research, Vol. 25, 1340-1357, (2016)
2015
52.
Relationship
between Enzyme/Substrate Properties and Enzyme Efficiency
in Hydrolases
Sergio
F. Sousa, Maria J. Ramos, Carmay Lim,
Pedro A. Fernandes
ACS Catalysis, Vol. 5, 5877-5887, (2015)
51.
Receptor-based
Virtual Screening Protocol for Drug Discovery
Nuno M. F. S.A. Cerqueira, Diana Gesto, Eduardo F. Oliveira, Diogo Santos-Martins, Natercia F. Bras, Sergio F. Sousa, Pedro A. Fernandes, Maria Joao Ramos
Archives of Biochemistry and Biophysics, Vol. 582, 56-67, (2015)
50.
Molecular
Dynamics Analysis of FAAH complexed with Anandamine
Sergio
F. Sousa, Joao TS Coimbra, Pedro A.
Fernandes, Tiziana Marino, Maria J. Ramos, Nino Russo
Frontiers in Quantum Methods and Applications in Chemistry and Physics, Vol. 29, 114-130, (2015)
2014
49. Prediction of Solvation Free Energies with Thermodynamic Integration using the General Amber Force Field
Silvia A. Martins, Sergio F. Sousa, Pedro A. Fernandes, Maria Joao Ramos
Journal of Chemical Theory and Computation, Vol. 10, 3570-3577, (2014)
48.
Classification
Study of Solvation Free Energies of Organic Molecules
Using Machine Learning Techniques
N.S.H.N. Moorthy, Silvia A. Martins, Sergio F. Sousa,
Maria J. Ramos, Pedro A. Fernandes
RSC Advances, Vol. 4, 61624-61630, (2014)
47. Enzymatic “tricks”: Carboxylate shift and Sulfur Shift
Sergio F. Sousa, Nuno M. F. S. A. Cerqueira, Natercia Bras, Pedro A. Fernandes, Maria Joao Ramos
International Journal of Quantum Chemistry, Vol. 114, 1253-1256, (2014)
46. Structural and Dynamics Analysis of Matrix Metalloproteinases MMP-2 complexed with Chemically Modified Tetracyclines
Bruna L. Marcial, Sergio F. Sousa, Helio F. Dos Santos, Maria Joao Ramos
Journal of Biomolecular Structure & Dynamics, Vol. 32, pp. 1907-1918, (2014)
45. Biomembrane simulations of 12 lipid types using the General-Amber Force Field in a tensionless ensemble
Joao T.S. Coimbra, Sergio F. Sousa, Pedro A. Fernandes, Maria Rangel, Maria Joao Ramos
Journal of Biomolecular Structure & Dynamics, Vol. 32, pp. 88-103, (2014)
2013
44. Farnesyltransferase Inhibitors: A Comprehensive Review Based On Quantitative Structural Analysis
N. S. Hari Narayana Moorthy, Sergio F. Sousa, Maria Joao Ramos, Pedro A. Fernandes
Current Medicinal Chemistry, Vol. 20, pp. 4888-4923, (2013)
43. Comparative analysis of the performance of commonly available density functionals in the determination of geometrical parameters for copper complexes
Sergio F. Sousa, Gaspar R. Pinto, Antonio J Ribeiro, Joao TS Coimbra, Pedro A. Fernandes, Maria Joao Ramos
Journal of Computational Chemistry, Vol. 34, pp. 2079-2090, (2013)
42. Parameters for Molecular Dynamics Simulations of Manganese-Containing Metalloproteins
Rui PP Neves, Sergio F. Sousa, Pedro A Fernandes, Maria Joao Ramos
Journal of Chemical Theory and Computation, Vol. 9, pp. 2718–2732, (2013)
41. Computational Alanine Scanning Mutagenesis: MM-PBSA vs TI
Sílvia A Martins, Marta AS Perez, Irina S Moreira, Sergio F. Sousa, Maria Joao Ramos, Pedro A Fernandes
Journal of Chemical Theory and Computation, Vol. 9, pp. 1311–1319, (2013)
40. Protein-ligand docking in the new millennium - A Retrospective of 10 years in the field
Sergio F. Sousa, Antonio J Ribeiro, Joao TS Coimbra, Rui PP Neves, Silvia A Martins, Hary NS Moorthy , Pedro A. Fernandes, Maria Joao Ramos
Current Medicinal Chemistry, Vol. 20 pp. 2296-314, (2013)
39. Comparative assessment of computational methods for the determination of solvation free energies in alcohol-based molecules
Sílvia A. Martins, Sergio F. Sousa
Journal of Computational Chemistry, Vol 34, pp. 1354-62, (2013)
38. Molecular Dynamics Analysis of a Series of 22 Potential Farnesyltransferase Substrates Containing a CaaX Motif
Sergio F. Sousa, Joao T.S. Coimbra, Diogo Paramos-de-Carvalho, Rita Pinto, Rodrigo S. Guimaraes, Vitor Teixeira, Pedro A. Fernandes, Maria Joao Ramos
Journal of Molecular Modeling, Vol. 19, pp. 673-88, (2013)
2012
37. Chemically Modified Tetracyclines as Inhibitors of MMP‑2 Matrix 2 Metalloproteinase: A Molecular and Structural Study
Bruna L. Marcial, Sergio F. Sousa, Ingrid L. Barbosa, Helio F. Dos Santos, Maria Joao Ramos
Journal of Physical Chemistry B, Vol. 116, pp. 13644-54 (2012)
36. Computational Enzymatic Catalysis – Clarifying Enzymatic Mechanisms with the help of computers
Sergio F. Sousa, Pedro A. Fernandes, Maria Joao Ramos
Physical Chemistry Chemical Physics, Vol. 14, pp. 12431-12441. (2012).
35. In silico Based Structural Analysis of Some Piperidine Analogs as Farnesyltransferase Inhibitors
N. S. Hari Narayana Moorthy, Sergio F. Sousa, Maria Joao Ramos, Pedro A. Fernandes
Medicinal Chemistry, Vol. 8, pp. 853-864. (2012).
34. Dehydration of a polyether type extraction agent and of the corresponding K(+) complex: insights into liquid-liquid extraction mechanisms by quantum chemical methods
Mario Valente, Sergio F. Sousa, Alexandre L. Magalhaes, Cristina Freire
Journal of Molecular Modeling, Vol. 18, pp. 4909-4915 (2012).
33. Decomplexation and Complexation of Alkali Metal Cations by a Crown-Ether-Type Podand in Dichloromethane: A Steered Molecular Dynamics Study
Mario Valente, Sergio F. Sousa, Alexandre L. Magalhaes, Cristina Freire
Theoretical Chemistry Accounts, Vol. 131, n.º 1171. (2012).
32. Tranfer of the K+ Cations Across a Water/Dichloromethane Interface: A Steered Molecular Dynamics Study with Implications in Cation Extraction
Mario Valente, Sergio F. Sousa, Alexandre L. Magalhaes, Cristina Freire
Journal of Physical Chemistry B, Vol. 116, pp. 1843-1849. (2012).
2011
31. Detection of Farnesyltransferase Interface Hot Spots Through Computational Alanine Scanning Mutagenesis
Marta A. S. Perez, Sergio F. Sousa, Eduardo F. T. Oliveira, Pedro A. Fernandes, Maria Joao Ramos
Journal of Physical Chemistry B, Vol. 115, pp. 15339-15354. (2011).
30. Structural Feature Study of Benzofuran Derivatives as Farnesyltransferase Inhibitors
N. S. Hari Narayana Moorthy, Sergio F. Sousa, Maria Joao Ramos, Pedro A. Fernandes
Journal of Enzyme Inhibition and Medicinal Chemistry, Vol. 26, pp. 777-791, (2011).
29. Complexation of Alkaline-Metal Cations by Crown-Ether Type Podands with Application in Solvent Extraction: Insights from Quantum Chemical Calculations
Mario Valente, Sergio F. Sousa, Alexandre L. Magalhaes, Cristina Freire
Journal of Molecular Modeling, Vol. 17, pp. 3275-3288, (2011).
28. In Silico Based Structural Analysis of Arylthiophene Derivatives for FTase Inhibitory Activity, HERG and other Toxic Effects
N. S. Hari Narayana Moorthy, Sergio F. Sousa, Maria Joao Ramos, Pedro A. Fernandes
Journal of Biomolecular Screening, Vol 16, pp. 1036-1047, (2011).
27. Detailed Atomistic Analysis of the HIV-1 Protein Interface
Sergio F. Sousa, Bruno Tamames, Pedro A. Fernandes, Maria Joao Ramos
Journal of Physical Chemistry B, Vol 115, pp. 7045-7057, (2011).
2010
26. Factors Influencing the Binding of a Potassium Cation to a Polyethylene Glycol Type Podand in Liquid-Liquid Extraction - A Molecular Dynamics Study
Mario Valente, Sergio F. Sousa, Alexandre L. Magalhaes, Cristina Freire
Theoretical Chemistry Accounts, Vol 127, pp. 681-687, (2010).
25. Crown-Ether Type Podands as Alkali Metal Cation Extractants: Influence of the Number of Oxygens in the Chain
Mario Valente, Sergio F. Sousa, Alexandre L. Magalhaes, Cristina Freire
Journal of Solution Chemistry, Vol 39, pp. 1230-1242, (2010).
24. Virtual Screening of Compound Libraries
Nuno
MFSA Cerqueira, Sergio
F. Sousa, Pedro
A. Fernandes, Maria Joao Ramos
Ligand-Macromolecular
Interactions in Drug Discovery: Methods and Protocols
in Methods in Molecular Biology , Vol 572, pp. 57-70, (2010).
23. Virtual Screening in Drug Design and Development
Sergio F. Sousa, Nuno MFSA Cerqueira, Pedro A. Fernandes, Maria Joao Ramos
Combinatorial Chemistry & High Throughput Screening, Vol 13, pp. 442-453, (2010).
22. Comparative Molecular Dynamics Study on the Complexation of Alkali Metal Cations by a Poly-Ethylene-Glycol Type Podand in Water and in Dicloromethane
Mario Valente, Sergio F. Sousa, Alexandre L. Magalhaes, Cristina Freire
Journal of Molecular Structure - Theochem, Vol 946, pp. 77-82, (2010).
2009
21. Gas-Phase Geometry Optimization of Biological Molecules as an Alternative to a Continuum Environment Description: Fact, Myth, or Fiction?
Sergio F. Sousa, Pedro A. Fernandes, Maria Joao Ramos
Journal of Physical Chemistry A, Vol 113, pp. 14231-14236, (2009).
20. Direct Covalent Modification as a Strategy to Inhibit Nuclear Factor-Kappa B
Vineet Pande, Sergio F. Sousa, Maria Joao Ramos
Current Medicinal Chemistry, Vol. 16, pp. 4261-4273, (2009).
19. The Zinc Proteome: a Tale of Stability and Functionality
Sergio F. Sousa, Ana B. Lopes, Pedro A. Fernandes, Maria Joao Ramos
Dalton Transactions, Vol. 38, pp. 7946-7956, (2009).
18. Comparative Analysis of the Performance of Commonly Available Density Functionals in the Determination of Geometrical Parameters for Zinc Complexes
Sergio F. Sousa, Emanuela S. Carvalho, Diana M. Ferreira, Isabel S. Tavares, Pedro A. Fernandes, Maria Joao Ramos, Jose A. N. F. Gomes
Journal of Computational Chemistry, Vol. 30, pp. 2752-2763, (2009).
17. The Search for the Mechanism in the Reaction Catalyzed by Farnesyltransferase
Sergio F. Sousa, Pedro A. Fernandes, Maria Joao Ramos
Chemistry - a European Journal, Vol. 15, pp. 4243-4247, (2009).
16. Molecular Dynamics Simulations on the Critical States of the Farnesyltransferase Enzyme
Sergio F. Sousa, Pedro A. Fernandes, Maria Joao Ramos
Bioorganic & Medicinal Chemistry, Vol. 17, pp. 3369-3378, (2009).
2008
15. Enzyme Flexibility and the Catalytic Mechanism of Farnesyltransferase: Targeting the Relation
Sergio F. Sousa, Pedro A. Fernandes, Maria Joao Ramos
Journal of Physical Chemistry B, Vol. 112, pp. 8681-8691, (2008).
Note: Selected Cover Art
14. Farnesyltransferase Inhibitors: A Detailed Chemical View on an Elusive Biological Problem
Sergio F. Sousa, Pedro A. Fernandes, Maria Joao Ramos
Current Medicinal Chemistry, Vol. 15, pp. 1478-1492, (2008).
13. Molecular Dynamics Analysis of Farnesyltransferase - A Closer Look into the Amino Acid Behavior
Sergio F. Sousa, Pedro A. Fernandes, Maria Joao Ramos
International Journal of Quantum Chemistry, Vol. 108, pp. 1939-1950, (2008).
2007
12. General Performance of Density Functionals - a Review
Sergio F. Sousa, Pedro A. Fernandes, Maria Joao Ramos
Journal of Physical Chemistry A, Vol. 111, pp. 10439-10452, (2007).
Note: Selected Cover Art
Note: 602 citations (ISI Web of Science) - Hot Paper (ISI Web of Science)
11. Analysis of Zinc-Ligand Bond-Lengths in Metalloproteins: Trends and Patterns
Bruno Tamames, Sergio F. Sousa, Juan Tamames, Pedro A. Fernandes, Maria Joao Ramos
Proteins, Structure, Function and Bioinformatics, Vol. 69, pp. 466-475, (2007).
10. Comparative Assessment of Theoretical Methods for the Determination of Geometrical Properties in Biological Zinc Complexes
Sergio F. Sousa, Pedro A. Fernandes, Maria Joao Ramos
Journal of Physical Chemistry B, Vol. 111, pp. 9146-9152, (2007).
9. The Carboxylate-Shift in Zinc Enzymes: A Computational Study
Sergio F. Sousa, Pedro A. Fernandes, Maria Joao Ramos
Journal of the American Chemical Society, Vol. 129, pp. 1378-1385, (2007).
8. Theoretical Studies on Farnesyltransferase: Evidence for Thioether Product Coordination to the Active-Site Zinc Sphere
Sergio F. Sousa, Pedro A. Fernandes, Maria Joao Ramos
Journal of Computational Chemistry, Vol. 28, pp. 1160-1168, (2007).
7. Theoretical Studies on Farnesyltransferase: The Distances Paradox Explained
Sergio F. Sousa, Pedro A. Fernandes, Maria Joao Ramos
Proteins, Structure, Function and Bioinformatics, Vol. 66, pp.205-216, (2007).
6. Effective Tailor-Made Force Field Parameterization of the Several Zn Coordination Environments in the Puzzling FTase Enzyme: Opening the Door to the Full Understanding of its Elusive Catalytic Mechanism
Sergio F. Sousa, Pedro A. Fernandes, Maria Joao Ramos
Theoretical Chemistry Accounts, Vol. 117, pp. 171-181, (2007).
2006
5. Protein-Ligand Docking: Current Status and Future Challenges
Sergio F. Sousa, Pedro A. Fernandes, Maria Joao Ramos
Proteins, Structure, Function and Bioinformatics, Vol. 65, pp. 15-26, (2006).
Note: 422 citations (ISI Web of Science)
2005
4. Farnesyltransferase: Theoretical Studies on Peptide Substrate Entrance - Thiol or Thiolate Coordination ?
Sergio F. Sousa, Pedro A. Fernandes, Maria Joao Ramos
Journal of Molecular Structure - THEOCHEM, Vol. 729, pp. 125-129, (2005).
3. Unravelling the Mechanism of the Farnesyltransferase Enzyme
Sergio F. Sousa, Pedro A. Fernandes, Maria Joao Ramos
Journal of Biological Inorganic Chemistry, Vol. 10, pp. 3-10, (2005).
2. Farnesyltransferase - New Insights into the Zinc-Coordination Sphere-Paradigm
Sergio F. Sousa, Pedro A. Fernandes, Maria Joao Ramos
Biophysical Journal, Vol. 88, pp. 483-494, (2005).
2003
1. New Designs in MRI Constrast Agents
P.A. Fernandes, A.T.P. Carvalho, A.T. Marques, A.L.F. Pereira, A.P.S. Madeira, A.S.P. Ribeiro, A.F.R. Carvalho, E.T.A. Ricardo, F.J.V. Pinto, H.A. Santos, H.D.G. Mangericao, H.M. Martins, H.D.B. Pinto, H.R.R. Santos, I.S. Moreira, M.J.V. Azeredo, R.P.S. Abreu, R.M.S. Oliveira, S.F.M. Sousa, R.J.A.M. Silva, Z.S. Mourao, M.J. Ramos.
Journal of Computer-Aided Molecular Design, Vol. 17, pp. 463-473, (2003).