Sergio Filipe Sousa
Computational Chemistry
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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


49Prediction 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)

47Enzymatic “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) 

43Comparative 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) 

42Parameters 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)

41Computational 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)

40Protein-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)

39Comparative 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).