Research
by cesarCURRENT PROJECTS
* Enhanced Sampling Methods.
* Free Energy Methods
* Drug Design/Discovery
PROFESSIONAL EXPERIENCE
2005 – Present: University of California, San Diego.
Postdoctoral Research Associate
Howard Hughes Medical Institute
Mccammon Research Group
EDUCATION
2001 – 2005: Federal University of Rio de Janeiro (Rio de Janeiro, Brazil)
Ph.D. : Research Advisor: Professor Ricardo Bicca de Alencastro.
Catalytic Activity of the Serine Protease of Human Cytomegalovirus: A Theoretical Study.
1996 – 2001: Federal University of Rio de Janeiro (Rio de Janeiro, Brazil)
B.S. in Chemical Engineering (with distinction)
PUBLICATIONS
23. Coupling Constant pH Simulations with Accelerated Molecular Dynamics Method
S. Williams,C. A. F. Oliveira, J. A. McCammon.
J. Chem. Theor Comp (submitted)
22. Inclusion of Receptor Flexibility in Docking Analyses of Metalloproteinases types 2 and 3 Reveals that Pyrone-Based Molecules Work as Conformation Selective Inhibitors
C. A. F. Oliveira, J. A. McCammon (in preparation).
21. Design of MMP2 inhibitors: Including Receptor Flexibility and Induced fit-Effects into Drug Design.
J. Durrant, C. A. F. Oliveira, J. A. McCammon.
J. Mol. Recognition (accepted)
20. Thioamide hydroxythiopyrones supersede amide hydroxythiopyrones in potency against anthrax lethal factor.
A. Agrawal, C. A. F. Oliveira, Y. Cheng, J. A. Jacobsen, J. A. McCammon, Seth M. Cohen
J. Med. Chem. 52, 1063–1074 (2009).
19. Coupling Accelerated Molecular Dynamics Methods with Thermodynamic Integration Simulations.
C. A. F. Oliveira, D. Hammelberg, J. A. McCammon.
J. Chem. Theor. Comp. 4, 1516-1525 (2008).
18. Biomolecular Association of the E9 – Im9 Colicin Dnase – Immunity Protein recognition in Water: A Multiple Copy and Accelerated Molecular Dynamics Simulation Study.
R. Baron, S. Wong, C. A. F. Oliveira, J. A. McCammon.
J. Phys. Chem. B 112, 16802–16814 (2008).
17. Reversible Folding of Trp-Cage Protein from Accelerated Molecular Dynamics Simulation.
C. A. F. Oliveira, D. Hammelberg, J. A. McCammon (in preparation)
16. Inhibition of Cathepsin B by Au(I) Complexes: A Kinetic and Computational Study.
S. S. Gunatilleke, C. A. F. Oliveira, J. A. McCammon, A. M. Barrios.
J. Biol. Inoorg. Chem. 13, 555-561, (2008)
15. Sampling of Slow Diffusive Conformational Transitions with Accelerated Molecular Dynamics.
D. Hammelberg, C. A. F. Oliveira, J. A. McCammon.
J. Chem. Phys. 127, 155102-155110, (2007).
14. Estimating Kinetic Rates from Accelerated Molecular Dynamics Simulations: Alanine Dipeptide in Explicit Solvent as a Case Study.
C. A. F. Oliveira, D. Hammelberg, J. A. McCammon.
J. Chem. Phys. 127, 175105-175112, (2007).
13. Molecular Dynamics Simulations of Metalloproteinases Types 2 and 3 Reveal Differences in the Dynamic Behavior of the S1’ Binding Pocket.
C. A. F. Oliveira, M. Zissen, J. Mongon, J. A. McCammon
Curr. Pharm. Des. 13, 3471-3475, (2007).
12. Human Cytomegalovirus Protease: Why is the Dimer Required for Catalytic Activity?
C. A. F. Oliveira, C. R. W. Guimarães, G. Barreiro, R. Bicca de Alencastro.
J. Chem. Theory Comput. 3, 278–288, (2007)
11. On the Application of Accelerated Molecular Dynamics to Liquid Water Simulations.
C. A. F. Oliveira, D. Hammelberg, J. A. McCammon.
J. Phys. Chem. B. 110, 22695-22701, (2006).
10. Evaluating Relative Octanol/Water Partition Coefficients of Thrombin Inhibitors via Free-Energy Perturbations.
C. A. F. Oliveira, C. R. W. Guimarães, H. Mello, A. Echevarria, R. Bicca de Alencastro.
Int. J. Quantum Chem. 102, 542-553 (2005).
9. On the Application of Simple Explicit Water Models to the Simulations of Biomolecules.
C. R. W. Guimarães, G. Barreiro, C. A. F. Oliveira, R. Bicca de Alencastro.
Braz. J. Phys. 34(1), 126-136 (2004).
8. Synthetic and Theoretical Studies on the Reduction of Electron Withdrawing Group Conjugated Olefins Using the Hantzsch 1,4-dihydropyridine Ester.
S. J. Garden, C. R. W. Guimarães, C. A. F. Oliveira, M. B. Correa, A. C. Pinto, R. Bicca de Alencastro.
J. Org. Chem. 68(23), 8815-8822 (2003).
7. Investigation of the Induced-Fit Mechanism and Catalytic Activity of the Human Cytomegalovirus Protease Homodimer via Molecular Dynamics Simulations.
C. A. F. Oliveira, C. R. W. Guimarães, G. Barreiro, R. Bicca de Alencastro.
Proteins 52(4), 483-491 (2003).
6. Metodologias em Modelagem Molecular de Biomoléculas.
R. Bicca de Alencastro, M.G. Albuquerque, O. A. Santos Filho, C. R. W. Guimarães, G. Barreiro, N. C. Romeiro, R. C. A. Martins, C. A. F. Oliveira.
In “A Arte de Vencer Desafios: Um Tributo a Claudio Costa Neto”, Editor M. A. Chaer do Nascimento, Rio de Janeiro, pp. 29-41 (2002).
5. A Molecular Dynamics Study on Liquid 1-Octanol. Part 2. The Water-Saturated 1-Octanol Solution.
C. A. F. de Oliveira, C. R. W. Guimarães, R. Bicca de Alencastro.
Int. J. Quantum Chem. 90(2), 786-791 (2002).
4. Detecção em Tempo Real de Vazamentos em Redes de Escoamento para Fluidos Incompressíveis: Uma Abordagem em Séries Temporais.
C. A. F. de Oliveira, O. Q. F. de Araújo, J. L. Medeiros.
Boletim Técnico da Petrobrás, Brasil, v.45, n. 2 (2002).
3. Instantaneus Leak Detection in Pipe Networks for Incompressible Fluids: A Time Series Approach.
C. A. F. de Oliveira, O. Q. F. de Araújo, J. L. Medeiros.
Procceedings of 3rd Enpromer, v. 1, p. 433-438 (2002).
2. Metodologias em Modelagem Molecular de Biomoléculas.
R. Bicca de Alencastro, M.G. Albuquerque, O. A. Santos Filho, C. R. W. Guimarães, G. Barreiro, N. C. Romeiro, R. C. A. Martins, C. A. F. Oliveira.[/i]
In: Santos, Hélio F.; Coura, Pablo Z.; Dantas, Sócrates O.; Barone, Paulo M. V. B. (Org.). Escola Brasileira de Estrutura Eletrônica. São Paulo, p. 191-201 (2002).
1. A Molecular Dynamics Study on Liquid 1-Octanol.
C. A. F. de Oliveira, C. R. W. Guimarães, R. Bicca de Alencastro.
Int. J. Quantum Chem.: Quantum Biol. Symp. 80(4-5), 999-1006 (2000).