Research
by cesarResearcher ID :
News: Anton Highlights
PROFESSIONAL EXPERIENCE
2011 – Present: University of California, San Diego.
Mccammon Research Group
Research Specialist
Howard Hughes Medical Institute
2005 – 2011: University of California, San Diego.
Mccammon Research Group
Postdoctoral Research Associate
Howard Hughes Medical Institute
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
33. Enhanced Sampling Using Windowed Replica Exchange Accelerated Molecular Dynamics.
M. Arrar, W. Sinko, M. Fajer, C. A. F. Oliveira , J. A. McCammon.
J. Chem. Theory. Comp (submitted)
32. TIR1/AFBs and Aux/IAAs Constitute a Combinatorial Co-receptor System to Perceive Auxin with Differential Sensitivities.
L. I. A. Calderón Villalobos, S. Lee, C. A. F. Oliveira , A. Ivetac, W. Brandt, L. Armitage, L. B. Sheard, X. Tan, G. Parry, H. Mao, J. A. Mccammon, N. Zheng, R. Napier, S. Kepinski, M. Estelle.
Nat. Chem. Biol. (Accepted)
31. Benzoic Acids Target Both cis- and trans-prenyl Transferases: A Crystallographic Investigation.
Y. Zhang, Y. Liu, W. Zhu, R. Cao, J. No, F. Lin, K. Li, K. Wang, K. Houlihan, A. Sankovsky, W. Sinko, C. A. F. Oliveira , J. A. McCammon and E. Oldfield
J. Am. Chem. Soc. (submitted)
30. Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations.
W. Sinko, C. A. F. Oliveira , J. A. McCammon
J. Chem. Theory. Comp. 8, 17-23 (2012) (* joint first-author)
29. Guide to Virtual Screening: Application to the Akt Phosphatase PHLPP.
In Methods in Molecular Biology: Computational Drug Discovery and Design.
W. Sinko, E. Sierecki, C. A. F. Oliveira , J. A. McCammon (in press).
COMPUTATIONAL DRUG DISCOVERY AND DESIGN
Methods in Molecular Biology, 819, 561-73 (2012)
28. Enhanced lipid diffusion and mixing in accelerated molecular dynamics.
Yi Wang, P. R. L. Markwick, C. A. F. Oliveira , J. A. McCammon
J. Chem. Theor. Comp. 7, 3199-3207 (2011)
27. Large-Scale Conformational Changes of Trypanosoma cruzi Proline Racemase Predicted by Accelerated Molecular Dynamics Simulation.
C. A. F. Oliveira, B. Grant, M. Zhou, J. A. McCammon
PLoS Comp. Biol. 7 (10), e1002178 (2011)
26. Pyrone-Based Inhibitors of Metalloproteinases Types 2 and 3 May Work as Conformation-Selective Inhibitors.
J. Durrant, C. A. F. Oliveira*, J. A. McCammon. (* joint first-author)
Chem. Biol. & Drug Design. 78, 191-198 (2011) (Cover).
25. Applying Molecular Dynamics Simulations to Identify Rarely Sampled Ligand-bound Conformational States of Undecaprenyl Pyrophosphate Synthase, an Antibacterial Target.
W. Sinko,C. A. F. Oliveira, S. Williams, A. V. Wynsberghe, E. Oldfield, J, A. McCammon.
Chem. Biol. & Drug Design. 7, 412-420 (2011) (Cover) (F1000)
24. POVME: An Algorithm for Measuring Binding-Pocket Volume.
J. Durrant, C. A. F. Oliveira, J. A. McCammon.
J. Mol. Graph. Model. 29, 773-776 (2011).
23. From Zn to Mn: The Study of Novel Manganese-Binding Groups in the Search for New Drugs against Tuberculosis.
S. L. Williams, C. A. F. Oliveira, H. Vazquez, J. A. McCammon
J. Chem. Biol. Drug Des. 77, 117-123 (2011).
22. From Sensors to Silencers: Quinoline- and Benzimidazole-Sulfonamides as Inhibitors for Zinc Proteases
M. Rouffet,C. A. F. Oliveira, J. A. McCammon, S. M. Cohen.
J. Am. Chem. Soc. 13, 8232–8233 (2010)
21. Coupling Constant pH Simulations with Accelerated Molecular Dynamics Method
S. Williams,C. A. F. Oliveira, J. A. McCammon.
J. Chem. Theory Comput. 6, 560–568 (2010)
20. Including Receptor Flexibility and Induced fit-Effects into the Design of MMP2 inhibitors.
J. Durrant, C. A. F. Oliveira, J. A. McCammon.
J. Mol. Recognition 23(2), 173-182 (2010). Special Issue Article
19. 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).
18. 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).
17. 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).
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. A Molecular Dynamics Study on Liquid 1-Octanol. Part 3. Evaluating Octanol/Water Partition Coefficients of Novel 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. 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).
2. 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 (2001).
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).
Cesar Augusto Fernandes de Oliveira César de Oliveira
Cesar Augusto F. de Oliveira C. A. F. CAF deOliveira DeOliveira