Carlos A. Del Carpio

Publications (71) View all

• Article: Applying Ultra-Accelerated Quantum Chemical Molecular Dynamics Technique for the Evaluation of Ligand Protein Interactions

  K. Kumar Sahu, Mohamed Ismael, S. Md. Abdur Rauf, A. Suzuki, R. Sahnoun, M. Koyama, H. Tsuboi, N. Hatakeyama, A. Endou, H. Takaba, C. A. Del Carpio, M. Kubo, A. Miyamoto
  Medicinal Chemistry Research 01/2010; 19:1. · 1.27 Impact Factor
• Article: A graph theoretical approach for assessing bio-macromolecular complex structural stability.

  Carlos Adriel Del Carpio, Mihai Iulian Florea, Ai Suzuki, Hideyuki Tsuboi, Nozomu Hatakeyama, Akira Endou, Hiromitsu Takaba, Eiichiro Ichiishi, Akira Miyamoto
  [show abstract] [hide abstract]
  ABSTRACT: Fast and proper assessment of bio macro-molecular complex structural rigidity as a measure of structural stability can be useful in systematic studies to predict molecular function, and can also enable the design of rapid scoring functions to rank automatically generated bio-molecular complexes. Based on the graph theoretical approach of Jacobs et al. [Jacobs DJ, Rader AJ, Kuhn LA, Thorpe MF (2001) Protein flexibility predictions using graph theory. Proteins: Struct Funct Genet 44:150-165] for expressing molecular flexibility, we propose a new scheme to analyze the structural stability of bio-molecular complexes. This analysis is performed in terms of the identification in interacting subunits of clusters of flappy amino acids (those constituting regions of potential internal motion) that undergo an increase in rigidity at complex formation. Gains in structural rigidity of the interacting subunits upon bio-molecular complex formation can be evaluated by expansion of the network of intra-molecular inter-atomic interactions to include inter-molecular inter-atomic interaction terms. We propose two indices for quantifying this change: one local, which can express localized (at the amino acid level) structural rigidity, the other global to express overall structural stability for the complex. The new system is validated with a series of protein complex structures reported in the protein data bank. Finally, the indices are used as scoring coefficients to rank automatically generated protein complex decoys.
  Journal of Molecular Modeling 05/2009; 15(11):1349-70. · 1.80 Impact Factor
• Article: A DFT study on the carbamates formation through the absorption of CO2 by AMP

  Mohamed Ismael, R. Sahnoun, A. Suzuki, M. Koyama, H. Tsuboi, N. Hatakeyama, A. Endou, H. Takaba, M. Kubo, S. Shimizu, C. A. Del Carpio, A. Miyamoto
  International Journal of Greenhouse Gas Control 01/2009; 3:612. · 5.11 Impact Factor
• Source

  Available from: Abdul Rajjak Shaikh

  Article: A DFT Study of the Heme Role in the N-Demethylation of Theophylline Mediated by Compound I of Cytochrome P450

  Mohamed Ismael, C. A. Del Carpio, A. R. Shaikh, H. Tsuboi, M. Koyama, A. Endou, M. Kubo, E. Broclawik, A. Miyamoto
  MATERIALS TRANSACTIONS 01/2007; 48:730. · 0.70 Impact Factor
• Source

  Available from: Abdul Rajjak Shaikh

  Article: Hyperconjugation with lone pair of morpholine nitrogen stabilizes transition state for phenyl hydroxylation in CYP3A4 metabolism of (S)-N-[1-(3-morpholin-4-yl phenyl) ethyl]-3- phenylacrylamide

  A. R. Shaikh, E. Broclawik, Mohamed Ismael, H. Tsuboi, M. Koyama, M. Kubo, C. A. Del Carpio, A. Miyamoto
  Chemical Physics Letters. 01/2006; 419:523.