Carlos A. Del Carpio |
|
|
|
Kyoto Institute of Technology
·
Drosophila Genetic Resource Center
|
Questions and Answers (4) View all
-
Answer added in Bioinformatics and Computational Biology4 Any good protein 3d structure model validation program on line?By Carlos Del Carpio · Kyoto Institute of TechnologyCarlos Del Carpio · Kyoto Institute of TechnologyThank you for the reply. I could find the right place.Thank you for the reply. I could find the right place.Following
-
Question asked in Bioinformatics and Computational Biology4 Any good protein 3d structure model validation program on line?Has anybody tried to install or use the MODCHECK suite to validate structural models of proteins? Is there any other better validation package? I hav... [more]Has anybody tried to install or use the MODCHECK suite to validate structural models of proteins? Is there any other better validation package? I have found VADAR, but its results are a bit ambiguous.They give a ftp site from which to download MODCHECK but it seems the page is no more taken care of... Could anybody comment on WHAT-IF, or WHAT-CHECK... Thank you very muchBy Carlos Del Carpio · Kyoto Institute of TechnologyFollowing
-
Answer added in Structural Bioinformatics and Structural Biology10 Which is the best free online tool available for protein-protein docking ?By Deepa Narayanan · Ethiraj College for WomenCarlos Del Carpio · Kyoto Institute of TechnologyMIAX is a system that I have been developing for years, so if you have your proteins, you can give me your PDB codes, and see what candidates I can pr... [more]MIAX is a system that I have been developing for years, so if you have your proteins, you can give me your PDB codes, and see what candidates I can predict for you... though as I told you before, there are not programs that will give you the close-to-native solution one may require...Following
-
Answer added in Structural Bioinformatics and Structural Biology10 Which is the best free online tool available for protein-protein docking ?By Deepa Narayanan · Ethiraj College for WomenCarlos Del Carpio · Kyoto Institute of TechnologyI don't think such a tool exists... There are programs that can give you candidates (servers, just make a google search), but not the exact solution..... [more]I don't think such a tool exists... There are programs that can give you candidates (servers, just make a google search), but not the exact solution... This problem as well as the protein 3D structure prediction problem are still matter of huge investigation...Following
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. MiyamotoMedicinal 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. MiyamotoInternational Journal of Greenhouse Gas Control 01/2009; 3:612. · 5.11 Impact Factor -
SourceAvailable 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. MiyamotoMATERIALS TRANSACTIONS 01/2007; 48:730. · 0.70 Impact Factor -
SourceAvailable 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. MiyamotoChemical Physics Letters. 01/2006; 419:523.