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Parameter sensitivity analysis of stochastic models: application to catalytic reaction networks.

Computational biology and chemistry

Damiani C, Filisetti A, Graudenzi A, Lecca P.
PMID: 23246776
Comput Biol Chem. 2013 Feb;42:5-17. doi: 10.1016/j.compbiolchem.2012.10.007. Epub 2012 Nov 07.

A general numerical methodology for parametric sensitivity analysis is proposed, which allows to determine the parameters exerting the greatest influence on the output of a stochastic computational model, especially when the knowledge about the actual value of a parameter...

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Damiani C, Filisetti A, Graudenzi A, et al. Parameter sensitivity analysis of stochastic models: application to catalytic reaction networks. Comput Biol Chem. 2012;42:5-17doi: 10.1016/j.compbiolchem.2012.10.007.
Damiani, C., Filisetti, A., Graudenzi, A., & Lecca, P. (2013). Parameter sensitivity analysis of stochastic models: application to catalytic reaction networks. Computational biology and chemistry, 425-17. https://doi.org/10.1016/j.compbiolchem.2012.10.007
Damiani, Chiara, et al. "Parameter sensitivity analysis of stochastic models: application to catalytic reaction networks." Computational biology and chemistry vol. 42 (2013): 5-17. doi: https://doi.org/10.1016/j.compbiolchem.2012.10.007
Damiani C, Filisetti A, Graudenzi A, Lecca P. Parameter sensitivity analysis of stochastic models: application to catalytic reaction networks. Comput Biol Chem. 2013 Feb;42:5-17. doi: 10.1016/j.compbiolchem.2012.10.007. Epub 2012 Nov 07. PMID: 23246776.
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Catalytic site identification--a web server to identify catalytic site structural matches throughout PDB.

Nucleic acids research

Kirshner DA, Nilmeier JP, Lightstone FC.
PMID: 23680785
Nucleic Acids Res. 2013 Jul;41:W256-65. doi: 10.1093/nar/gkt403. Epub 2013 May 16.

The catalytic site identification web server provides the innovative capability to find structural matches to a user-specified catalytic site among all Protein Data Bank proteins rapidly (in less than a minute). The server also can examine a user-specified protein...

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Kirshner DA, Nilmeier JP, Lightstone FC. Catalytic site identification--a web server to identify catalytic site structural matches throughout PDB. Nucleic Acids Res. 2013;41:W256-65doi: 10.1093/nar/gkt403.
Kirshner, D. A., Nilmeier, J. P., & Lightstone, F. C. (2013). Catalytic site identification--a web server to identify catalytic site structural matches throughout PDB. Nucleic acids research, 41W256-65. https://doi.org/10.1093/nar/gkt403
Kirshner, Daniel A, et al. "Catalytic site identification--a web server to identify catalytic site structural matches throughout PDB." Nucleic acids research vol. 41 (2013): W256-65. doi: https://doi.org/10.1093/nar/gkt403
Kirshner DA, Nilmeier JP, Lightstone FC. Catalytic site identification--a web server to identify catalytic site structural matches throughout PDB. Nucleic Acids Res. 2013 Jul;41:W256-65. doi: 10.1093/nar/gkt403. Epub 2013 May 16. PMID: 23680785; PMCID: PMC3692059.
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The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes.

Nucleic acids research

Furnham N, Holliday GL, de Beer TA, Jacobsen JO, Pearson WR, Thornton JM.
PMID: 24319146
Nucleic Acids Res. 2014 Jan;42:D485-9. doi: 10.1093/nar/gkt1243. Epub 2013 Dec 06.

Understanding which are the catalytic residues in an enzyme and what function they perform is crucial to many biology studies, particularly those leading to new therapeutics and enzyme design. The original version of the Catalytic Site Atlas (CSA) (http://www.ebi.ac.uk/thornton-srv/databases/CSA)...

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Furnham N, Holliday GL, de Beer TA, et al. The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes. Nucleic Acids Res. 2013;42:D485-9doi: 10.1093/nar/gkt1243.
Furnham, N., Holliday, G. L., de Beer, T. A., Jacobsen, J. O., Pearson, W. R., & Thornton, J. M. (2014). The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes. Nucleic acids research, 42D485-9. https://doi.org/10.1093/nar/gkt1243
Furnham, Nicholas, et al. "The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes." Nucleic acids research vol. 42 (2014): D485-9. doi: https://doi.org/10.1093/nar/gkt1243
Furnham N, Holliday GL, de Beer TA, Jacobsen JO, Pearson WR, Thornton JM. The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes. Nucleic Acids Res. 2014 Jan;42:D485-9. doi: 10.1093/nar/gkt1243. Epub 2013 Dec 06. PMID: 24319146; PMCID: PMC3964973.
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EzCatDB: the enzyme reaction database, 2015 update.

Nucleic acids research

Nagano N, Nakayama N, Ikeda K, Fukuie M, Yokota K, Doi T, Kato T, Tomii K.
PMID: 25324316
Nucleic Acids Res. 2015 Jan;43:D453-8. doi: 10.1093/nar/gku946. Epub 2014 Oct 16.

The EzCatDB database (http://ezcatdb.cbrc.jp/EzCatDB/) has emphasized manual classification of enzyme reactions from the viewpoints of enzyme active-site structures and their catalytic mechanisms based on literature information, amino acid sequences of enzymes (UniProtKB) and the corresponding tertiary structures from the...

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Nagano N, Nakayama N, Ikeda K, et al. EzCatDB: the enzyme reaction database, 2015 update. Nucleic Acids Res. 2014;43:D453-8doi: 10.1093/nar/gku946.
Nagano, N., Nakayama, N., Ikeda, K., Fukuie, M., Yokota, K., Doi, T., Kato, T., & Tomii, K. (2015). EzCatDB: the enzyme reaction database, 2015 update. Nucleic acids research, 43D453-8. https://doi.org/10.1093/nar/gku946
Nagano, Nozomi, et al. "EzCatDB: the enzyme reaction database, 2015 update." Nucleic acids research vol. 43 (2015): D453-8. doi: https://doi.org/10.1093/nar/gku946
Nagano N, Nakayama N, Ikeda K, Fukuie M, Yokota K, Doi T, Kato T, Tomii K. EzCatDB: the enzyme reaction database, 2015 update. Nucleic Acids Res. 2015 Jan;43:D453-8. doi: 10.1093/nar/gku946. Epub 2014 Oct 16. PMID: 25324316; PMCID: PMC4384017.
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Key role of the REC lobe during CRISPR-Cas9 activation by 'sensing', 'regulating', and 'locking' the catalytic HNH domain.

Quarterly reviews of biophysics

Palermo G, Chen JS, Ricci CG, Rivalta I, Jinek M, Batista VS, Doudna JA, McCammon JA.
PMID: 30555184
Q Rev Biophys. 2018;51. doi: 10.1017/S0033583518000070. Epub 2018 Aug 03.

Understanding the conformational dynamics of CRISPR (clustered regularly interspaced short palindromic repeat)-Cas9 is of the utmost importance for improving its genome editing capability. Here, molecular dynamics simulations performed using Anton-2 - a specialized supercomputer capturing micro-to-millisecond biophysical events in...

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Palermo G, Chen JS, Ricci CG, et al. Key role of the REC lobe during CRISPR-Cas9 activation by 'sensing', 'regulating', and 'locking' the catalytic HNH domain. Q Rev Biophys. 2018;51doi: 10.1017/S0033583518000070.
Palermo, G., Chen, J. S., Ricci, C. G., Rivalta, I., Jinek, M., Batista, V. S., Doudna, J. A., & McCammon, J. A. (2018). Key role of the REC lobe during CRISPR-Cas9 activation by 'sensing', 'regulating', and 'locking' the catalytic HNH domain. Quarterly reviews of biophysics, 51. https://doi.org/10.1017/S0033583518000070
Palermo, Giulia, et al. "Key role of the REC lobe during CRISPR-Cas9 activation by 'sensing', 'regulating', and 'locking' the catalytic HNH domain." Quarterly reviews of biophysics vol. 51 (2018). doi: https://doi.org/10.1017/S0033583518000070
Palermo G, Chen JS, Ricci CG, Rivalta I, Jinek M, Batista VS, Doudna JA, McCammon JA. Key role of the REC lobe during CRISPR-Cas9 activation by 'sensing', 'regulating', and 'locking' the catalytic HNH domain. Q Rev Biophys. 2018;51. doi: 10.1017/S0033583518000070. Epub 2018 Aug 03. PMID: 30555184; PMCID: PMC6292676.
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Showing 1 to 5 of 5 entries