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Interpretation of Quantitative Structure-Activity Relationship Models: Past, Present, and Future.

Journal of chemical information and modeling

Polishchuk P.
PMID: 28949520
J Chem Inf Model. 2017 Nov 27;57(11):2618-2639. doi: 10.1021/acs.jcim.7b00274. Epub 2017 Oct 13.

This paper is an overview of the most significant and impactful interpretation approaches of quantitative structure-activity relationship (QSAR) models, their development, and application. The evolution of the interpretation paradigm from "model → descriptors → (structure)" to "model → structure"...

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Polishchuk P. Interpretation of Quantitative Structure-Activity Relationship Models: Past, Present, and Future. J Chem Inf Model. 2017;57(11):2618-2639doi: 10.1021/acs.jcim.7b00274.
Polishchuk, P. (2017). Interpretation of Quantitative Structure-Activity Relationship Models: Past, Present, and Future. Journal of chemical information and modeling, 57(11), 2618-2639. https://doi.org/10.1021/acs.jcim.7b00274
Polishchuk, Pavel. "Interpretation of Quantitative Structure-Activity Relationship Models: Past, Present, and Future." Journal of chemical information and modeling vol. 57,11 (2017): 2618-2639. doi: https://doi.org/10.1021/acs.jcim.7b00274
Polishchuk P. Interpretation of Quantitative Structure-Activity Relationship Models: Past, Present, and Future. J Chem Inf Model. 2017 Nov 27;57(11):2618-2639. doi: 10.1021/acs.jcim.7b00274. Epub 2017 Oct 13. PMID: 28949520.
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Correction to Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation.

Journal of chemical information and modeling

Zhang J, Tuguldur B, van der Spoel D.
PMID: 27058595
J Chem Inf Model. 2016 Apr 25;56(4):819-20. doi: 10.1021/acs.jcim.6b00081. Epub 2016 Apr 08.

No abstract available.

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Zhang J, Tuguldur B, van der Spoel D. Correction to Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation. J Chem Inf Model. 2016;56(4):819-20doi: 10.1021/acs.jcim.6b00081.
Zhang, J., Tuguldur, B., & van der Spoel, D. (2016). Correction to Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation. Journal of chemical information and modeling, 56(4), 819-20. https://doi.org/10.1021/acs.jcim.6b00081
Zhang, Jin, et al. "Correction to Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation." Journal of chemical information and modeling vol. 56,4 (2016): 819-20. doi: https://doi.org/10.1021/acs.jcim.6b00081
Zhang J, Tuguldur B, van der Spoel D. Correction to Force Field Benchmark of Organic Liquids. 2. Gibbs Energy of Solvation. J Chem Inf Model. 2016 Apr 25;56(4):819-20. doi: 10.1021/acs.jcim.6b00081. Epub 2016 Apr 08. PMID: 27058595.
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An Additive Definition of Molecular Complexity.

Journal of chemical information and modeling

Böttcher T.
PMID: 26857537
J Chem Inf Model. 2016 Mar 28;56(3):462-70. doi: 10.1021/acs.jcim.5b00723. Epub 2016 Feb 22.

A framework for molecular complexity is established that is based on information theory and consistent with chemical knowledge. The resulting complexity index Cm is derived from abstracting the information content of a molecule by the degrees of freedom in...

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Böttcher T. An Additive Definition of Molecular Complexity. J Chem Inf Model. 2016;56(3):462-70doi: 10.1021/acs.jcim.5b00723.
Böttcher, T. (2016). An Additive Definition of Molecular Complexity. Journal of chemical information and modeling, 56(3), 462-70. https://doi.org/10.1021/acs.jcim.5b00723
Böttcher, Thomas. "An Additive Definition of Molecular Complexity." Journal of chemical information and modeling vol. 56,3 (2016): 462-70. doi: https://doi.org/10.1021/acs.jcim.5b00723
Böttcher T. An Additive Definition of Molecular Complexity. J Chem Inf Model. 2016 Mar 28;56(3):462-70. doi: 10.1021/acs.jcim.5b00723. Epub 2016 Feb 22. PMID: 26857537.
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What is the smallest saturated acyclic alkane that cannot be made?.

Journal of chemical information and modeling

de Silva KM, Goodman JM.
PMID: 15667132
J Chem Inf Model. 2005 Jan-Feb;45(1):81-7. doi: 10.1021/ci0497657.

Saturated acyclic alkanes may show a high degree of strain if they have many branches close to each other. We report calculations which indicate how strained a molecule may become before it falls apart rapidly at room temperature and...

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de Silva KM, Goodman JM. What is the smallest saturated acyclic alkane that cannot be made?. J Chem Inf Model. 2005;45(1):81-7doi: 10.1021/ci0497657.
de Silva, K. M., & Goodman, J. M. (2005). What is the smallest saturated acyclic alkane that cannot be made?. Journal of chemical information and modeling, 45(1), 81-7. https://doi.org/10.1021/ci0497657
de Silva, K M Nalin, and Goodman, Jonathan M. "What is the smallest saturated acyclic alkane that cannot be made?." Journal of chemical information and modeling vol. 45,1 (2005): 81-7. doi: https://doi.org/10.1021/ci0497657
de Silva KM, Goodman JM. What is the smallest saturated acyclic alkane that cannot be made?. J Chem Inf Model. 2005 Jan-Feb;45(1):81-7. doi: 10.1021/ci0497657. PMID: 15667132.
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Linear and nonlinear methods in modeling the aqueous solubility of organic compounds.

Journal of chemical information and modeling

Catana C, Gao H, Orrenius C, Stouten PF.
PMID: 15667142
J Chem Inf Model. 2005 Jan-Feb;45(1):170-6. doi: 10.1021/ci049797u.

Solubility data for 930 diverse compounds have been analyzed using linear Partial Least Square (PLS) and nonlinear PLS methods, Continuum Regression (CR), and Neural Networks (NN). 1D and 2D descriptors from MOE package in combination with E-state or ISIS...

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Catana C, Gao H, Orrenius C, et al. Linear and nonlinear methods in modeling the aqueous solubility of organic compounds. J Chem Inf Model. 2005;45(1):170-6doi: 10.1021/ci049797u.
Catana, C., Gao, H., Orrenius, C., & Stouten, P. F. (2005). Linear and nonlinear methods in modeling the aqueous solubility of organic compounds. Journal of chemical information and modeling, 45(1), 170-6. https://doi.org/10.1021/ci049797u
Catana, Cornel, et al. "Linear and nonlinear methods in modeling the aqueous solubility of organic compounds." Journal of chemical information and modeling vol. 45,1 (2005): 170-6. doi: https://doi.org/10.1021/ci049797u
Catana C, Gao H, Orrenius C, Stouten PF. Linear and nonlinear methods in modeling the aqueous solubility of organic compounds. J Chem Inf Model. 2005 Jan-Feb;45(1):170-6. doi: 10.1021/ci049797u. PMID: 15667142.
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Reaction-MQL: line notation for functional transformation.

Journal of chemical information and modeling

Reisen FH, Schneider G, Proschak E.
PMID: 19090785
J Chem Inf Model. 2009 Jan;49(1):6-12. doi: 10.1021/ci800215t.

Representation of chemical reactions is pivotal for different purposes in cheminformatics. We present an extension of the molecular query language (MQL), which combines readable style with meaningful rules for string representation of reactions and unambiguous product formation. The concept...

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Reisen FH, Schneider G, Proschak E. Reaction-MQL: line notation for functional transformation. J Chem Inf Model. 2009;49(1):6-12doi: 10.1021/ci800215t.
Reisen, F. H., Schneider, G., & Proschak, E. (2009). Reaction-MQL: line notation for functional transformation. Journal of chemical information and modeling, 49(1), 6-12. https://doi.org/10.1021/ci800215t
Reisen, Felix H, et al. "Reaction-MQL: line notation for functional transformation." Journal of chemical information and modeling vol. 49,1 (2009): 6-12. doi: https://doi.org/10.1021/ci800215t
Reisen FH, Schneider G, Proschak E. Reaction-MQL: line notation for functional transformation. J Chem Inf Model. 2009 Jan;49(1):6-12. doi: 10.1021/ci800215t. PMID: 19090785.
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Mechanism of the Kolbe-Schmitt reaction. Structure of the intermediate potassium phenoxide-CO(2) complex.

Journal of chemical information and modeling

Marković Z, Marković S, Manojlović N, Predojević-Simović J.
PMID: 17511442
J Chem Inf Model. 2007 Jul-Aug;47(4):1520-5. doi: 10.1021/ci700068b. Epub 2007 May 19.

Our investigation elucidates the structure of the intermediate in the first stage of the carboxylation reaction of potassium phenoxide. Under the reduced pressure of carbon dioxide the complex is not solvated with the CO(2) molecules. Under the conditions of...

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Marković Z, Marković S, Manojlović N, et al. Mechanism of the Kolbe-Schmitt reaction. Structure of the intermediate potassium phenoxide-CO(2) complex. J Chem Inf Model. 2007;47(4):1520-5doi: 10.1021/ci700068b.
Marković, Z., Marković, S., Manojlović, N., & Predojević-Simović, J. (2007). Mechanism of the Kolbe-Schmitt reaction. Structure of the intermediate potassium phenoxide-CO(2) complex. Journal of chemical information and modeling, 47(4), 1520-5. https://doi.org/10.1021/ci700068b
Marković, Zoran, et al. "Mechanism of the Kolbe-Schmitt reaction. Structure of the intermediate potassium phenoxide-CO(2) complex." Journal of chemical information and modeling vol. 47,4 (2007): 1520-5. doi: https://doi.org/10.1021/ci700068b
Marković Z, Marković S, Manojlović N, Predojević-Simović J. Mechanism of the Kolbe-Schmitt reaction. Structure of the intermediate potassium phenoxide-CO(2) complex. J Chem Inf Model. 2007 Jul-Aug;47(4):1520-5. doi: 10.1021/ci700068b. Epub 2007 May 19. PMID: 17511442.
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Kohonen network study of aromatic compounds based on electronic and nonelectronic structure descriptors.

Journal of chemical information and modeling

Panek JJ, Jezierska A, Vracko M.
PMID: 15807487
J Chem Inf Model. 2005 Mar-Apr;45(2):264-72. doi: 10.1021/ci049752t.

Atoms in Molecules (AIM) and Electron Localization Function (ELF) methodologies were applied to describe the electronic structure of 88 aromatic compounds. The analyzed database contains molecules substituted by nucleophilic and electrophilic groups which are responsible for electron density distribution...

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Panek JJ, Jezierska A, Vracko M. Kohonen network study of aromatic compounds based on electronic and nonelectronic structure descriptors. J Chem Inf Model. 2005;45(2):264-72doi: 10.1021/ci049752t.
Panek, J. J., Jezierska, A., & Vracko, M. (2005). Kohonen network study of aromatic compounds based on electronic and nonelectronic structure descriptors. Journal of chemical information and modeling, 45(2), 264-72. https://doi.org/10.1021/ci049752t
Panek, Jarosław J, et al. "Kohonen network study of aromatic compounds based on electronic and nonelectronic structure descriptors." Journal of chemical information and modeling vol. 45,2 (2005): 264-72. doi: https://doi.org/10.1021/ci049752t
Panek JJ, Jezierska A, Vracko M. Kohonen network study of aromatic compounds based on electronic and nonelectronic structure descriptors. J Chem Inf Model. 2005 Mar-Apr;45(2):264-72. doi: 10.1021/ci049752t. PMID: 15807487.
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Chemical markup, XML, and the world wide web. 6. CMLReact, an XML vocabulary for chemical reactions.

Journal of chemical information and modeling

Holliday GL, Murray-Rust P, Rzepa HS.
PMID: 16426051
J Chem Inf Model. 2006 Jan-Feb;46(1):145-57. doi: 10.1021/ci0502698.

A set of components (CMLReact) for managing chemical and biochemical reactions has been added to CML. These can be combined to support most of the strategies for the formal representation of reactions. The elements, attributes, and types are formally...

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Holliday GL, Murray-Rust P, Rzepa HS. Chemical markup, XML, and the world wide web. 6. CMLReact, an XML vocabulary for chemical reactions. J Chem Inf Model. 2006;46(1):145-57doi: 10.1021/ci0502698.
Holliday, G. L., Murray-Rust, P., & Rzepa, H. S. (2006). Chemical markup, XML, and the world wide web. 6. CMLReact, an XML vocabulary for chemical reactions. Journal of chemical information and modeling, 46(1), 145-57. https://doi.org/10.1021/ci0502698
Holliday, Gemma L, et al. "Chemical markup, XML, and the world wide web. 6. CMLReact, an XML vocabulary for chemical reactions." Journal of chemical information and modeling vol. 46,1 (2006): 145-57. doi: https://doi.org/10.1021/ci0502698
Holliday GL, Murray-Rust P, Rzepa HS. Chemical markup, XML, and the world wide web. 6. CMLReact, an XML vocabulary for chemical reactions. J Chem Inf Model. 2006 Jan-Feb;46(1):145-57. doi: 10.1021/ci0502698. PMID: 16426051.
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Simultaneous feature selection and parameter optimisation using an artificial ant colony: case study of melting point prediction.

Chemistry Central journal

O'Boyle NM, Palmer DS, Nigsch F, Mitchell JB.
PMID: 18959785
Chem Cent J. 2008 Oct 29;2:21. doi: 10.1186/1752-153X-2-21.

BACKGROUND: We present a novel feature selection algorithm, Winnowing Artificial Ant Colony (WAAC), that performs simultaneous feature selection and model parameter optimisation for the development of predictive quantitative structure-property relationship (QSPR) models. The WAAC algorithm is an extension of...

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O'Boyle NM, Palmer DS, Nigsch F, et al. Simultaneous feature selection and parameter optimisation using an artificial ant colony: case study of melting point prediction. Chem Cent J. 2008;2:21doi: 10.1186/1752-153X-2-21.
O'Boyle, N. M., Palmer, D. S., Nigsch, F., & Mitchell, J. B. (2008). Simultaneous feature selection and parameter optimisation using an artificial ant colony: case study of melting point prediction. Chemistry Central journal, 221. https://doi.org/10.1186/1752-153X-2-21
O'Boyle, Noel M, et al. "Simultaneous feature selection and parameter optimisation using an artificial ant colony: case study of melting point prediction." Chemistry Central journal vol. 2 (2008): 21. doi: https://doi.org/10.1186/1752-153X-2-21
O'Boyle NM, Palmer DS, Nigsch F, Mitchell JB. Simultaneous feature selection and parameter optimisation using an artificial ant colony: case study of melting point prediction. Chem Cent J. 2008 Oct 29;2:21. doi: 10.1186/1752-153X-2-21. PMID: 18959785; PMCID: PMC2603525.
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Modeling of the spread of an effluent and the overturning length scale near an underwater source in the northern Adriatic.

Journal of chemical information and modeling

Malacic V, Mozetic P.
PMID: 16309245
J Chem Inf Model. 2005 Nov-Dec;45(6):1491-501. doi: 10.1021/ci050201s.

No abstract available.

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Malacic V, Mozetic P. Modeling of the spread of an effluent and the overturning length scale near an underwater source in the northern Adriatic. J Chem Inf Model. 2005;45(6):1491-501doi: 10.1021/ci050201s.
Malacic, V., & Mozetic, P. (2005). Modeling of the spread of an effluent and the overturning length scale near an underwater source in the northern Adriatic. Journal of chemical information and modeling, 45(6), 1491-501. https://doi.org/10.1021/ci050201s
Malacic, Vlado, and Mozetic, Patricija. "Modeling of the spread of an effluent and the overturning length scale near an underwater source in the northern Adriatic." Journal of chemical information and modeling vol. 45,6 (2005): 1491-501. doi: https://doi.org/10.1021/ci050201s
Malacic V, Mozetic P. Modeling of the spread of an effluent and the overturning length scale near an underwater source in the northern Adriatic. J Chem Inf Model. 2005 Nov-Dec;45(6):1491-501. doi: 10.1021/ci050201s. PMID: 16309245.
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Prediction of properties from simulations: a re-examination with modern statistical methods.

Journal of chemical information and modeling

Mansson RA, Frey JG, Essex JW, Welsh AH.
PMID: 16309286
J Chem Inf Model. 2005 Nov-Dec;45(6):1791-803. doi: 10.1021/ci050056i.

We discuss models fit to data collected by Duffy and Jorgensen to predict solvation free energies and partition equilibria of drugs, organic molecules, aromatic heterocycles, and other molecules. These data were originally examined using linear regression, but here more...

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Mansson RA, Frey JG, Essex JW, et al. Prediction of properties from simulations: a re-examination with modern statistical methods. J Chem Inf Model. 2005;45(6):1791-803doi: 10.1021/ci050056i.
Mansson, R. A., Frey, J. G., Essex, J. W., & Welsh, A. H. (2005). Prediction of properties from simulations: a re-examination with modern statistical methods. Journal of chemical information and modeling, 45(6), 1791-803. https://doi.org/10.1021/ci050056i
Mansson, R A, et al. "Prediction of properties from simulations: a re-examination with modern statistical methods." Journal of chemical information and modeling vol. 45,6 (2005): 1791-803. doi: https://doi.org/10.1021/ci050056i
Mansson RA, Frey JG, Essex JW, Welsh AH. Prediction of properties from simulations: a re-examination with modern statistical methods. J Chem Inf Model. 2005 Nov-Dec;45(6):1791-803. doi: 10.1021/ci050056i. PMID: 16309286.
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Showing 1 to 12 of 609 entries