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Partial order in chemistry.

Combinatorial chemistry & high throughput screening

Brüggemann R.
PMID: 18991572
Comb Chem High Throughput Screen. 2008 Nov;11(9):687-90. doi: 10.2174/138620708786306023.

In chemistry, there is broad use of graphs and graph-theoretical invariants derived from them. Less known are directed graphs, as e.g., motivated in reaction networks. Here, the focus is on directed graphs derived from order theory. General approaches based...

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Brüggemann R. Partial order in chemistry. Comb Chem High Throughput Screen. 2008;11(9):687-90doi: 10.2174/138620708786306023.
Brüggemann, R. (2008). Partial order in chemistry. Combinatorial chemistry & high throughput screening, 11(9), 687-90. https://doi.org/10.2174/138620708786306023
Brüggemann, Rainer. "Partial order in chemistry." Combinatorial chemistry & high throughput screening vol. 11,9 (2008): 687-90. doi: https://doi.org/10.2174/138620708786306023
Brüggemann R. Partial order in chemistry. Comb Chem High Throughput Screen. 2008 Nov;11(9):687-90. doi: 10.2174/138620708786306023. PMID: 18991572.
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Collection and preparation of molecular databases for virtual screening.

SAR and QSAR in environmental research

Saxena AK, Prathipati P.
PMID: 16920660
SAR QSAR Environ Res. 2006 Aug;17(4):371-92. doi: 10.1080/10629360600884462.

Drug discovery and development research is undergoing a paradigm shift from a linear and sequential nature of the various steps involved in the drug discovery process of the past to the more parallel approach of the present, due to...

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Saxena AK, Prathipati P. Collection and preparation of molecular databases for virtual screening. SAR QSAR Environ Res. 2006;17(4):371-92doi: 10.1080/10629360600884462.
Saxena, A. K., & Prathipati, P. (2006). Collection and preparation of molecular databases for virtual screening. SAR and QSAR in environmental research, 17(4), 371-92. https://doi.org/10.1080/10629360600884462
Saxena, A K, and Prathipati, P. "Collection and preparation of molecular databases for virtual screening." SAR and QSAR in environmental research vol. 17,4 (2006): 371-92. doi: https://doi.org/10.1080/10629360600884462
Saxena AK, Prathipati P. Collection and preparation of molecular databases for virtual screening. SAR QSAR Environ Res. 2006 Aug;17(4):371-92. doi: 10.1080/10629360600884462. PMID: 16920660.
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Multilayer formulation of the fragment molecular orbital method (FMO).

The journal of physical chemistry. A

Fedorov DG, Ishida T, Kitaura K.
PMID: 16833570
J Phys Chem A. 2005 Mar 24;109(11):2638-46. doi: 10.1021/jp047186z.

The fragment molecular orbital method (FMO) has been generalized to allow for multilayer structure. Fragments are assigned to layers, and each layer can be described with a different basis set and/or level of electron correlation. Interlayer boundaries are treated...

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Fedorov DG, Ishida T, Kitaura K. Multilayer formulation of the fragment molecular orbital method (FMO). J Phys Chem A. 2005;109(11):2638-46doi: 10.1021/jp047186z.
Fedorov, D. G., Ishida, T., & Kitaura, K. (2005). Multilayer formulation of the fragment molecular orbital method (FMO). The journal of physical chemistry. A, 109(11), 2638-46. https://doi.org/10.1021/jp047186z
Fedorov, Dmitri G, et al. "Multilayer formulation of the fragment molecular orbital method (FMO)." The journal of physical chemistry. A vol. 109,11 (2005): 2638-46. doi: https://doi.org/10.1021/jp047186z
Fedorov DG, Ishida T, Kitaura K. Multilayer formulation of the fragment molecular orbital method (FMO). J Phys Chem A. 2005 Mar 24;109(11):2638-46. doi: 10.1021/jp047186z. PMID: 16833570.
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Effect of steric molecular field settings on CoMFA predictivity.

Journal of molecular modeling

Mittal RR, McKinnon RA, Sorich MJ.
PMID: 18038162
J Mol Model. 2008 Jan;14(1):59-67. doi: 10.1007/s00894-007-0252-1. Epub 2007 Nov 24.

Steric molecular field can be represented in a number of ways in comparative molecular field analysis (CoMFA). This study aimed to investigate whether the choice of steric molecular field settings significantly influences the predictive performance of CoMFA and, if...

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Mittal RR, McKinnon RA, Sorich MJ. Effect of steric molecular field settings on CoMFA predictivity. J Mol Model. 2007;14(1):59-67doi: 10.1007/s00894-007-0252-1.
Mittal, R. R., McKinnon, R. A., & Sorich, M. J. (2008). Effect of steric molecular field settings on CoMFA predictivity. Journal of molecular modeling, 14(1), 59-67. https://doi.org/10.1007/s00894-007-0252-1
Mittal, Ruchi R, et al. "Effect of steric molecular field settings on CoMFA predictivity." Journal of molecular modeling vol. 14,1 (2008): 59-67. doi: https://doi.org/10.1007/s00894-007-0252-1
Mittal RR, McKinnon RA, Sorich MJ. Effect of steric molecular field settings on CoMFA predictivity. J Mol Model. 2008 Jan;14(1):59-67. doi: 10.1007/s00894-007-0252-1. Epub 2007 Nov 24. PMID: 18038162.
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The electronic structure of inorganic benzenes: valence bond and ring-current descriptions.

Inorganic chemistry

Engelberts JJ, Havenith RW, van Lenthe JH, Jenneskens LW, Fowler PW.
PMID: 16022524
Inorg Chem. 2005 Jul 25;44(15):5266-72. doi: 10.1021/ic050017o.

Valence bond (VB) theory and ring-current maps have been used to study the electronic structure of inorganic benzene analogues X(6)H(6) (X = C (1), Si (2)), X(6) (X = N (3), P (4)), X(3)Y(3)H(6) (X,Y = B,N (5), B,P...

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Engelberts JJ, Havenith RW, van Lenthe JH, et al. The electronic structure of inorganic benzenes: valence bond and ring-current descriptions. Inorg Chem. 2005;44(15):5266-72doi: 10.1021/ic050017o.
Engelberts, J. J., Havenith, R. W., van Lenthe, J. H., Jenneskens, L. W., & Fowler, P. W. (2005). The electronic structure of inorganic benzenes: valence bond and ring-current descriptions. Inorganic chemistry, 44(15), 5266-72. https://doi.org/10.1021/ic050017o
Engelberts, Jeroen J, et al. "The electronic structure of inorganic benzenes: valence bond and ring-current descriptions." Inorganic chemistry vol. 44,15 (2005): 5266-72. doi: https://doi.org/10.1021/ic050017o
Engelberts JJ, Havenith RW, van Lenthe JH, Jenneskens LW, Fowler PW. The electronic structure of inorganic benzenes: valence bond and ring-current descriptions. Inorg Chem. 2005 Jul 25;44(15):5266-72. doi: 10.1021/ic050017o. PMID: 16022524.
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Effect of linear surface-charge non-uniformities on the electrokinetic ionic-current rectification in conical nanopores.

Journal of colloid and interface science

Qian S, Joo SW, Ai Y, Cheney MA, Hou W.
PMID: 18977486
J Colloid Interface Sci. 2009 Jan 15;329(2):376-83. doi: 10.1016/j.jcis.2008.10.012. Epub 2008 Nov 01.

The electrokinetic ionic-current rectification in a conical nanopore with linearly varying surface-charge distributions is studied theoretically by using a continuum model composed of a coupled system of the Nernst-Planck equations for the ionic-concentration field and the Poisson equation for...

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Qian S, Joo SW, Ai Y, et al. Effect of linear surface-charge non-uniformities on the electrokinetic ionic-current rectification in conical nanopores. J Colloid Interface Sci. 2008;329(2):376-83doi: 10.1016/j.jcis.2008.10.012.
Qian, S., Joo, S. W., Ai, Y., Cheney, M. A., & Hou, W. (2009). Effect of linear surface-charge non-uniformities on the electrokinetic ionic-current rectification in conical nanopores. Journal of colloid and interface science, 329(2), 376-83. https://doi.org/10.1016/j.jcis.2008.10.012
Qian, Shizhi, et al. "Effect of linear surface-charge non-uniformities on the electrokinetic ionic-current rectification in conical nanopores." Journal of colloid and interface science vol. 329,2 (2009): 376-83. doi: https://doi.org/10.1016/j.jcis.2008.10.012
Qian S, Joo SW, Ai Y, Cheney MA, Hou W. Effect of linear surface-charge non-uniformities on the electrokinetic ionic-current rectification in conical nanopores. J Colloid Interface Sci. 2009 Jan 15;329(2):376-83. doi: 10.1016/j.jcis.2008.10.012. Epub 2008 Nov 01. PMID: 18977486.
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Virtual computational chemistry laboratory--design and description.

Journal of computer-aided molecular design

Tetko IV, Gasteiger J, Todeschini R, Mauri A, Livingstone D, Ertl P, Palyulin VA, Radchenko EV, Zefirov NS, Makarenko AS, Tanchuk VY, Prokopenko VV.
PMID: 16231203
J Comput Aided Mol Des. 2005 Jun;19(6):453-63. doi: 10.1007/s10822-005-8694-y.

Internet technology offers an excellent opportunity for the development of tools by the cooperative effort of various groups and institutions. We have developed a multi-platform software system, Virtual Computational Chemistry Laboratory, http://www.vcclab.org, allowing the computational chemist to perform a...

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Tetko IV, Gasteiger J, Todeschini R, et al. Virtual computational chemistry laboratory--design and description. J Comput Aided Mol Des. 2005;19(6):453-63doi: 10.1007/s10822-005-8694-y.
Tetko, I. V., Gasteiger, J., Todeschini, R., Mauri, A., Livingstone, D., Ertl, P., Palyulin, V. A., Radchenko, E. V., Zefirov, N. S., Makarenko, A. S., Tanchuk, V. Y., & Prokopenko, V. V. (2005). Virtual computational chemistry laboratory--design and description. Journal of computer-aided molecular design, 19(6), 453-63. https://doi.org/10.1007/s10822-005-8694-y
Tetko, Igor V, et al. "Virtual computational chemistry laboratory--design and description." Journal of computer-aided molecular design vol. 19,6 (2005): 453-63. doi: https://doi.org/10.1007/s10822-005-8694-y
Tetko IV, Gasteiger J, Todeschini R, Mauri A, Livingstone D, Ertl P, Palyulin VA, Radchenko EV, Zefirov NS, Makarenko AS, Tanchuk VY, Prokopenko VV. Virtual computational chemistry laboratory--design and description. J Comput Aided Mol Des. 2005 Jun;19(6):453-63. doi: 10.1007/s10822-005-8694-y. PMID: 16231203.
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Reparameterized Austin Model 1 for quantitative structure-property relationships in liquid media.

Journal of molecular modeling

Dobchev DA, Karelson M.
PMID: 16404615
J Mol Model. 2006 Mar;12(4):503-12. doi: 10.1007/s00894-005-0080-0. Epub 2006 Jan 11.

A reparameterization of the quantum-chemical AM1 (Austin Model 1) model has been carried out using a nonlinear optimization based on a modification of the Levenberg-Marquardt technique. The optimum numerical values for the one-electron resonance integral parameters (beta (s) and...

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Dobchev DA, Karelson M. Reparameterized Austin Model 1 for quantitative structure-property relationships in liquid media. J Mol Model. 2006;12(4):503-12doi: 10.1007/s00894-005-0080-0.
Dobchev, D. A., & Karelson, M. (2006). Reparameterized Austin Model 1 for quantitative structure-property relationships in liquid media. Journal of molecular modeling, 12(4), 503-12. https://doi.org/10.1007/s00894-005-0080-0
Dobchev, Dimitar A, and Karelson, Mati. "Reparameterized Austin Model 1 for quantitative structure-property relationships in liquid media." Journal of molecular modeling vol. 12,4 (2006): 503-12. doi: https://doi.org/10.1007/s00894-005-0080-0
Dobchev DA, Karelson M. Reparameterized Austin Model 1 for quantitative structure-property relationships in liquid media. J Mol Model. 2006 Mar;12(4):503-12. doi: 10.1007/s00894-005-0080-0. Epub 2006 Jan 11. PMID: 16404615.
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SBMLmerge, a system for combining biochemical network models.

Genome informatics. International Conference on Genome Informatics

Schulz M, Uhlendorf J, Klipp E, Liebermeister W.
PMID: 17503356
Genome Inform. 2006;17(1):62-71.

The Systems Biology Markup Language (SBML) is an XML-based format for representing mathematical models of biochemical reaction networks, and it is likely to become a main standard in the systems biology community. As published mathematical models in cell biology...

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Schulz M, Uhlendorf J, Klipp E, et al. SBMLmerge, a system for combining biochemical network models. Genome Inform. 2006;17(1):62-71
Schulz, M., Uhlendorf, J., Klipp, E., & Liebermeister, W. (2006). SBMLmerge, a system for combining biochemical network models. Genome informatics. International Conference on Genome Informatics, 17(1), 62-71.
Schulz, Marvin, et al. "SBMLmerge, a system for combining biochemical network models." Genome informatics. International Conference on Genome Informatics vol. 17,1 (2006): 62-71.
Schulz M, Uhlendorf J, Klipp E, Liebermeister W. SBMLmerge, a system for combining biochemical network models. Genome Inform. 2006;17(1):62-71. PMID: 17503356.
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Contact line and contact angle dynamics in superhydrophobic channels.

Langmuir : the ACS journal of surfaces and colloids

Zhang J, Kwok DY.
PMID: 16700586
Langmuir. 2006 May 23;22(11):4998-5004. doi: 10.1021/la053375c.

The dynamics of the wetting and movement of a three-phase contact line confined between two superhydrophobic surfaces were studied using a mean-field free-energy lattice Boltzmann model. Principle features of superhydrophobic surfaces, such as trapped vapor/air between rough microstructures, high...

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Zhang J, Kwok DY. Contact line and contact angle dynamics in superhydrophobic channels. Langmuir. 2006;22(11):4998-5004doi: 10.1021/la053375c.
Zhang, J., & Kwok, D. Y. (2006). Contact line and contact angle dynamics in superhydrophobic channels. Langmuir : the ACS journal of surfaces and colloids, 22(11), 4998-5004. https://doi.org/10.1021/la053375c
Zhang, Junfeng, and Kwok, Daniel Y. "Contact line and contact angle dynamics in superhydrophobic channels." Langmuir : the ACS journal of surfaces and colloids vol. 22,11 (2006): 4998-5004. doi: https://doi.org/10.1021/la053375c
Zhang J, Kwok DY. Contact line and contact angle dynamics in superhydrophobic channels. Langmuir. 2006 May 23;22(11):4998-5004. doi: 10.1021/la053375c. PMID: 16700586.
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The spatial extent of contaminants and the landscape scale: an analysis of the wildlife, conservation biology, and population modeling literature.

Environmental toxicology and chemistry

Carlsen TM, Coty JD, Kercher JR.
PMID: 15285375
Environ Toxicol Chem. 2004 Mar;23(3):798-811. doi: 10.1897/02-202.

Many contaminant releases to the terrestrial environment are of small areal extent. Thus, rather than evaluating the ecological impact on species in the immediate vicinity of the release, it may be more ecologically meaningful to determine if population impacts...

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Carlsen TM, Coty JD, Kercher JR. The spatial extent of contaminants and the landscape scale: an analysis of the wildlife, conservation biology, and population modeling literature. Environ Toxicol Chem. 2004;23(3):798-811doi: 10.1897/02-202.
Carlsen, T. M., Coty, J. D., & Kercher, J. R. (2004). The spatial extent of contaminants and the landscape scale: an analysis of the wildlife, conservation biology, and population modeling literature. Environmental toxicology and chemistry, 23(3), 798-811. https://doi.org/10.1897/02-202
Carlsen, Tina M, et al. "The spatial extent of contaminants and the landscape scale: an analysis of the wildlife, conservation biology, and population modeling literature." Environmental toxicology and chemistry vol. 23,3 (2004): 798-811. doi: https://doi.org/10.1897/02-202
Carlsen TM, Coty JD, Kercher JR. The spatial extent of contaminants and the landscape scale: an analysis of the wildlife, conservation biology, and population modeling literature. Environ Toxicol Chem. 2004 Mar;23(3):798-811. doi: 10.1897/02-202. PMID: 15285375.
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Systematic generation of chemical structures for rational drug design based on QSAR models.

Current computer-aided drug design

Funatsu K, Miyao T, Arakawa M.
PMID: 20550510
Curr Comput Aided Drug Des. 2011 Mar;7(1):1-9. doi: 10.2174/157340911793743556.

The first step in the process of drug development is to determine those lead compounds that demonstrate significant biological activity with regard to a target protein. Because this process is often costly and time consuming, there is a need...

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Funatsu K, Miyao T, Arakawa M. Systematic generation of chemical structures for rational drug design based on QSAR models. Curr Comput Aided Drug Des. 2011;7(1):1-9doi: 10.2174/157340911793743556.
Funatsu, K., Miyao, T., & Arakawa, M. (2011). Systematic generation of chemical structures for rational drug design based on QSAR models. Current computer-aided drug design, 7(1), 1-9. https://doi.org/10.2174/157340911793743556
Funatsu, Kimito, et al. "Systematic generation of chemical structures for rational drug design based on QSAR models." Current computer-aided drug design vol. 7,1 (2011): 1-9. doi: https://doi.org/10.2174/157340911793743556
Funatsu K, Miyao T, Arakawa M. Systematic generation of chemical structures for rational drug design based on QSAR models. Curr Comput Aided Drug Des. 2011 Mar;7(1):1-9. doi: 10.2174/157340911793743556. PMID: 20550510.
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Showing 13 to 24 of 125 entries