Search

Your search keyword '"Tämm, Kaido"' showing total 48 results
Start Over Author "Tämm, Kaido"
48 results on '"Tämm, Kaido"'

1. CompSafeNano project: NanoInformatics approaches for safe-by-design nanomaterials

Author

Zouraris, Dimitrios, Mavrogiorgis, Angelos, Tsoumanis, Andreas, Saarimäki, Laura Aliisa, del Giudice, Giusy, Federico, Antonio, Serra, Angela, Greco, Dario, Rouse, Ian, Subbotina, Julia, Lobaskin, Vladimir, Jagiello, Karolina, Ciura, Krzesimir, Judzinska, Beata, Mikolajczyk, Alicja, Sosnowska, Anita, Puzyn, Tomasz, Gulumian, Mary, Wepener, Victor, Martinez, Diego S.T., Petry, Romana, El Yamani, Naouale, Rundén-Pran, Elise, Murugadoss, Sivakumar, Shaposhnikov, Sergey, Minadakis, Vasileios, Tsiros, Periklis, Sarimveis, Harry, Longhin, Eleonora Marta, SenGupta, Tanima, Olsen, Ann-Karin Hardie, Skakalova, Viera, Hutar, Peter, Dusinska, Maria, Papadiamantis, Anastasios G., Gheorghe, L. Cristiana, Reilly, Katie, Brun, Emilie, Ullah, Sami, Cambier, Sebastien, Serchi, Tommaso, Tämm, Kaido, Lorusso, Candida, Dondero, Francesco, Melagrakis, Evangelos, Fraz, Muhammad Moazam, Melagraki, Georgia, Lynch, Iseult, and Afantitis, Antreas

Published
2025
Full Text
View/download PDF

3. A computational view on nanomaterial intrinsic and extrinsic features for nanosafety and sustainability

Author

Mancardi, Giulia, Mikolajczyk, Alicja, Annapoorani, Vigneshwari K., Bahl, Aileen, Blekos, Kostas, Burk, Jaanus, Çetin, Yarkın A., Chairetakis, Konstantinos, Dutta, Sutapa, Escorihuela, Laura, Jagiello, Karolina, Singhal, Ankush, van der Pol, Rianne, Bañares, Miguel A., Buchete, Nicolae-Viorel, Calatayud, Monica, Dumit, Verónica I., Gardini, Davide, Jeliazkova, Nina, Haase, Andrea, Marcoulaki, Effie, Martorell, Benjamí, Puzyn, Tomasz, Agur Sevink, G.J., Simeone, Felice C., Tämm, Kaido, and Chiavazzo, Eliodoro

Published
2023
Full Text
View/download PDF

7. NanoConstruct: A Web Application Builder of Ellipsoidal Nanoparticles for the investigation of their crystal growth, their stability, and the calculation of their atomistic descriptors

Author

Kolokathis, Panagiotis D., primary, Zouraris, Dimitrios, additional, Voyiatzis, Evangelos, additional, Sidiropoulos, Nikolaos K., additional, Tsoumanis, Andreas, additional, Melagraki, Georgia, additional, Tämm, Kaido, additional, Lynch, Iseult, additional, and Afantitis, Antreas, additional

Published
2024
Full Text
View/download PDF

10. An Integrated Data-Driven Strategy for Safe-by-Design Nanoparticles: The FP7 MODERN Project

Author

Brehm, Martin, Kafka, Alexander, Bamler, Markus, Kühne, Ralph, Schüürmann, Gerrit, Sikk, Lauri, Burk, Jaanus, Burk, Peeter, Tamm, Tarmo, Tämm, Kaido, Pokhrel, Suman, Mädler, Lutz, Kahru, Anne, Aruoja, Villem, Sihtmäe, Mariliis, Scott-Fordsmand, Janeck, Sorensen, Peter B., Escorihuela, Laura, Roca, Carlos P., Fernández, Alberto, Giralt, Francesc, Rallo, Robert, Tran, Lang, editor, Bañares, Miguel A., editor, and Rallo, Robert, editor

Published
2017
Full Text
View/download PDF

17. Machine learning and materials modelling interpretation of in vivo toxicological response to TiO2 nanoparticles library (UV and non-UV exposure)

Author

Gomes, Susana I. L., primary, Amorim, Mónica J. B., additional, Pokhrel, Suman, additional, Mädler, Lutz, additional, Fasano, Matteo, additional, Chiavazzo, Eliodoro, additional, Asinari, Pietro, additional, Jänes, Jaak, additional, Tämm, Kaido, additional, Burk, Jaanus, additional, and Scott-Fordsmand, Janeck J., additional

Published
2021
Full Text
View/download PDF

18. Can an InChI for Nano Address the Need for a Simplified Representation of Complex Nanomaterials across Experimental and Nanoinformatics Studies?

Author

Lynch, Iseult, primary, Afantitis, Antreas, additional, Exner, Thomas, additional, Himly, Martin, additional, Lobaskin, Vladimir, additional, Doganis, Philip, additional, Maier, Dieter, additional, Sanabria, Natasha, additional, Papadiamantis, Anastasios G., additional, Rybinska-Fryca, Anna, additional, Gromelski, Maciej, additional, Puzyn, Tomasz, additional, Willighagen, Egon, additional, Johnston, Blair D., additional, Gulumian, Mary, additional, Matzke, Marianne, additional, Green Etxabe, Amaia, additional, Bossa, Nathan, additional, Serra, Angela, additional, Liampa, Irene, additional, Harper, Stacey, additional, Tämm, Kaido, additional, Jensen, Alexander CØ, additional, Kohonen, Pekka, additional, Slater, Luke, additional, Tsoumanis, Andreas, additional, Greco, Dario, additional, Winkler, David A., additional, Sarimveis, Haralambos, additional, and Melagraki, Georgia, additional

Published
2020
Full Text
View/download PDF

19. Predicting Cytotoxicity of Metal Oxide Nanoparticles Using Isalos Analytics Platform

Author

Papadiamantis, Anastasios G., primary, Jänes, Jaak, additional, Voyiatzis, Evangelos, additional, Sikk, Lauri, additional, Burk, Jaanus, additional, Burk, Peeter, additional, Tsoumanis, Andreas, additional, Ha, My Kieu, additional, Yoon, Tae Hyun, additional, Valsami-Jones, Eugenia, additional, Lynch, Iseult, additional, Melagraki, Georgia, additional, Tämm, Kaido, additional, and Afantitis, Antreas, additional

Published
2020
Full Text
View/download PDF

20. Can an InChI for Nano Address the Need for a Simplified Representation of Complex Nanomaterials across Experimental and Nanoinformatics Studies?

Author

Lynch, Iseult, Anreas Afantitis, Exner, Thomas, Himley, Martin, Lobaskin, Vladimir, Doganis, Phillip, Maier, Dieter, Sanabria, Natasha, Rybinska-Fryca, Anna, Gromelski, Maciej, Puzyn, Tomasz, Willighagen, Egon, Johnston, Blair, Gulumian, Mary, Matzke, Marianne, Etxabe, Amaia Green, Bossa, Nathan, Serra, Angela, Liampa, Irene, Harper, Stacey, Tämm, Kaido, Jensen, Alexander CØ, Kohonen, Pekka, Slater, Luke, Tsoumanis, Andreas, Greco, Dario, Winkler, David, Haralambos Sarimveis, and Melagraki, Georgia

Subjects
FOS: Nanotechnology, 100708 Nanomaterials
Abstract

Chemoinformatics has developed efficient ways of representing chemical structures for small molecules as simple text strings, simplified molecular-input line-entry system (SMILES) and the IUPAC International Chemical Identifier (InChI), which are machine-readable. In particular, InChIs have been extended to encode formalized representations of mixtures and reactions, and work is ongoing to represent polymers and other macromolecules in this way. The next frontier is encoding the multi-component structures of nanomaterials (NMs) in a machine-readable format to enable linking of datasets for nanoinformatics and regulatory applications. A workshop organized by the H2020 research infrastructure NanoCommons and the nanoinformatics project NanoSolveIT analysed issues involved in developing an InChI for NMs (NInChI). The layers needed to captureNMstructures include but are not limited to: core composition (possibly multi-layered); surface topography; surface coatings or functionalization; doping with other chemicals; and representation of impurities. NM distributions (size, shape, composition, surface properties, etc.), types of chemical linkages connecting surface functionalization and coating molecules to the core, and various crystallographic forms exhibited by NMs also need to be considered. Six case studies were conducted to elucidate requirements for unambiguous description of NMs. The suggested NInChI layers are intended to stimulate further analysis that will lead to the first version of a “nano” extension to the InChI standard.

Published
2020
Full Text
View/download PDF

28. Comparison of prominent methods for computational studies of lanthanoid cation complexation.

Author

Luhaste, Liisa, Tämm, Kaido, Sikk, Lauri, Pupart, Anni, Toomsalu, Eve, and Burk, Peeter

Subjects
*RARE earth metals, *QUANTUM chemistry, *BINDING energy, *CATIONS, *DENSITY functional theory
Abstract

We compared different computational methods (quantum chemical and DFT) for calculations of binding energies of 8- and 9-coordinated lanthanoid-aqua complexes. We used nine computational methods and compared the results with those obtained by the CCSD(T) method. All the nine methods provided relatively similar results and calculated energies correlated very well with the CCSD(T) obtained energies for complexes of this type. The comparison of basis sets revealed that combination of Dolg's (5s5p4d)/[4s4p3d] + 2s1p1d basis set for lanthanoids and the cc-pvdz basis set for non-lanthanoids can be suggested as optimal for further studies of lanthanoids cation complexation. [ABSTRACT FROM AUTHOR]

Published
2018
Full Text
View/download PDF

29. Macrocyclic peptidomimetics with antimicrobial activity: synthesis, bioassay, and molecular modeling studies

Author

Ibrahim, Mohamed A., primary, Panda, Siva S., additional, Oliferenko, Alexander A., additional, Oliferenko, Polina V., additional, Girgis, Adel S., additional, Elagawany, Mohamed, additional, Küçükbay, F. Zehra, additional, Panda, Chandramukhi S., additional, Pillai, Girinath G., additional, Samir, Ahmed, additional, Tämm, Kaido, additional, Hall, C. Dennis, additional, and Katritzky, Alan R., additional

Published
2015
Full Text
View/download PDF

34. QSAR study of pharmacological permeabilities

Author

Karelson, Mati, primary, Karelson, Gunnar, additional, Tamm, Tarmo, additional, Tulp, Indrek, additional, Jänes, Jaak, additional, Tämm, Kaido, additional, Lomaka, Andre, additional, Savchenko, Deniss, additional, and Dobchev, Dimitar, additional

Published
2009
Full Text
View/download PDF

36. Skin Permeation Rate as a Function of Chemical Structure

Author

Katritzky, Alan R., primary, Dobchev, Dimitar A., additional, Fara, Dan C., additional, Hür, Evrim, additional, Tämm, Kaido, additional, Kurunczi, Ludovic, additional, Karelson, Mati, additional, Varnek, Alexandre, additional, and Solov'ev, Vitaly P., additional

Published
2006
Full Text
View/download PDF

41. Skin Permeation Rate as a Function of Chemical Structure

Author

R. Katritzky, Alan, A. Dobchev, Dimitar, C. Fara, Dan, Hür, Evrim, Tämm, Kaido, Kurunczi, Ludovic, Karelson, Mati, Varnek, Alexandre, and P. Solov'ev, Vitaly

Abstract

Multilinear and nonlinear QSAR models were built for the skin permeation rate (Log Kp) of a set of 143 diverse compounds. Satisfactory models were obtained by three approaches applied:  (i) CODESSA PRO, (ii) Neural Network modeling using large pools of theoretical molecular descriptors, and (iii) ISIDA modeling based on fragment descriptors. The predictive abilities of the models were assessed by internal and external validations. The descriptors involved in the equations are discussed from the physicochemical point of view to illuminate the factors that influence skin permeation.

Published
2006

42. Aqueous Biphasic Systems. Partitioning of Organic Molecules:  A QSPR Treatment

Author

R. Katritzky, Alan, Tämm, Kaido, Kuanar, Minati, C. Fara, Dan, Oliferenko, Alexander, Oliferenko, Polina, G. Huddleston, Jonathan, and D. Rogers, Robin

Abstract

The partitioning of 29 small organic probes in a PEG-2000/(NH4)2SO4biphasic system was investigated using a quantitative structure−property relationship (QSPR) approach. A three-descriptor equation with the squared correlation coefficient (R2) of 0.97 for the partition coefficient (log D) was obtained. All descriptors were derived solely from the chemical structure of the compounds. Using the same descriptors, a three-parameter model was also obtained for log P(octanol/water, R2 0.89); predicted log Pvalues were used as an external descriptor for modeling log D.

Published
2004
Full Text
View/download PDF

44. Machine learning and materials modelling interpretation of in vivo toxicological response to TiO 2 nanoparticles library (UV and non-UV exposure).

Author

Gomes SIL, Amorim MJB, Pokhrel S, Mädler L, Fasano M, Chiavazzo E, Asinari P, Jänes J, Tämm K, Burk J, and Scott-Fordsmand JJ

Subjects
Animals, Machine Learning, Titanium toxicity, Metal Nanoparticles, Nanoparticles toxicity, Oligochaeta
Abstract

Assessing the risks of nanomaterials/nanoparticles (NMs/NPs) under various environmental conditions requires a more systematic approach, including the comparison of effects across many NMs with identified different but related characters/descriptors. Hence, there is an urgent need to provide coherent (eco)toxicological datasets containing comprehensive toxicity information relating to a diverse spectra of NPs characters. These datasets are test benches for developing holistic methodologies with broader applicability. In the present study we assessed the effects of a custom design Fe-doped TiO 2 NPs library, using the soil invertebrate Enchytraeus crypticus (Oligochaeta), via a 5-day pulse via aqueous exposure followed by a 21-days recovery period in soil (survival, reproduction assessment). Obviously, when testing TiO 2 , realistic conditions should include UV exposure. The 11 Fe-TiO 2 library contains NPs of size range between 5-27 nm with varying %Fe (enabling the photoactivation of TiO 2 at energy wavelengths in the visible-light range). The NPs were each described by 122 descriptors, being a mixture of measured and atomistic model descriptors. The data were explored using single and univariate statistical methods, combined with machine learning and multiscale modelling techniques. An iterative pruning process was adopted for identifying automatically the most significant descriptors. TiO 2 NPs toxicity decreased when combined with UV. Notably, the short-term water exposure induced lasting biological responses even after longer-term recovery in clean exposure. The correspondence with Fe-content correlated with the band-gap hence the reduction of UV oxidative stress. The inclusion of both measured and modelled materials data benefitted the explanation of the results, when combined with machine learning.

Published
2021
Full Text
View/download PDF

45. Robust Modeling and Scaffold Hopping: Case Study Based on HIV Reverse Transcriptase Inhibitors Type-1 Data.

Author

Pillai GG, Mederos L, Panda CS, Gronski A, Burk P, Hall CD, Katritzky AR, Tämm K, and Karelson M

Subjects
Algorithms, HIV Reverse Transcriptase chemistry, HIV-1 enzymology, Linear Models, Models, Molecular, HIV Reverse Transcriptase antagonists & inhibitors, Quantitative Structure-Activity Relationship, Reverse Transcriptase Inhibitors chemistry
Abstract

Background: Human immunodeficiency virus type 1 (HIV-1) is the causative agent of AIDS occurs across mucosal surfaces or by direct inoculation., Objective: The objective of this study was to consider chemically diverse scaffold sets of HIV-1 Reverse Transcriptase Inhibitors (HIV-1 RTI) subjected to ideal oriented QSAR with large descriptor space., Method: We generated a four-parameter QSAR model based on 111 data points, which provided an optimum prediction of HIV-1 RTI for overall 367 experimentally measured compounds., Results: The robustness of the model is demonstrated by its statistical validation (Ntraining = 111, R2 = 0.85, Q2lmo = 0.84) and by the prediction of HIV-1 inhibition activity for experimentally measured compounds., Conclusion: Finally, 5 novel hit compounds were designed in silico by using a virtual screening approach. The new hits met all the pharmacophore constraints and predicted pIC50 values within the binding ability of HIV-1 RT protein targets.

Published
2016
Full Text
View/download PDF

46. Theoretical modeling of HPV: QSAR and novodesign with fragment approach.

Author

Pillai GG, Sikk L, Tamm T, Karelson M, Burk P, and Tämm K

Subjects
Human papillomavirus 6 enzymology, Humans, Inhibitory Concentration 50, Molecular Structure, Adenosine Triphosphatases antagonists & inhibitors, DNA Helicases antagonists & inhibitors, Drug Design, Enzyme Inhibitors chemistry, Enzyme Inhibitors pharmacology, Human papillomavirus 6 drug effects, Quantitative Structure-Activity Relationship
Abstract

Structure-activity relationships in a data set of HPV6-E1 helicase ATPase inhibitors were investigated based on two different sets of descriptors. Statistically significant four parameter Quantitative Structure-Activity Relationships (QSAR) models were constructed and validated in both cases (R(2)=0.849; R(2) cv=0.811; F=52.20; s(2)=0.25; N=42). A Fragment based QSAR (FQSAR) approach was applied for developing a fragment-QSAR equation, which enabled the construction of virtual structures for novel ATPase inhibitors with desired or pre-defined activity.

Published
2014
Full Text
View/download PDF

47. Fragment-based development of HCV protease inhibitors for the treatment of hepatitis C.

Author

Karelson M, Dobchev DA, Karelson G, Tamm T, Tämm K, Nikonov A, Mutso M, and Merits A

Subjects
Computer Simulation, Hepacivirus drug effects, Hepatitis C drug therapy, Hepatitis C enzymology, Humans, Linear Models, Models, Biological, Antiviral Agents chemistry, Antiviral Agents pharmacology, Hepacivirus enzymology, Peptide Hydrolases metabolism, Protease Inhibitors chemistry, Protease Inhibitors pharmacology, Quantitative Structure-Activity Relationship
Abstract

A novel computational technology based on fragmentation of the chemical compounds has been used for the fast and efficient prediction of activities of prospective protease inhibitors of the hepatitis C virus. This study spans over a discovery cycle from the theoretical prediction of new HCV NS3 protease inhibitors to the first cytotoxicity experimental tests of the best candidates. The measured cytotoxicity of the compounds indicated that at least two candidates would be suitable further development of drugs.

Published
2012
Full Text
View/download PDF

48. Aqueous biphasic systems. Partitioning of organic molecules: a QSPR treatment.

Author

Katritzky AR, Tämm K, Kuanar M, Fara DC, Oliferenko A, Oliferenko P, Huddleston JG, and Rogers RD

Abstract

The partitioning of 29 small organic probes in a PEG-2000/(NH4)2SO4 biphasic system was investigated using a quantitative structure-property relationship (QSPR) approach. A three-descriptor equation with the squared correlation coefficient (R2) of 0.97 for the partition coefficient (log D) was obtained. All descriptors were derived solely from the chemical structure of the compounds. Using the same descriptors, a three-parameter model was also obtained for log P (octanol/water, R2=0.89); predicted log P values were used as an external descriptor for modeling log D.

Published
2004
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results