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MD-TASK: a software suite for analyzing molecular dynamics trajectories.

Bioinformatics (Oxford, England)

Brown DK, Penkler DL, Sheik Amamuddy O, Ross C, Atilgan AR, Atilgan C, Tastan Bishop Ö.
PMID: 28575169
Bioinformatics. 2017 Sep 01;33(17):2768-2771. doi: 10.1093/bioinformatics/btx349.

SUMMARY: Molecular dynamics (MD) determines the physical motions of atoms of a biological macromolecule in a cell-like environment and is an important method in structural bioinformatics. Traditionally, measurements such as root mean square deviation, root mean square fluctuation, radius...

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Brown DK, Penkler DL, Sheik Amamuddy O, et al. MD-TASK: a software suite for analyzing molecular dynamics trajectories. Bioinformatics. 2017;33(17):2768-2771doi: 10.1093/bioinformatics/btx349.
Brown, D. K., Penkler, D. L., Sheik Amamuddy, O., Ross, C., Atilgan, A. R., Atilgan, C., & Tastan Bishop, �. �. (2017). MD-TASK: a software suite for analyzing molecular dynamics trajectories. Bioinformatics (Oxford, England), 33(17), 2768-2771. https://doi.org/10.1093/bioinformatics/btx349
Brown, David K, et al. "MD-TASK: a software suite for analyzing molecular dynamics trajectories." Bioinformatics (Oxford, England) vol. 33,17 (2017): 2768-2771. doi: https://doi.org/10.1093/bioinformatics/btx349
Brown DK, Penkler DL, Sheik Amamuddy O, Ross C, Atilgan AR, Atilgan C, Tastan Bishop Ö. MD-TASK: a software suite for analyzing molecular dynamics trajectories. Bioinformatics. 2017 Sep 01;33(17):2768-2771. doi: 10.1093/bioinformatics/btx349. PMID: 28575169; PMCID: PMC5860072.
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Metabolic Engineering of .

Journal of agricultural and food chemistry

Hou Y, Liu X, Li S, Zhang X, Yu S, Zhao GR.
PMID: 32627549
J Agric Food Chem. 2020 Aug 05;68(31):8370-8380. doi: 10.1021/acs.jafc.0c02949. Epub 2020 Jul 21.

Betalains are emerging natural pigments with high tinctorial strength and stability, physiological activities, and fluorescent properties for potential application in food, cosmetic, and pharmaceutical industries. Betalains including yellow betaxanthins and red betacyanins are mainly restricted in the Caryophyllales plants....

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Hou Y, Liu X, Li S, et al. Metabolic Engineering of . J Agric Food Chem. 2020;68(31):8370-8380doi: 10.1021/acs.jafc.0c02949.
Hou, Y., Liu, X., Li, S., Zhang, X., Yu, S., & Zhao, G. R. (2020). Metabolic Engineering of . Journal of agricultural and food chemistry, 68(31), 8370-8380. https://doi.org/10.1021/acs.jafc.0c02949
Hou, Yanan, et al. "Metabolic Engineering of ." Journal of agricultural and food chemistry vol. 68,31 (2020): 8370-8380. doi: https://doi.org/10.1021/acs.jafc.0c02949
Hou Y, Liu X, Li S, Zhang X, Yu S, Zhao GR. Metabolic Engineering of . J Agric Food Chem. 2020 Aug 05;68(31):8370-8380. doi: 10.1021/acs.jafc.0c02949. Epub 2020 Jul 21. PMID: 32627549.
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Chemical constituents of .

Journal of Asian natural products research

Xu DL, Pan YC, Li L, ShangGuan YN, Zhang SB, Liu GY, Cheng L, Xiao SJ.
PMID: 30612468
J Asian Nat Prod Res. 2019 Dec;21(12):1184-1189. doi: 10.1080/10286020.2018.1516212. Epub 2019 Jan 06.

A new triphenanthrene compound named 2,2',2'',7,7',7''-hexahydroxy-4,4',4''-trimethoxy-[9,9',9'',10,10',10'']-hexahydro-1,8,1',6''-triphenanthrene (

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Xu DL, Pan YC, Li L, et al. Chemical constituents of . J Asian Nat Prod Res. 2019;21(12):1184-1189doi: 10.1080/10286020.2018.1516212.
Xu, D. L., Pan, Y. C., Li, L., ShangGuan, Y. N., Zhang, S. B., Liu, G. Y., Cheng, L., & Xiao, S. J. (2019). Chemical constituents of . Journal of Asian natural products research, 21(12), 1184-1189. https://doi.org/10.1080/10286020.2018.1516212
Xu, De-Lin, et al. "Chemical constituents of ." Journal of Asian natural products research vol. 21,12 (2019): 1184-1189. doi: https://doi.org/10.1080/10286020.2018.1516212
Xu DL, Pan YC, Li L, ShangGuan YN, Zhang SB, Liu GY, Cheng L, Xiao SJ. Chemical constituents of . J Asian Nat Prod Res. 2019 Dec;21(12):1184-1189. doi: 10.1080/10286020.2018.1516212. Epub 2019 Jan 06. PMID: 30612468.
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Guiding Lights: Tissue Bioprinting Using Photoactivated Materials.

Chemical reviews

Lee M, Rizzo R, Surman F, Zenobi-Wong M.
PMID: 32662642
Chem Rev. 2020 Oct 14;120(19):10950-11027. doi: 10.1021/acs.chemrev.0c00077. Epub 2020 Jul 14.

Photoactivated materials have found widespread use in biological and medical applications and are playing an increasingly important role in the nascent field of three-dimensional (3D) bioprinting. Light can be used as a trigger to drive the formation or the...

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Lee M, Rizzo R, Surman F, et al. Guiding Lights: Tissue Bioprinting Using Photoactivated Materials. Chem Rev. 2020;120(19):10950-11027doi: 10.1021/acs.chemrev.0c00077.
Lee, M., Rizzo, R., Surman, F., & Zenobi-Wong, M. (2020). Guiding Lights: Tissue Bioprinting Using Photoactivated Materials. Chemical reviews, 120(19), 10950-11027. https://doi.org/10.1021/acs.chemrev.0c00077
Lee, Mihyun, et al. "Guiding Lights: Tissue Bioprinting Using Photoactivated Materials." Chemical reviews vol. 120,19 (2020): 10950-11027. doi: https://doi.org/10.1021/acs.chemrev.0c00077
Lee M, Rizzo R, Surman F, Zenobi-Wong M. Guiding Lights: Tissue Bioprinting Using Photoactivated Materials. Chem Rev. 2020 Oct 14;120(19):10950-11027. doi: 10.1021/acs.chemrev.0c00077. Epub 2020 Jul 14. PMID: 32662642.
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Obituary: Toshio Fujita, QSAR pioneer.

Journal of computer-aided molecular design

Akamatsu M, Oprea TI.
PMID: 29119351
J Comput Aided Mol Des. 2017 Nov;31(11):959-960. doi: 10.1007/s10822-017-0078-6. Epub 2017 Nov 08.

This is the obituary for Toshio Fujita, pioneer of the quantitative structure activity relationship (QSAR) paradigm.

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Akamatsu M, Oprea TI. Obituary: Toshio Fujita, QSAR pioneer. J Comput Aided Mol Des. 2017;31(11):959-960doi: 10.1007/s10822-017-0078-6.
Akamatsu, M., & Oprea, T. I. (2017). Obituary: Toshio Fujita, QSAR pioneer. Journal of computer-aided molecular design, 31(11), 959-960. https://doi.org/10.1007/s10822-017-0078-6
Akamatsu, Miki, and Oprea, Tudor I. "Obituary: Toshio Fujita, QSAR pioneer." Journal of computer-aided molecular design vol. 31,11 (2017): 959-960. doi: https://doi.org/10.1007/s10822-017-0078-6
Akamatsu M, Oprea TI. Obituary: Toshio Fujita, QSAR pioneer. J Comput Aided Mol Des. 2017 Nov;31(11):959-960. doi: 10.1007/s10822-017-0078-6. Epub 2017 Nov 08. PMID: 29119351.
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Synthesis of [2]catenanes by template-directed clipping approach.

The Journal of organic chemistry

Li Z, Liu W, Wu J, Liu SH, Yin J.
PMID: 22839768
J Org Chem. 2012 Aug 17;77(16):7129-35. doi: 10.1021/jo3012804. Epub 2012 Aug 09.

A series of [2]catenanes were efficiently synthesized in high yields by a template-directed clipping approach with the formation of one macrocycle around another macrocycle containing a dialkylammonium recognition site. Their structures were identified by the NMR spectra and ESI...

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Li Z, Liu W, Wu J, et al. Synthesis of [2]catenanes by template-directed clipping approach. J Org Chem. 2012;77(16):7129-35doi: 10.1021/jo3012804.
Li, Z., Liu, W., Wu, J., Liu, S. H., & Yin, J. (2012). Synthesis of [2]catenanes by template-directed clipping approach. The Journal of organic chemistry, 77(16), 7129-35. https://doi.org/10.1021/jo3012804
Li, Ziyong, et al. "Synthesis of [2]catenanes by template-directed clipping approach." The Journal of organic chemistry vol. 77,16 (2012): 7129-35. doi: https://doi.org/10.1021/jo3012804
Li Z, Liu W, Wu J, Liu SH, Yin J. Synthesis of [2]catenanes by template-directed clipping approach. J Org Chem. 2012 Aug 17;77(16):7129-35. doi: 10.1021/jo3012804. Epub 2012 Aug 09. PMID: 22839768.
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Recent advances in drug design methods: where will they lead?.

BioEssays : news and reviews in molecular, cellular and developmental biology

Dean PM.
PMID: 7980495
Bioessays. 1994 Sep;16(9):683-7. doi: 10.1002/bies.950160915.

Drug design methods have made significant new advances over the last ten years, mainly in the areas of molecular modelling. In more recent times important developments in theory have led to a different type of modelling becoming possible, the...

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Dean PM. Recent advances in drug design methods: where will they lead?. Bioessays. 1994;16(9):683-7doi: 10.1002/bies.950160915.
Dean, P. M. (1994). Recent advances in drug design methods: where will they lead?. BioEssays : news and reviews in molecular, cellular and developmental biology, 16(9), 683-7. https://doi.org/10.1002/bies.950160915
Dean, P M. "Recent advances in drug design methods: where will they lead?." BioEssays : news and reviews in molecular, cellular and developmental biology vol. 16,9 (1994): 683-7. doi: https://doi.org/10.1002/bies.950160915
Dean PM. Recent advances in drug design methods: where will they lead?. Bioessays. 1994 Sep;16(9):683-7. doi: 10.1002/bies.950160915. PMID: 7980495.
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Structural, chemical topological, electrotopological and electronic structure hypotheses.

Combinatorial chemistry & high throughput screening

Torrens F.
PMID: 14683486
Comb Chem High Throughput Screen. 2003 Dec;6(8):801-9. doi: 10.2174/138620703771826919.

The first important hypothesis in the prediction of properties of synthesized molecules is the structural hypothesis. In the study of drug-receptor interactions, the case where the three-dimensional structure of the receptor is known allows the application of molecular simulation...

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Torrens F. Structural, chemical topological, electrotopological and electronic structure hypotheses. Comb Chem High Throughput Screen. 2003;6(8):801-9doi: 10.2174/138620703771826919.
Torrens, F. (2003). Structural, chemical topological, electrotopological and electronic structure hypotheses. Combinatorial chemistry & high throughput screening, 6(8), 801-9. https://doi.org/10.2174/138620703771826919
Torrens, F. "Structural, chemical topological, electrotopological and electronic structure hypotheses." Combinatorial chemistry & high throughput screening vol. 6,8 (2003): 801-9. doi: https://doi.org/10.2174/138620703771826919
Torrens F. Structural, chemical topological, electrotopological and electronic structure hypotheses. Comb Chem High Throughput Screen. 2003 Dec;6(8):801-9. doi: 10.2174/138620703771826919. PMID: 14683486.
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Two new norlignans from the aerial parts of .

Natural product research

Nhung LTH, Huong PTM, Anh NT, Tai BH, Nhiem NX, Doan VV, Hoang NH, Seo Y, Kim SH, Kiem PV.
PMID: 32498564
Nat Prod Res. 2022 Jan;36(1):157-164. doi: 10.1080/14786419.2020.1771707. Epub 2020 Jun 05.

Two new norlignans, pouzolignan N (

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Nhung LTH, Huong PTM, Anh NT, et al. Two new norlignans from the aerial parts of . Nat Prod Res. 2020;36(1):157-164doi: 10.1080/14786419.2020.1771707.
Nhung, L. T. H., Huong, P. T. M., Anh, N. T., Tai, B. H., Nhiem, N. X., Doan, V. V., Hoang, N. H., Seo, Y., Kim, S. H., & Kiem, P. V. (2022). Two new norlignans from the aerial parts of . Natural product research, 36(1), 157-164. https://doi.org/10.1080/14786419.2020.1771707
Nhung, Le Thi Hong, et al. "Two new norlignans from the aerial parts of ." Natural product research vol. 36,1 (2022): 157-164. doi: https://doi.org/10.1080/14786419.2020.1771707
Nhung LTH, Huong PTM, Anh NT, Tai BH, Nhiem NX, Doan VV, Hoang NH, Seo Y, Kim SH, Kiem PV. Two new norlignans from the aerial parts of . Nat Prod Res. 2022 Jan;36(1):157-164. doi: 10.1080/14786419.2020.1771707. Epub 2020 Jun 05. PMID: 32498564.
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Cryo-EM, XFELs and the structure conundrum in structural biology.

Nature methods

Ourmazd A.
PMID: 31534229
Nat Methods. 2019 Oct;16(10):941-944. doi: 10.1038/s41592-019-0587-4.

No abstract available.

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Ourmazd A. Cryo-EM, XFELs and the structure conundrum in structural biology. Nat Methods. 2019;16(10):941-944doi: 10.1038/s41592-019-0587-4.
Ourmazd, A. (2019). Cryo-EM, XFELs and the structure conundrum in structural biology. Nature methods, 16(10), 941-944. https://doi.org/10.1038/s41592-019-0587-4
Ourmazd, Abbas. "Cryo-EM, XFELs and the structure conundrum in structural biology." Nature methods vol. 16,10 (2019): 941-944. doi: https://doi.org/10.1038/s41592-019-0587-4
Ourmazd A. Cryo-EM, XFELs and the structure conundrum in structural biology. Nat Methods. 2019 Oct;16(10):941-944. doi: 10.1038/s41592-019-0587-4. PMID: 31534229.
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Structure-Based Design of Biologically Active Compounds.

Molecules (Basel, Switzerland)

Gemma S.
PMID: 32650470
Molecules. 2020 Jul 08;25(14). doi: 10.3390/molecules25143115.

The past decades have witnessed tremendous progress in the detailed structural knowledge of proteins as potential or validated drug targets and the discovery of new drugs based on this wealth of knowledge progressed in parallel [...].

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Gemma S. Structure-Based Design of Biologically Active Compounds. Molecules. 2020;25(14)doi: 10.3390/molecules25143115.
Gemma, S. (2020). Structure-Based Design of Biologically Active Compounds. Molecules (Basel, Switzerland), 25(14), . https://doi.org/10.3390/molecules25143115
Gemma, Sandra. "Structure-Based Design of Biologically Active Compounds." Molecules (Basel, Switzerland) vol. 25,14 (2020). doi: https://doi.org/10.3390/molecules25143115
Gemma S. Structure-Based Design of Biologically Active Compounds. Molecules. 2020 Jul 08;25(14). doi: 10.3390/molecules25143115. PMID: 32650470; PMCID: PMC7397263.
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MLatom 2: An Integrative Platform for Atomistic Machine Learning.

Topics in current chemistry (Cham)

Dral PO, Ge F, Xue BX, Hou YF, Pinheiro M, Huang J, Barbatti M.
PMID: 34101036
Top Curr Chem (Cham). 2021 Jun 08;379(4):27. doi: 10.1007/s41061-021-00339-5.

Atomistic machine learning (AML) simulations are used in chemistry at an ever-increasing pace. A large number of AML models has been developed, but their implementations are scattered among different packages, each with its own conventions for input and output....

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Dral PO, Ge F, Xue BX, et al. MLatom 2: An Integrative Platform for Atomistic Machine Learning. Top Curr Chem (Cham). 2021;379(4):27doi: 10.1007/s41061-021-00339-5.
Dral, P. O., Ge, F., Xue, B. X., Hou, Y. F., Pinheiro, M., Huang, J., & Barbatti, M. (2021). MLatom 2: An Integrative Platform for Atomistic Machine Learning. Topics in current chemistry (Cham), 379(4), 27. https://doi.org/10.1007/s41061-021-00339-5
Dral, Pavlo O, et al. "MLatom 2: An Integrative Platform for Atomistic Machine Learning." Topics in current chemistry (Cham) vol. 379,4 (2021): 27. doi: https://doi.org/10.1007/s41061-021-00339-5
Dral PO, Ge F, Xue BX, Hou YF, Pinheiro M, Huang J, Barbatti M. MLatom 2: An Integrative Platform for Atomistic Machine Learning. Top Curr Chem (Cham). 2021 Jun 08;379(4):27. doi: 10.1007/s41061-021-00339-5. PMID: 34101036; PMCID: PMC8187220.
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Showing 13 to 24 of 158 entries