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Virtual Environment for Studying the Docking Interactions of Rigid Biomolecules with Haptics.

Journal of chemical information and modeling

Iakovou G, Hayward S, Laycock SD.
PMID: 28437105
J Chem Inf Model. 2017 May 22;57(5):1142-1152. doi: 10.1021/acs.jcim.7b00051. Epub 2017 May 03.

Haptic technology facilitates user interaction with the virtual world via the sense of touch. In molecular docking, haptics enables the user to sense the interaction forces during the docking process. Here we describe a haptics-assisted interactive software tool, called...

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Iakovou G, Hayward S, Laycock SD. Virtual Environment for Studying the Docking Interactions of Rigid Biomolecules with Haptics. J Chem Inf Model. 2017;57(5):1142-1152doi: 10.1021/acs.jcim.7b00051.
Iakovou, G., Hayward, S., & Laycock, S. D. (2017). Virtual Environment for Studying the Docking Interactions of Rigid Biomolecules with Haptics. Journal of chemical information and modeling, 57(5), 1142-1152. https://doi.org/10.1021/acs.jcim.7b00051
Iakovou, Georgios, et al. "Virtual Environment for Studying the Docking Interactions of Rigid Biomolecules with Haptics." Journal of chemical information and modeling vol. 57,5 (2017): 1142-1152. doi: https://doi.org/10.1021/acs.jcim.7b00051
Iakovou G, Hayward S, Laycock SD. Virtual Environment for Studying the Docking Interactions of Rigid Biomolecules with Haptics. J Chem Inf Model. 2017 May 22;57(5):1142-1152. doi: 10.1021/acs.jcim.7b00051. Epub 2017 May 03. PMID: 28437105.
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[Computational chemistry in structure-based drug design].

Yao xue xue bao = Acta pharmaceutica Sinica

Cao R, Li W, Sun HZ, Zhou Y, Huang N.
PMID: 24133970
Yao Xue Xue Bao. 2013 Jul;48(7):1041-52.

Today, the understanding of the sequence and structure of biologically relevant targets is growing rapidly and researchers from many disciplines, physics and computational science in particular, are making significant contributions to modern biology and drug discovery. However, it remains...

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Cao R, Li W, Sun HZ, et al. [Computational chemistry in structure-based drug design]. Yao Xue Xue Bao. 2013;48(7):1041-52
Cao, R., Li, W., Sun, H. Z., Zhou, Y., & Huang, N. (2013). [Computational chemistry in structure-based drug design]. Yao xue xue bao = Acta pharmaceutica Sinica, 48(7), 1041-52.
Cao, Ran, et al. "[Computational chemistry in structure-based drug design]." Yao xue xue bao = Acta pharmaceutica Sinica vol. 48,7 (2013): 1041-52.
Cao R, Li W, Sun HZ, Zhou Y, Huang N. [Computational chemistry in structure-based drug design]. Yao Xue Xue Bao. 2013 Jul;48(7):1041-52. Chinese. PMID: 24133970.
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Applications of docking and molecular dynamics in drug design.

Current computer-aided drug design

Yang G, Yang Z.
PMID: 24138395
Curr Comput Aided Drug Des. 2013 Dec;9(4):506. doi: 10.2174/157340990904131213160459.

No abstract available.

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Yang G, Yang Z. Applications of docking and molecular dynamics in drug design. Curr Comput Aided Drug Des. 2013;9(4):506doi: 10.2174/157340990904131213160459.
Yang, G., & Yang, Z. (2013). Applications of docking and molecular dynamics in drug design. Current computer-aided drug design, 9(4), 506. https://doi.org/10.2174/157340990904131213160459
Yang, Gang, and Yang, Zhiwei. "Applications of docking and molecular dynamics in drug design." Current computer-aided drug design vol. 9,4 (2013): 506. doi: https://doi.org/10.2174/157340990904131213160459
Yang G, Yang Z. Applications of docking and molecular dynamics in drug design. Curr Comput Aided Drug Des. 2013 Dec;9(4):506. doi: 10.2174/157340990904131213160459. PMID: 24138395.
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Molecular characterization, pathogen-host interaction pathway and in silico approaches for vaccine design against COVID-19.

Journal of chemical neuroanatomy

Singh N, Rai SN, Singh V, Singh MP.
PMID: 33091590
J Chem Neuroanat. 2020 Dec;110:101874. doi: 10.1016/j.jchemneu.2020.101874. Epub 2020 Oct 19.

COVID-19 has forsaken the world because of extremely high infection rates and high mortality rates. At present we have neither medicine nor vaccine to prevent this pandemic. Lockdowns, curfews, isolations, quarantines, and social distancing are the only ways to...

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Singh N, Rai SN, Singh V, et al. Molecular characterization, pathogen-host interaction pathway and in silico approaches for vaccine design against COVID-19. J Chem Neuroanat. 2020;110:101874doi: 10.1016/j.jchemneu.2020.101874.
Singh, N., Rai, S. N., Singh, V., & Singh, M. P. (2020). Molecular characterization, pathogen-host interaction pathway and in silico approaches for vaccine design against COVID-19. Journal of chemical neuroanatomy, 110101874. https://doi.org/10.1016/j.jchemneu.2020.101874
Singh, Nidhi, et al. "Molecular characterization, pathogen-host interaction pathway and in silico approaches for vaccine design against COVID-19." Journal of chemical neuroanatomy vol. 110 (2020): 101874. doi: https://doi.org/10.1016/j.jchemneu.2020.101874
Singh N, Rai SN, Singh V, Singh MP. Molecular characterization, pathogen-host interaction pathway and in silico approaches for vaccine design against COVID-19. J Chem Neuroanat. 2020 Dec;110:101874. doi: 10.1016/j.jchemneu.2020.101874. Epub 2020 Oct 19. PMID: 33091590; PMCID: PMC7571424.
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A Structure-Based Drug Discovery Paradigm.

International journal of molecular sciences

Batool M, Ahmad B, Choi S.
PMID: 31174387
Int J Mol Sci. 2019 Jun 06;20(11). doi: 10.3390/ijms20112783.

Structure-based drug design is becoming an essential tool for faster and more cost-efficient lead discovery relative to the traditional method. Genomic, proteomic, and structural studies have provided hundreds of new targets and opportunities for future drug discovery. This situation...

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Batool M, Ahmad B, Choi S. A Structure-Based Drug Discovery Paradigm. Int J Mol Sci. 2019;20(11)doi: 10.3390/ijms20112783.
Batool, M., Ahmad, B., & Choi, S. (2019). A Structure-Based Drug Discovery Paradigm. International journal of molecular sciences, 20(11), . https://doi.org/10.3390/ijms20112783
Batool, Maria, et al. "A Structure-Based Drug Discovery Paradigm." International journal of molecular sciences vol. 20,11 (2019). doi: https://doi.org/10.3390/ijms20112783
Batool M, Ahmad B, Choi S. A Structure-Based Drug Discovery Paradigm. Int J Mol Sci. 2019 Jun 06;20(11). doi: 10.3390/ijms20112783. PMID: 31174387; PMCID: PMC6601033.
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Novel motif is capable of determining CCR and CCR-like proteins based on the divergence of CCRs in plants.

Tree physiology

Chao N, Jiang WT, Wang XC, Jiang XN, Gai Y.
PMID: 31748812
Tree Physiol. 2019 Dec 01;39(12):2019-2026. doi: 10.1093/treephys/tpz098.

Cinnamoyl-coenzyme A reductases (CCRs) have been reported as key enzymes involved in monolignol biosynthesis. In this study, a motif-aware workflow based on a new signature motif effectively distinguished CCRs from CCR-like proteins. The divergence of CCRs and CCR-like sequences...

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Chao N, Jiang WT, Wang XC, et al. Novel motif is capable of determining CCR and CCR-like proteins based on the divergence of CCRs in plants. Tree Physiol. 2019;39(12):2019-2026doi: 10.1093/treephys/tpz098.
Chao, N., Jiang, W. T., Wang, X. C., Jiang, X. N., & Gai, Y. (2019). Novel motif is capable of determining CCR and CCR-like proteins based on the divergence of CCRs in plants. Tree physiology, 39(12), 2019-2026. https://doi.org/10.1093/treephys/tpz098
Chao, Nan, et al. "Novel motif is capable of determining CCR and CCR-like proteins based on the divergence of CCRs in plants." Tree physiology vol. 39,12 (2019): 2019-2026. doi: https://doi.org/10.1093/treephys/tpz098
Chao N, Jiang WT, Wang XC, Jiang XN, Gai Y. Novel motif is capable of determining CCR and CCR-like proteins based on the divergence of CCRs in plants. Tree Physiol. 2019 Dec 01;39(12):2019-2026. doi: 10.1093/treephys/tpz098. PMID: 31748812.
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Subtle differences in chemical pattern between human toll-like receptor 8 agonists and antagonists: Emerging chemical patterns analysis.

Chemical biology & drug design

Huang S, Mei H, Zhang D, Shi T, Chen L, Kuang Z, Heng Y, Pan X, Lu L.
PMID: 31293023
Chem Biol Drug Des. 2019 Oct;94(4):1824-1834. doi: 10.1111/cbdd.13590. Epub 2019 Aug 09.

Due to the potencies in the treatments of cancer, infectious diseases, and autoimmune diseases, the developments of human TLR8 (hTLR8) agonists and antagonists have attracted widespread attentions. The hTLR8 agonists and antagonists have similar structures but with completely opposite...

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Huang S, Mei H, Zhang D, et al. Subtle differences in chemical pattern between human toll-like receptor 8 agonists and antagonists: Emerging chemical patterns analysis. Chem Biol Drug Des. 2019;94(4):1824-1834doi: 10.1111/cbdd.13590.
Huang, S., Mei, H., Zhang, D., Shi, T., Chen, L., Kuang, Z., Heng, Y., Pan, X., & Lu, L. (2019). Subtle differences in chemical pattern between human toll-like receptor 8 agonists and antagonists: Emerging chemical patterns analysis. Chemical biology & drug design, 94(4), 1824-1834. https://doi.org/10.1111/cbdd.13590
Huang, Shuheng, et al. "Subtle differences in chemical pattern between human toll-like receptor 8 agonists and antagonists: Emerging chemical patterns analysis." Chemical biology & drug design vol. 94,4 (2019): 1824-1834. doi: https://doi.org/10.1111/cbdd.13590
Huang S, Mei H, Zhang D, Shi T, Chen L, Kuang Z, Heng Y, Pan X, Lu L. Subtle differences in chemical pattern between human toll-like receptor 8 agonists and antagonists: Emerging chemical patterns analysis. Chem Biol Drug Des. 2019 Oct;94(4):1824-1834. doi: 10.1111/cbdd.13590. Epub 2019 Aug 09. PMID: 31293023.
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New Experimental and Computational Tools for Drug Discovery: Medicinal Chemistry, Molecular Docking, and Machine Learning - Part-VI.

Current topics in medicinal chemistry

Monteagudo MC, González-Díaz H.
PMID: 30499403
Curr Top Med Chem. 2018;18(27):2325-2326. doi: 10.2174/1568026619666181130122945.

No abstract available.

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Monteagudo MC, González-Díaz H. New Experimental and Computational Tools for Drug Discovery: Medicinal Chemistry, Molecular Docking, and Machine Learning - Part-VI. Curr Top Med Chem. 2018;18(27):2325-2326doi: 10.2174/1568026619666181130122945.
Monteagudo, M. C., & González-Díaz, H. (2018). New Experimental and Computational Tools for Drug Discovery: Medicinal Chemistry, Molecular Docking, and Machine Learning - Part-VI. Current topics in medicinal chemistry, 18(27), 2325-2326. https://doi.org/10.2174/1568026619666181130122945
Monteagudo, Maykel Cruz, and González-Díaz, Humbert. "New Experimental and Computational Tools for Drug Discovery: Medicinal Chemistry, Molecular Docking, and Machine Learning - Part-VI." Current topics in medicinal chemistry vol. 18,27 (2018): 2325-2326. doi: https://doi.org/10.2174/1568026619666181130122945
Monteagudo MC, González-Díaz H. New Experimental and Computational Tools for Drug Discovery: Medicinal Chemistry, Molecular Docking, and Machine Learning - Part-VI. Curr Top Med Chem. 2018;18(27):2325-2326. doi: 10.2174/1568026619666181130122945. PMID: 30499403.
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Rapid Identification of Potential Drug Candidates from Multi-Million Compounds' Repositories. Combination of 2D Similarity Search with 3D Ligand/Structure Based Methods and In Vitro Screening.

Molecules (Basel, Switzerland)

Szilágyi K, Flachner B, Hajdú I, Szaszkó M, Dobi K, Lőrincz Z, Cseh S, Dormán G.
PMID: 34577064
Molecules. 2021 Sep 15;26(18). doi: 10.3390/molecules26185593.

Rapid in silico selection of target focused libraries from commercial repositories is an attractive and cost-effective approach in early drug discovery. If structures of active compounds are available, rapid 2D similarity search can be performed on multimillion compounds' databases....

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Szilágyi K, Flachner B, Hajdú I, et al. Rapid Identification of Potential Drug Candidates from Multi-Million Compounds' Repositories. Combination of 2D Similarity Search with 3D Ligand/Structure Based Methods and In Vitro Screening. Molecules. 2021;26(18)doi: 10.3390/molecules26185593.
Szilágyi, K., Flachner, B., Hajdú, I., Szaszkó, M., Dobi, K., Lőrincz, Z., Cseh, S., & Dormán, G. (2021). Rapid Identification of Potential Drug Candidates from Multi-Million Compounds' Repositories. Combination of 2D Similarity Search with 3D Ligand/Structure Based Methods and In Vitro Screening. Molecules (Basel, Switzerland), 26(18), . https://doi.org/10.3390/molecules26185593
Szilágyi, Katalin, et al. "Rapid Identification of Potential Drug Candidates from Multi-Million Compounds' Repositories. Combination of 2D Similarity Search with 3D Ligand/Structure Based Methods and In Vitro Screening." Molecules (Basel, Switzerland) vol. 26,18 (2021). doi: https://doi.org/10.3390/molecules26185593
Szilágyi K, Flachner B, Hajdú I, Szaszkó M, Dobi K, Lőrincz Z, Cseh S, Dormán G. Rapid Identification of Potential Drug Candidates from Multi-Million Compounds' Repositories. Combination of 2D Similarity Search with 3D Ligand/Structure Based Methods and In Vitro Screening. Molecules. 2021 Sep 15;26(18). doi: 10.3390/molecules26185593. PMID: 34577064; PMCID: PMC8468386.
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The impact of compound library size on the performance of scoring functions for structure-based virtual screening.

Briefings in bioinformatics

Fresnais L, Ballester PJ.
PMID: 32568385
Brief Bioinform. 2021 May 20;22(3). doi: 10.1093/bib/bbaa095.

Larger training datasets have been shown to improve the accuracy of machine learning (ML)-based scoring functions (SFs) for structure-based virtual screening (SBVS). In addition, massive test sets for SBVS, known as ultra-large compound libraries, have been demonstrated to enable...

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Fresnais L, Ballester PJ. The impact of compound library size on the performance of scoring functions for structure-based virtual screening. Brief Bioinform. 2021;22(3)doi: 10.1093/bib/bbaa095.
Fresnais, L., & Ballester, P. J. (2021). The impact of compound library size on the performance of scoring functions for structure-based virtual screening. Briefings in bioinformatics, 22(3), . https://doi.org/10.1093/bib/bbaa095
Fresnais, Louison, and Ballester, Pedro J. "The impact of compound library size on the performance of scoring functions for structure-based virtual screening." Briefings in bioinformatics vol. 22,3 (2021). doi: https://doi.org/10.1093/bib/bbaa095
Fresnais L, Ballester PJ. The impact of compound library size on the performance of scoring functions for structure-based virtual screening. Brief Bioinform. 2021 May 20;22(3). doi: 10.1093/bib/bbaa095. PMID: 32568385.
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EDock-ML: A web server for using ensemble docking with machine learning to aid drug discovery.

Protein science : a publication of the Protein Society

Chandak T, Wong CF.
PMID: 33733530
Protein Sci. 2021 May;30(5):1087-1097. doi: 10.1002/pro.4065. Epub 2021 Mar 25.

EDock-ML is a web server that facilitates the use of ensemble docking with machine learning to help decide whether a compound is worthwhile to be considered further in a drug discovery process. Ensemble docking provides an economical way to...

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Chandak T, Wong CF. EDock-ML: A web server for using ensemble docking with machine learning to aid drug discovery. Protein Sci. 2021;30(5):1087-1097doi: 10.1002/pro.4065.
Chandak, T., & Wong, C. F. (2021). EDock-ML: A web server for using ensemble docking with machine learning to aid drug discovery. Protein science : a publication of the Protein Society, 30(5), 1087-1097. https://doi.org/10.1002/pro.4065
Chandak, Tanay, and Wong, Chung F. "EDock-ML: A web server for using ensemble docking with machine learning to aid drug discovery." Protein science : a publication of the Protein Society vol. 30,5 (2021): 1087-1097. doi: https://doi.org/10.1002/pro.4065
Chandak T, Wong CF. EDock-ML: A web server for using ensemble docking with machine learning to aid drug discovery. Protein Sci. 2021 May;30(5):1087-1097. doi: 10.1002/pro.4065. Epub 2021 Mar 25. PMID: 33733530; PMCID: PMC8040857.
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Identification of Phelligridin-Based Compounds as Novel Human CD73 Inhibitors.

Journal of chemical information and modeling

Lyu S, Zhao Y, Zeng X, Chen X, Meng Q, Ding Z, Zhao W, Qi Y, Gao Y, Du J.
PMID: 33656342
J Chem Inf Model. 2021 Mar 22;61(3):1275-1286. doi: 10.1021/acs.jcim.0c00961. Epub 2021 Mar 03.

As an emerging immune checkpoint, CD73 has received more attention in the past decade. Inhibition of CD73 enzymatic activity can enhance antitumor immunity. Several CD73 inhibitors have been identified by in vitro assays in recent years, but they remain...

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Lyu S, Zhao Y, Zeng X, et al. Identification of Phelligridin-Based Compounds as Novel Human CD73 Inhibitors. J Chem Inf Model. 2021;61(3):1275-1286doi: 10.1021/acs.jcim.0c00961.
Lyu, S., Zhao, Y., Zeng, X., Chen, X., Meng, Q., Ding, Z., Zhao, W., Qi, Y., Gao, Y., & Du, J. (2021). Identification of Phelligridin-Based Compounds as Novel Human CD73 Inhibitors. Journal of chemical information and modeling, 61(3), 1275-1286. https://doi.org/10.1021/acs.jcim.0c00961
Lyu, Sifan, et al. "Identification of Phelligridin-Based Compounds as Novel Human CD73 Inhibitors." Journal of chemical information and modeling vol. 61,3 (2021): 1275-1286. doi: https://doi.org/10.1021/acs.jcim.0c00961
Lyu S, Zhao Y, Zeng X, Chen X, Meng Q, Ding Z, Zhao W, Qi Y, Gao Y, Du J. Identification of Phelligridin-Based Compounds as Novel Human CD73 Inhibitors. J Chem Inf Model. 2021 Mar 22;61(3):1275-1286. doi: 10.1021/acs.jcim.0c00961. Epub 2021 Mar 03. PMID: 33656342.
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Showing 13 to 24 of 76 entries