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Journal articles on the topic 'Ligand design'

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Published: 4 June 2021

Last updated: 10 March 2023

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1

Apostolakist, J., and A. Caflisch. "Computational Ligand Design." Combinatorial Chemistry & High Throughput Screening 2, no. 2 (April 1999): 91–104. http://dx.doi.org/10.2174/1386207302666220203193501.

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Abstract: A variety of computational tools that are used to assist drug design are reviewed. Particular emphasis is given to the limitations and merits of different methodologies. Recently, a number of general methods have been proposed for clustering compounds in classes of drug like and non-drug-like molecules. The usefulness of this classification for drug design is discussed. The estimation of (relative) binding affinities is from a theoretical point of view the most challenging part of ligand design. We review three methods for the estimation of binding energies. Firstly, quantitative structure-activity relationships (QSAR) are presented. These have gained significantly from recent developments of experimental techniques for combinatorial synthesis and high-throughput screening as well as the use of powerful computational procedures like genetic algorithms and neural networks for the derivation of models. Secondly, empirical energy functions are shown to lead to more general models than standard QSAR, since they are fitted to a variety of complexes. They have been used recently with considerable success. Thirdly, we briefly outline free energy calculations based on molecular dynamics simulations, the method with the most sound theoretical foundation. Recent developments are reestablishing the interest in this approach. In the last part of this review structure-based ligand design programs are described. These are closely related to docking, with the difference that in design, unlike in most docking procedures, ligands are built on a fragment-by-fragment basis. Finally, a short description of our approach to computational combinatorial ligand design is given.

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2

Caflisch, Amedeo, Rudolf Wälchli, and Claus Ehrhardt. "Computer-Aided Design of Thrombin Inhibitors." Physiology 13, no. 4 (August 1998): 182–89. http://dx.doi.org/10.1152/physiologyonline.1998.13.4.182.

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Computer-aided ligand design is an active, challenging, and multidisciplinary research field that blends knowledge of biochemistry, physics, and computer sciences. Whenever it is possible to experimentally determine or to model the three-dimensional structure of a pharmacologically relevant enzyme or receptor, computational approaches can be used to design specific high-affinity ligands. This article describes methods, applications, and perspectives of computer-assisted ligand design.

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3

Zhang, Bihan, Jishi Chen, Yitao Cao, Osburg Jin Huang Chai, and Jianping Xie. "Ligand Design in Ligand‐Protected Gold Nanoclusters." Small 17, no. 27 (January 28, 2021): 2004381. http://dx.doi.org/10.1002/smll.202004381.

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4

Nash, Jessica A., Matthew D. Manning, Alexey V. Gulyuk, Aleksey E. Kuznetsov, and Yaroslava G. Yingling. "Gold nanoparticle design for RNA compaction." Biointerphases 17, no. 6 (November 2022): 061001. http://dx.doi.org/10.1116/6.0002043.

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RNA-based therapeutics hold a great promise in treating a variety of diseases. However, double-stranded RNAs (dsRNAs) are inherently unstable, highly charged, and stiff macromolecules that require a delivery vehicle. Cationic ligand functionalized gold nanoparticles (AuNPs) are able to compact nucleic acids and assist in RNA delivery. Here, we use large-scale all-atom molecular dynamics simulations to show that correlations between ligand length, metal core size, and ligand excess free volume control the ability of nanoparticles to bend dsRNA far below its persistence length. The analysis of ammonium binding sites showed that longer ligands that bind deep within the major groove did not cause bending. By limiting ligand length and, thus, excess free volume, we have designed nanoparticles with controlled internal binding to RNA's major groove. NPs that are able to induce RNA bending cause a periodic variation in RNA's major groove width. Density functional theory studies on smaller models support large-scale simulations. Our results are expected to have significant implications in packaging of nucleic acids for their applications in nanotechnology and gene delivery.

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5

Date, Richard W., Eva Fernandez Iglesias, Kathryn E. Rowe, James M. Elliott, and Duncan W. Bruce. "Metallomesogens by ligand design." Dalton Trans., no. 10 (2003): 1914–31. http://dx.doi.org/10.1039/b212610a.

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6

Fryzuk, Michael D. "Ligand Design Virtual Issue." Inorganic Chemistry 54, no. 20 (October 19, 2015): 9671–74. http://dx.doi.org/10.1021/acs.inorgchem.5b02191.

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7

Ishiguro, Masaji. "Modeling of receptor–ligand complex and ligand design." Japanese Journal of Pesticide Science 43, no. 1 (February 20, 2018): 54–59. http://dx.doi.org/10.1584/jpestics.w18-20.

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8

Hendrati, Diana, Erianti Siska Purnamasari, Syulastri Effendi, and Santhy Wyantuti. "Pemantapan Proses Sintesis Ligan Dibutilditiokarbamat (DBDTK) Sebagai Pengekstrak Logam Tanah Jarang Berdasarkan Desain Eksperimen." ALCHEMY Jurnal Penelitian Kimia 14, no. 2 (September 3, 2018): 219. http://dx.doi.org/10.20961/alchemy.14.2.15006.219-235.

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<p>Gadolinium (Gd) merupakan salah satu logam tanah jarang, dimana logam tanah jarang dapat diekstrak dari mineral salah satunya mineral monasit. Logam Gd biasanya digunakan sebagai bahan dasar <em>contrast agent</em> dalam dunia kesehatan. Ligan dibutilditiokarbamat mampu membentuk senyawa kompleks dengan cara mengikat logam sehingga membentuk khelat yang dapat digunakan untuk ekstraksi. Tujuan dari penelitian ini adalah memantapkan sintesis ligan dibutilditiokarbamat berdasarkan desain eksperimen dan karakterisasi kompleks antara Gd(III) dengan ligan dibutilditiokarbamat hasil sintesis. Penelitian ini diawali dengan pembuatan desain eksperimen untuk sintesis ligan dan ekstraksi Gd(III) dengan ligan, kemudian proses sintesis dan ekstraksi dilakukan sesuai dengan desain eksperimen, hasil sintesis dan ekstraksi dikarakterisasi menggunakan metode spektroskopi serta diuji kelarutannya dalam pelarut organik. Data yang diperoleh menunjukkan bahwa sintesis ligan dibutilditiokarbamat optimal pada suhu 4 °C, perbandingan dibutilamin dan karbondisulfida yaitu 1 : 3 dengan perbandingan mol ammonia terhadap dibutilamin yaitu 1 : 4, sedangkan kondisi optimal untuk ekstraksi Gd(III) dengan ligan yaitu pada pH 6, dengan perbandingan mol Gd(III) dan ligan yaitu 1 : 4 dan lama ekstraksi 60 menit. Oleh karena itu ligan dibutilditiokarbamat hasil sintesis berpotensi digunakan sebagai ekstraktan untuk ekstraksi Gd(III). Hasil prediksi ligan berdasarkan desain eksperimen yaitu sebesar 56,12% sedangkan prediksi ekstraksi Gd(III) dengan ligan hasil sintesis diperoleh sebesar 78,41%.</p><p><strong>The Consolidation of Dibutyldithiocarbamate (DBDTC) Synthesis as Gadolinium Metal Extraction Based On Experimental Design. </strong>Gadolinium (Gd) is one of the rare-earth elements, whereas rare-earth elements can be extracted from monazite. Gd is usually used as raw material for synthesizing contrast agent<em> </em>in medicine field. Dibuthyldithiocarbamate ligand can form a complex compound with metal. This ligand will bind a metal and then forming chelate which is used for extraction. The purpose of this research is to ensure procedure of dibuthyldithiocarbamate ligand synthesis based on the design of experiment and to study the characterization of reaction result between Gd(III) and dibuthyldithiocarbamate ligand which this ligand is synthesis result. This research begins with making design of experiment for ligand synthesis and Gd(III) extraction with ligand, then perform the process of synthesis and extraction according to the design of experiment, the result of synthesis and extraction were characterized by spectroscopy method and solubility tested in organic solvent. The data was collected indicate that the optimal condition of dibuthyldithiocarbamate ligan synthesis at 4 °C (temperature), the ratio of di-n-butylamine and carbon disulphide is 1:3 with the mole ratio of ammonia to the di-n-butylamine 1:4, while the optimal conditions for gadolinium extraction with ligand at pH 6, the mol ratio of gadolinium and ligand is 1:4 and 60 minutes extraction time. Hence, dibuthyldithiocarbamate ligand can be used as extractan for extracting Gd(III). The prediction of ligand based on the experimental design is 56.12% while the prediction of Gd(III) extraction with ligand of the synthesis result is obtained equal to 78.41%. The conclusion of this research is that the synthesis of dibuthyldithiocarbamate ligand based on the experimental design can be developed for large-scale synthesis.</p>

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9

Hendrati, Diana, Erianti Siska Purnamasari, Syulastri Effendi, and Santhy Wyantuti. "Pemantapan Proses Sintesis Ligan Dibutilditiokarbamat (DBDTK) Sebagai Pengekstrak Logam Tanah Jarang Berdasarkan Desain Eksperimen." ALCHEMY Jurnal Penelitian Kimia 14, no. 1 (February 15, 2018): 195. http://dx.doi.org/10.20961/alchemy.14.1.15006.195-203.

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<p>Gadolinium (Gd) merupakan salah satu logam tanah jarang, dimana logam tanah jarang dapat diekstrak dari mineral salah satunya mineral monasit. Logam Gd biasanya digunakan sebagai bahan dasar <em>contrast agent</em> dalam dunia kesehatan. Ligan dibutilditiokarbamat mampu membentuk senyawa kompleks dengan cara mengikat logam sehingga membentuk khelat yang dapat digunakan untuk ekstraksi. Tujuan dari penelitian ini adalah memantapkan sintesis ligan dibutilditiokarbamat berdasarkan desain eksperimen dan karakterisasi kompleks antara Gd(III) dengan ligan dibutilditiokarbamat hasil sintesis. Penelitian ini diawali dengan pembuatan desain eksperimen untuk sintesis ligan dan ekstraksi Gd(III) dengan ligan, kemudian proses sintesis dan ekstraksi dilakukan sesuai dengan desain eksperimen, hasil sintesis dan ekstraksi dikarakterisasi menggunakan metode spektroskopi serta diuji kelarutannya dalam pelarut organik. Data yang diperoleh menunjukkan bahwa sintesis ligan dibutilditiokarbamat optimal pada suhu 4 °C, perbandingan dibutilamin dan karbondisulfida yaitu 1 : 3 dengan perbandingan mol ammonia terhadap dibutilamin yaitu 1 : 4, sedangkan kondisi optimal untuk ekstraksi Gd(III) dengan ligan yaitu pada pH 6, dengan perbandingan mol Gd(III) dan ligan yaitu 1 : 4 dan lama ekstraksi 60 menit. Oleh karena itu ligan dibutilditiokarbamat hasil sintesis berpotensi digunakan sebagai ekstraktan untuk ekstraksi Gd(III). Hasil prediksi ligan berdasarkan desain eksperimen yaitu sebesar 56,12% sedangkan prediksi ekstraksi Gd(III) dengan ligan hasil sintesis diperoleh sebesar 78,41%. Kesimpulan dari penelitian ini bahwa sintesis ligan dibutilditiokarbamat berdasarkan desain eksperimen dapat dikembangkan untuk sintesis skala besar.</p><p>Gadolinium (Gd) is one of the rare-earth elements, whereas rare-earth elements can be extracted from monazite. Gd is usually used as raw material for synthesizing contrast agent<em> </em>in medicine field. Dibuthyldithiocarbamate ligand can form a complex compound with metal. This ligand will bind a metal and then forming chelate which is used for extraction. The purpose of this research is to ensure procedure of dibuthyldithiocarbamate ligand synthesis based on the design of experiment and to study the characterization of reaction result between Gd(III) and dibuthyldithiocarbamate ligand which this ligand is synthesis result. This research begins with making design of experiment for ligand synthesis and Gd(III) extraction with ligand, then perform the process of synthesis and extraction according to the design of experiment, the result of synthesis and extraction were characterized by spectroscopy method and solubility tested in organic solvent. The data was collected indicate that the optimal condition of dibuthyldithiocarbamate ligan synthesis at 4 °C (temperature), the ratio of di-n-butylamine and carbon disulphide is 1:3 with the mole ratio of ammonia to the di-n-butylamine 1:4, while the optimal conditions for gadolinium extraction with ligand at pH 6, the mol ratio of gadolinium and ligand is 1:4 and 60 minutes extraction time. Hence, dibuthyldithiocarbamate ligand can be used as extractan for extracting Gd(III). The prediction of ligand based on the experimental design is 56.12% while the prediction of Gd(III) extraction with ligand of the synthesis result is obtained equal to 78.41%. The conclusion of this research is that the synthesis of dibuthyldithiocarbamate ligand based on the experimental design can be developed for large-scale synthesis.</p>

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10

Hendrati, Diana, Erianti Siska Purnamasari, Syulastri Effendi, and Santhy Wyantuti. "Pemantapan Proses Sistesis Ligan Dibutilditiokarbamat (DBDTK) sebagai Pengekstrak Logam Tanah Jarang berdasarkan Desain Eksperimen." ALCHEMY Jurnal Penelitian Kimia 14, no. 1 (February 15, 2018): 84. http://dx.doi.org/10.20961/alchemy.14.1.15006.84-99.

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<p>Gadolinium (Gd) merupakan salah satu logam tanah jarang, dimana logam tanah jarang dapat diekstrak dari mineral salah satunya mineral monasit. Logam Gd biasanya digunakan sebagai bahan dasar <em>contrast agent</em> dalam dunia kesehatan. Ligan dibutilditiokarbamat mampu membentuk senyawa kompleks dengan cara mengikat logam sehingga membentuk khelat yang dapat digunakan untuk ekstraksi. Tujuan dari penelitian ini adalah memantapkan sintesis ligan dibutilditiokarbamat berdasarkan desain eksperimen dan karakterisasi kompleks antara Gd(III) dengan ligan dibutilditiokarbamat hasil sintesis. Penelitian ini diawali dengan pembuatan desain eksperimen untuk sintesis ligan dan ekstraksi Gd(III) dengan ligan, kemudian proses sintesis dan ekstraksi dilakukan sesuai dengan desain eksperimen, hasil sintesis dan ekstraksi dikarakterisasi menggunakan metode spektroskopi serta diuji kelarutannya dalam pelarut organik. Data yang diperoleh menunjukkan bahwa sintesis ligan dibutilditiokarbamat optimal pada suhu 4 °C, perbandingan dibutilamin dan karbondisulfida yaitu 1:3 dengan perbandingan mol ammonia terhadap dibutilamin yaitu 1:4, sedangkan kondisi optimal untuk ekstraksi Gd(III) dengan ligan yaitu pada pH 6, dengan perbandingan mol Gd(III) dan ligan yaitu 1:4 dan lama ekstraksi 60 menit. Oleh karena itu ligan dibutilditiokarbamat hasil sintesis berpotensi digunakan sebagai ekstraktan untuk ekstraksi Gd(III). Hasil prediksi ligan berdasarkan desain eksperimen yaitu sebesar 56,12 % sedangkan prediksi ekstraksi Gd(III) dengan ligan hasil sintesis diperoleh sebesar 78,41 %. Kesimpulan dari penelitian ini bahwa sintesis ligan dibutilditiokarbamat berdasarkan desain eksperimen dapat dikembangkan untuk sintesis skala besar.</p><p>Gadolinium (Gd) is one of the rare-earth elements, whereas rare-earth elements can be extracted from monazite. Gd is usually used as raw material for synthesizing contrast agent<em> </em>in medicine field. Dibuthyldithiocarbamate ligand can form a complex compound with metal. This ligand will bind a metal and then forming chelate which is used for extraction. The purpose of this research is to ensure procedure of dibuthyldithiocarbamate ligand synthesis based on the design of experiment and to study the characterization of reaction result between Gd(III) and dibuthyldithiocarbamate ligand which this ligand is synthesis result. This research begins with making design of experiment for ligand synthesis and Gd(III) extraction with ligand, then perform the process of synthesis and extraction according to the design of experiment, the result of synthesis and extraction were characterized by spectroscopy method and solubility tested in organic solvent. The data was collected indicate that the optimal condition of dibuthyldithiocarbamate ligan synthesis at 4 °C (temperature), the ratio of di-n-butylamine and carbon disulphide is 1:3 with the mole ratio of ammonia to the di-n-butylamine 1:4, while the optimal conditions for gadolinium extraction with ligand at pH 6, the mol ratio of gadolinium and ligand is 1:4 and 60 minutes extraction time. Hence, dibuthyldithiocarbamate ligand can be used as extractan for extracting Gd(III). The prediction of ligand based on the experimental design is 56.12 % while the prediction of Gd(III) extraction with ligand of the synthesis result is obtained equal to 78.41 %. The conclusion of this research is that the synthesis of dibuthyldithiocarbamate ligand based on the experimental design can be developed for large-scale synthesis.</p>

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11

Heller, Markus, and Horst Kessler. "NMR spectroscopy in drug design." Pure and Applied Chemistry 73, no. 9 (September 1, 2001): 1429–36. http://dx.doi.org/10.1351/pac200173091429.

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The process of preclinical drug discovery consists of two steps: finding of initial hits (binding ligands to a medicinal relevant target, usually a protein) and lead optimization. Nuclear magnetic resonance spectroscopy is a powerful tool that can provide valuable information to every step of drug development. NMR is commonly used for characterizing the structure and molecular dynamics of target or ligand molecules. During the structure-based lead optimization, NMR provides insight into the structural and dynamical properties of the target-ligand complex. Recently, the use of NMR in the lead finding process by screening technologies has been shown. For the latter use, new techniques have also been developed. Those techniques, in combination with high throughput, have lead to an efficient screening of libraries composed of small molecules. In this article, the role of NMR during the discovery of a drug candidate is described.

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12

Mehta, Simpi, and Seema R. Pathak. "INSILICO DRUG DESIGN AND MOLECULAR DOCKING STUDIES OF NOVEL COUMARIN DERIVATIVES AS ANTI-CANCER AGENTS." Asian Journal of Pharmaceutical and Clinical Research 10, no. 4 (April 1, 2017): 335. http://dx.doi.org/10.22159/ajpcr.2017.v10i4.16826.

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Objective: Cancer is the major worldwide problem. It arises due to uncontrolled growth of cells. In the present study a series of novel coumarin derivatives were designed and computationallyoptimized to investigate the interaction between designed ligands and 10 pdb files of five selected proteins. The objective here was to analyse in silico anticancerous activity of designed ligands to reduce cost and time for getting novel anticancerous drug with minimum side effects.Methods: Docking studies were performed to find outmaximum interaction between designed ligands and selected five proteins using Schrondinger software Maestro. Capecitabin has been used as reference compound. Structures of selected proteins were downloaded from protein data bank.Results: All the designed ligands showed mild to excellent binding with proteins.Most of the ligands exhibited better interaction compared to reference compoundcapacitabin with all pdb files. Some of designed ligands amongst (1-7) showed excellent docking score with all pdb files(2v5z, 2v60, 2v61) ofAmine oxidase. Conclusion: All the designed ligands were docked with ten pdb files of five different proteins and it was found that out of seven designed ligand, ligand 4 showed best binding (docking score -10.139 ) with pdb 2v5z of protein Amine oxidase. Docked ligand cavity of ligand 4 showed important hydrophobic/non polar residues such asIle199,Ile316,Trp119,Phe168,Ile198,Cys172,Tyr188,Tyr398,Tyr435,Phe343,Tyr60,Leu328,Leu171 and showed pi-pi interaction with Tyr326.Further wet lab studies are continued in our laboratory to confirm and find out efficiency and activity of target compounds.Keywords: Docking, Mono Amine Oxidase, Coumarin derivatives, Anticancerous activity, binding energy, Ramachandran Plot, Hydrophobic residue.

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13

Bremner, J., R. Griffith, and B. Coban. "Ligand Design for Alpha1 Adrenoceptors." Current Medicinal Chemistry 8, no. 6 (May 1, 2001): 607–20. http://dx.doi.org/10.2174/0929867013373110.

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14

Stalke, D. "Charge density based ligand design." Acta Crystallographica Section A Foundations of Crystallography 64, a1 (August 23, 2008): C69. http://dx.doi.org/10.1107/s010876730809778x.

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Zabłocka, Maria, Alain Igau, Victorio Cadierno, Marek Koprowski, and Jean-Pierre Majoral. "α-Phosphino-Imine Ligand Design." Phosphorus, Sulfur, and Silicon and the Related Elements 177, no. 8-9 (August 2002): 1965. http://dx.doi.org/10.1080/10426500213421.

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16

Funk, Michael A. "Learning from diminutive ligand design." Science 362, no. 6411 (October 11, 2018): 195.5–196. http://dx.doi.org/10.1126/science.362.6411.195-e.

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17

Chan, Ting-Fung, and X. F. Steven Zheng. "De novo chemical ligand design ▾." Drug Discovery Today 7, no. 15 (August 2002): 802–3. http://dx.doi.org/10.1016/s1359-6446(02)02363-2.

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Love, Jason. "Reactions facilitated by ligand design." Dalton Transactions 45, no. 40 (2016): 15700–15701. http://dx.doi.org/10.1039/c6dt90177h.

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Nin-Hill, Alba, Nicolas Pierre Friedrich Mueller, Carla Molteni, Carme Rovira, and Mercedes Alfonso-Prieto. "Photopharmacology of Ion Channels through the Light of the Computational Microscope." International Journal of Molecular Sciences 22, no. 21 (November 8, 2021): 12072. http://dx.doi.org/10.3390/ijms222112072.

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The optical control and investigation of neuronal activity can be achieved and carried out with photoswitchable ligands. Such compounds are designed in a modular fashion, combining a known ligand of the target protein and a photochromic group, as well as an additional electrophilic group for tethered ligands. Such a design strategy can be optimized by including structural data. In addition to experimental structures, computational methods (such as homology modeling, molecular docking, molecular dynamics and enhanced sampling techniques) can provide structural insights to guide photoswitch design and to understand the observed light-regulated effects. This review discusses the application of such structure-based computational methods to photoswitchable ligands targeting voltage- and ligand-gated ion channels. Structural mapping may help identify residues near the ligand binding pocket amenable for mutagenesis and covalent attachment. Modeling of the target protein in a complex with the photoswitchable ligand can shed light on the different activities of the two photoswitch isomers and the effect of site-directed mutations on photoswitch binding, as well as ion channel subtype selectivity. The examples presented here show how the integration of computational modeling with experimental data can greatly facilitate photoswitchable ligand design and optimization. Recent advances in structural biology, both experimental and computational, are expected to further strengthen this rational photopharmacology approach.

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Rother, Kristian, Mathias Dunkel, Elke Michalsky, Silke Trissl, Andrean Goede, Ulf Leser, and Robert Preissner. "A structural keystone for drug design." Journal of Integrative Bioinformatics 3, no. 1 (June 1, 2006): 21–31. http://dx.doi.org/10.1515/jib-2006-19.

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Abstract 3D-structures of proteins and potential ligands are the cornerstones of rational drug design. The first brick to build upon is selecting a protein target and finding out whether biologically active compounds are known. Both tasks require more information than the structures themselves provide. For this purpose we have built a web resource bridging protein and ligand databases. It consists of three parts: i) A data warehouse on annotation of protein structures that integrates many well-known databases such as Swiss-Prot, SCOP, ENZYME and others. ii) A conformational library of structures of approved drugs. iii) A conformational library of ligands from the PDB, linking the realms of proteins and small molecules. The data collection contains structures of 30,000 proteins, 5,000 different ligands from 70,000 ligand-protein complexes, and 2,500 known drugs. Sets of protein structures can be refined by criteria like protein fold, family, metabolic pathway, resolution and textual annotation. The structures of organic compounds (drugs and ligands) can be searched considering chemical formula, trivial and trade names as well as medical classification codes for drugs (ATC). Retrieving structures by 2D-similarity has been implemented for all small molecules using Tanimoto coefficients. For the drug structures, 110,000 structural conformers have been calculated to account for structural flexibility. Two substances can be compared online by 3D-superimposition, where the pair of conformers that fits best is detected. Together, these web-accessible resources can be used to identify promising drug candidates. They have been used in-house to find alternatives to substances with a known binding activity but adverse side effects.

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Wang, Weibo, Gerald B. Hammond, and Bo Xu. "Ligand Effects and Ligand Design in Homogeneous Gold(I) Catalysis." Journal of the American Chemical Society 134, no. 12 (March 16, 2012): 5697–705. http://dx.doi.org/10.1021/ja3011397.

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22

Dugal-Tessier, Julien, Gregory R Dake, and Derek P Gates. "Chiral Ligand Design: A Bidentate Ligand Incorporating an Acyclic Phosphaalkene." Angewandte Chemie International Edition 47, no. 42 (October 6, 2008): 8064–67. http://dx.doi.org/10.1002/anie.200802949.

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Dugal-Tessier, Julien, Gregory R Dake, and Derek P Gates. "Chiral Ligand Design: A Bidentate Ligand Incorporating an Acyclic Phosphaalkene." Angewandte Chemie 120, no. 42 (October 6, 2008): 8184–87. http://dx.doi.org/10.1002/ange.200802949.

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Payne, Philippa R., Jason A. Bexrud, David C. Leitch, and Laurel L. Schafer. "Asymmetric hydroamination catalyzed by in situ generated chiral amidate and ureate complexes of zirconium — Probing the role of the tether in ligand design." Canadian Journal of Chemistry 89, no. 10 (October 2011): 1222–29. http://dx.doi.org/10.1139/v11-091.

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Simple chiral proligands have been synthesized from inexpensive chiral starting materials. These amidate and ureate ligands support zirconium complexes that successfully catalyze intramolecular hydroamination with up to 26% ee. Several elements necessary for successful ligand design are highlighted and discussed. In particular, the strict control of metal geometry through multidentate tethered ligands is determined to be an essential aspect of future ligand development.

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Chen, Xinyue, Wafaa W. Qoutah, Paul Free, Jonathan Hobley, David G. Fernig, and David Paramelle. "Features of Thiolated Ligands Promoting Resistance to Ligand Exchange in Self-Assembled Monolayers on Gold Nanoparticles." Australian Journal of Chemistry 65, no. 3 (2012): 266. http://dx.doi.org/10.1071/ch11432.

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An important feature necessary for biological stability of gold nanoparticles is resistance to ligand exchange. Here, we design and synthesize self-assembled monolayers of mixtures of small ligands on gold nanoparticles promoting high resistance to ligand exchange. We use as ligands short thiolated peptidols, e.g. H-CVVVT-ol, and ethylene glycol terminated alkane thiols (HS-C11-EG4). We present a straightforward method to evaluate the relative stability of each ligand shell against ligand exchange with small thiolated molecules. The results show that a ligand with a ‘thin’ stem, such as HS-C11-EG4, is an important feature to build a highly packed self-assembled monolayer and provide high resistance to ligand exchange. The greatest resistance to ligand exchange was found for the mixed ligand shells of the pentapeptidols H-CAVLT-ol or H-CAVYT-ol and the ligand HS-C11-EG4 at 30:70 (mole/mole). Mixtures of ligands of very different diameters, such as the peptidol H-CFFFY-ol and the ligand HS-C11-EG4, provide only a slightly lower stability against ligand exchange. These ligand shells are thus likely to be suitable for long-term use in biological environments. The method developed here provides a rapid screening tool to identify nanoparticles likely to be suitable for use in biological and biomedical applications.

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Hasegawa, Tokio, Mayo Osaka, Yusaku Miyamae, Katsutoshi Nishino, Hiroko Isoda, Kiyokazu Kawada, Mohamed Neffati, Kazuhiro Irie, and Masaya Nagao. "Two Types of PPARγ Ligands Identified in the Extract of Artemisia campestris." Chemistry 3, no. 2 (May 23, 2021): 647–57. http://dx.doi.org/10.3390/chemistry3020045.

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The 70% ethanol extract of Artemisia campestris was screened to find PPARγ ligands using the PPARγ ligand-responsive chimera luciferase reporter system. Capillartemisin B was identified as a PPARγ ligand that stimulated lipid accumulation in 3T3-L1 cells. By further purification of PPARγ ligands from a large-scale preparation of the methanol extract of Artemisia campestris, we isolated and identified eupatilin and santaflavone as PPARγ ligands. Weak PPARγ ligand activity of eupatilin or santaflavone in reporter assay was enhanced by a PPARγ antagonist, GW9662, suggesting that santaflavone or eupatilin and GW9662 bound simultaneously to the multiple sub-pockets of the PPARγ ligand-binding domain (LBD) and cooperatively activated PPARγ. Docking simulation suggested that eupatilin binds to the Ω-pocket but not to the AF-2 pocket of Y-shaped PPARγ LBD where artepillin C that differs from capillartemisin B at the C-5′ position without hydroxy group binds. Eupatilin or santaflavone with or without GW9662 did not stimulate lipid accumulation in differentiated 3T3-L1 cells, suggesting that binding of each compound alone or with GW9662 to the Ω-pocket which stimulated the PPARγ-responsive reporter expression was not enough to stimulate lipid accumulation. The PPARγ ligands found in this study have a potential to design the fragment-based drug design of a novel PPARγ ligand that cover the Y-shaped PPARγ LBD.

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MATSUI, Masakazu. "Ligand design for ion size recognition." Bunseki kagaku 45, no. 3 (1996): 209–23. http://dx.doi.org/10.2116/bunsekikagaku.45.209.

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De Benedetti, Pier, and Francesca Fanelli. "Ligand-Receptor Communication and Drug Design." Current Protein & Peptide Science 10, no. 2 (April 1, 2009): 186–93. http://dx.doi.org/10.2174/138920309787847581.

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29

Riccardi, Laura, Vito Genna, and Marco De Vivo. "Metal–ligand interactions in drug design." Nature Reviews Chemistry 2, no. 7 (June 26, 2018): 100–112. http://dx.doi.org/10.1038/s41570-018-0018-6.

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30

Peris, Eduardo, and Robert H. Crabtree. "Key factors in pincer ligand design." Chemical Society Reviews 47, no. 6 (2018): 1959–68. http://dx.doi.org/10.1039/c7cs00693d.

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31

Kangas, Erik, and Bruce Tidor. "Electrostatic specificity in molecular ligand design." Journal of Chemical Physics 112, no. 20 (May 22, 2000): 9120–31. http://dx.doi.org/10.1063/1.481522.

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Durand, Derek J., and Natalie Fey. "Computational Ligand Descriptors for Catalyst Design." Chemical Reviews 119, no. 11 (February 25, 2019): 6561–94. http://dx.doi.org/10.1021/acs.chemrev.8b00588.

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Yang, Wei, and Luhua Lai. "Computational design of ligand-binding proteins." Current Opinion in Structural Biology 45 (August 2017): 67–73. http://dx.doi.org/10.1016/j.sbi.2016.11.021.

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Williams, Alan F. "Ligand design for hollow spherical complexes." Coordination Chemistry Reviews 255, no. 17-18 (September 2011): 2104–10. http://dx.doi.org/10.1016/j.ccr.2011.03.021.

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35

La Croix, Andrew D., Andrew O’Hara, Kemar R. Reid, Noah J. Orfield, Sokrates T. Pantelides, Sandra J. Rosenthal, and Janet E. Macdonald. "Design of a Hole Trapping Ligand." Nano Letters 17, no. 2 (January 19, 2017): 909–14. http://dx.doi.org/10.1021/acs.nanolett.6b04213.

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Zhang, Yanling, Jianrui Song, Xiaojun Zhang, and Yuanyuan Xiao. "Ligand-Receptor Interactions and Drug Design." Biochemistry Insights 8s1 (January 2015): BCI.S37978. http://dx.doi.org/10.4137/bci.s37978.

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Belshaw, Peter J., Joseph G. Schoepfer, Karen-Qianye Liu, Kim L. Morrison, and Stuart L. Schreiber. "Rationales Design neuer Rezeptor-Ligand-Kombinationen." Angewandte Chemie 107, no. 19 (October 2, 1995): 2313–17. http://dx.doi.org/10.1002/ange.19951071920.

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38

Timms, Dave. "Ligand design: Identification of interaction sites." Journal of Chemical Technology & Biotechnology 57, no. 3 (April 24, 2007): 291–93. http://dx.doi.org/10.1002/jctb.280570321.

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39

Giri, Nabin, and Jianlin Cheng. "Improving Protein–Ligand Interaction Modeling with cryo-EM Data, Templates, and Deep Learning in 2021 Ligand Model Challenge." Biomolecules 13, no. 1 (January 9, 2023): 132. http://dx.doi.org/10.3390/biom13010132.

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Elucidating protein–ligand interaction is crucial for studying the function of proteins and compounds in an organism and critical for drug discovery and design. The problem of protein–ligand interaction is traditionally tackled by molecular docking and simulation, which is based on physical forces and statistical potentials and cannot effectively leverage cryo-EM data and existing protein structural information in the protein–ligand modeling process. In this work, we developed a deep learning bioinformatics pipeline (DeepProLigand) to predict protein–ligand interactions from cryo-EM density maps of proteins and ligands. DeepProLigand first uses a deep learning method to predict the structure of proteins from cryo-EM maps, which is averaged with a reference (template) structure of the proteins to produce a combined structure to add ligands. The ligands are then identified and added into the structure to generate a protein–ligand complex structure, which is further refined. The method based on the deep learning prediction and template-based modeling was blindly tested in the 2021 EMDataResource Ligand Challenge and was ranked first in fitting ligands to cryo-EM density maps. These results demonstrate that the deep learning bioinformatics approach is a promising direction for modeling protein–ligand interactions on cryo-EM data using prior structural information.

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Jiang, Xiaolin, Jiahui Zhang, Dongmei Zhao, and Yuehui Li. "Aldehyde effect and ligand discovery in Ru-catalyzed dehydrogenative cross-coupling of alcohols to esters." Chemical Communications 55, no. 19 (2019): 2797–800. http://dx.doi.org/10.1039/c8cc10315a.

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Mikhailov, Oleg V. "Template Synthesis (Self-Assembly) of Macrocycles: Theory and Practice." Molecules 27, no. 15 (July 28, 2022): 4829. http://dx.doi.org/10.3390/molecules27154829.

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For more than 60 years, in coordination chemistry (and since the beginning of the 21st century, in molecular nanotechnology, too), there has been very significant interest in template synthesis reactions, in which the design of coordination compounds (metal complexes) with complex ligands is carried out not according to the classical scheme [metal ion + ligand → complex], but according to scheme [metal ion + “building blocks” of the future ligand (the so-called ligand synthons or ligsons) → complex] [...]

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Zheng, Fang, and Chang-Guo Zhan. "Computational Modeling of Solvent Effects on Protein-Ligand Interactions Using Fully Polarizable Continuum Model and Rational Drug Design." Communications in Computational Physics 13, no. 1 (January 2013): 31–60. http://dx.doi.org/10.4208/cicp.130911.121011s.

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AbstractThis is a brief review of the computational modeling of protein-ligand interactions using a recently developed fully polarizable continuum model (FPCM) and rational drug design. Computational modeling has become a powerful tool in understanding detailed protein-ligand interactions at molecular level and in rational drug design. To study the binding of a protein with multiple molecular species of a ligand, one must accurately determine both the relative free energies of all of the molecular species in solution and the corresponding microscopic binding free energies for all of the molecular species binding with the protein. In this paper, we aim to provide a brief overview of the recent development in computational modeling of the solvent effects on the detailed protein-ligand interactions involving multiple molecular species of a ligand related to rational drug design. In particular, we first briefly discuss the main challenges in computational modeling of the detailed protein-ligand interactions involving the multiple molecular species and then focus on the FPCM model and its applications. The FPCM method allows accurate determination of the solvent effects in the first-principles quantum mechanism (QM) calculations on molecules in solution. The combined use of the FPCM-based QM calculations and other computational modeling and simulations enables us to accurately account for a protein binding with multiple molecular species of a ligand in solution. Based on the computational modeling of the detailed protein-ligand interactions, possible new drugs may be designed rationally as either small-molecule ligands of the protein or engineered proteins that bind/metabolize the ligand. The computational drug design has successfully led to discovery and development of promising drugs.

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43

Üngör, Ökten, Dilyara Igimbayeva, Alina Dragulescu-Andrasi, Sandugash Yergeshbayeva, Teresa Delgado, Samuel M. Greer, Gabrielle Donalson, Minyoung Jo, Rakhmetulla Erkasov, and Michael Shatruk. "Pyridyl-Thioethers as Capping Ligands for the Design of Heteroleptic Fe(II) Complexes with Spin-Crossover Behavior." Magnetochemistry 7, no. 10 (October 1, 2021): 134. http://dx.doi.org/10.3390/magnetochemistry7100134.

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Mononuclear heteroleptic complexes [Fe(tpma)(bimz)](ClO4)2 (1a), [Fe(tpma)(bimz)](BF4)2 (1b), [Fe(bpte)(bimz)](ClO4)2 (2a), and [Fe(bpte)(bimz)](BF4)2 (2b) (tpma = tris(2-pyridylmethyl)amine, bpte = S,S′-bis(2-pyridylmethyl)-1,2-thioethane, bimz = 2,2′-biimidazoline) were prepared by reacting the corresponding Fe(II) salts with stoichiometric amounts of the ligands. All complexes exhibit temperature-induced spin crossover (SCO), but the SCO temperature is substantially lower for complexes 1a and 1b as compared to 2a and 2b, indicating the stronger ligand field afforded by the N2S2-coordinating bpte ligand relative to the N4-coordinating tpma. Our findings suggest that ligands with mixed N/S coordination can be employed to discover new SCO complexes and to tune the transition temperature of known SCO compounds by substituting for purely N-coordinating ligands.

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44

Piromchom, Jureepan, Jintana Othong, Jaursup Boonmak, Ilpo Mutikainen, and Sujittra Youngme. "A novel one-dimensional metal–organic framework with a μ-cyanido-argentate group:catena-poly[[(5,5′-dimethyl-2,2′-bipyridyl-κ2N,N′)silver(I)]-μ-cyanido-κ2N:C]." Acta Crystallographica Section C Structural Chemistry 71, no. 12 (November 7, 2015): 1057–61. http://dx.doi.org/10.1107/s2053229615020288.

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The design and synthesis of metal coordination and supramolecular frameworks containingN-donor ligands and dicyanidoargentate units is of interest due to their potential applications in the fields of molecular magnetism, catalysis, nonlinear optics and luminescence. In the design and synthesis of extended frameworks, supramolecular interactions, such as hydrogen bonding, π–π stacking and van der Waals interactions, have been exploited for molecular recognition associated with biological activity and for the engineering of molecular solids.The title compound, [Ag(CN)(C12H12N2)]n, crystallizes with the AgIcation on a twofold axis, half a cyanide ligand disordered about a centre of inversion and half a twofold-symmetric 5,5′-dimethyl-2,2′-bipyridine (5,5′-dmbpy) ligand in the asymmetric unit. Each AgIcation exhibits a distorted tetrahedral geometry; the coordination environment comprises one C(N) atom and one N(C) atom from substitutionally disordered cyanide bridging ligands, and two N atoms from a bidentate chelating 5,5′-dmbpy ligand. The cyanide ligand links adjacent AgIcations to generate a one-dimensional zigzag chain. These chains are linked togetherviaweak nonclassical intermolecular interactions, generating a two-dimensional supramolecular network.

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45

Yuan, Xiaojing, and Yechun Xu. "Recent Trends and Applications of Molecular Modeling in GPCR–Ligand Recognition and Structure-Based Drug Design." International Journal of Molecular Sciences 19, no. 7 (July 20, 2018): 2105. http://dx.doi.org/10.3390/ijms19072105.

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G protein-coupled receptors represent the largest family of human membrane proteins and are modulated by a variety of drugs and endogenous ligands. Molecular modeling techniques, especially enhanced sampling methods, have provided significant insight into the mechanism of GPCR–ligand recognition. Notably, the crucial role of the membrane in the ligand-receptor association process has earned much attention. Additionally, docking, together with more accurate free energy calculation methods, is playing an important role in the design of novel compounds targeting GPCRs. Here, we summarize the recent progress in the computational studies focusing on the above issues. In the future, with continuous improvement in both computational hardware and algorithms, molecular modeling would serve as an indispensable tool in a wider scope of the research concerning GPCR–ligand recognition as well as drug design targeting GPCRs.

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46

Borisov, D. V., and A. V. Veselovsky. "Ligand-receptor binding kinetics in drug design." Biomeditsinskaya Khimiya 66, no. 1 (January 2020): 42–53. http://dx.doi.org/10.18097/pbmc20206601042.

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Traditionally, the thermodynamic values of affinity are considered as the main criterion for the development of new drugs. Usually, these values for drugs are measured in vitro at steady concentrations of the receptor and ligand, which are differed from in vivo environment. Recent studies have shown that the kinetics of the process of drug binding to its receptor make significant contribution in the drug effectiveness. This has increased attention in characterizing and predicting the rate constants of association and dissociation of the receptor ligand at the stage of preclinical studies of drug candidates. A drug with a long residence time can determine ligand-receptor selectivity (kinetic selectivity), maintain pharmacological activity of the drug at its low concentration in vivo. The paper discusses the theoretical basis of protein-ligand binding, molecular determinants that control the kinetics of the drug-receptor binding. Understanding the molecular features underlying the kinetics of receptor-ligand binding will contribute to the rational design of drugs with desired properties.

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47

Whitesides, George M., and Vijay M. Krishnamurthy. "Designing ligands to bind proteins." Quarterly Reviews of Biophysics 38, no. 4 (November 2005): 385–95. http://dx.doi.org/10.1017/s0033583506004240.

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The ability to design drugs (so-called ‘rational drug design’) has been one of the long-term objectives of chemistry for 50 years. It is an exceptionally difficult problem, and many of its parts lie outside the expertise of chemistry. The much more limited problem – how to design tight-binding ligands (rational ligand design) – would seem to be one that chemistry could solve, but has also proved remarkably recalcitrant. The question is ‘Why is it so difficult?’ and the answer is ‘We still don't entirely know’. This perspective discusses some of the technical issues – potential functions, protein plasticity, enthalpy/entropy compensation, and others – that contribute, and suggests areas where fundamental understanding of protein–ligand interactions falls short of what is needed. It surveys recent technological developments (in particular, isothermal titration calorimetry) that will, hopefully, make now the time for serious progress in this area. It concludes with the calorimetric examination of the association of a series of systematically varied ligands with a model protein. The counterintuitive thermodynamic results observed serve to illustrate that, even in relatively simple systems, understanding protein–ligand association is challenging.

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48

Hendlich, Manfred. "Databases for Protein–Ligand Complexes." Acta Crystallographica Section D Biological Crystallography 54, no. 6 (November 1, 1998): 1178–82. http://dx.doi.org/10.1107/s0907444998007124.

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Recent advances in experimental techniques have led to an enormous explosion of available data about protein–ligand complexes. To exploit the information that is hidden in these large data, collection tools for managing and accessing huge data collections are needed. This paper discusses databases for protein–ligand data which are accessibleviathe World Wide Web. A strong focus is placed on the ReLiBase database system which is a new three-dimensional database for storing and analysing structures of protein–ligand complexes currently deposited in the Brookhaven Protein Data Bank (PDB). ReLiBase contains efficient query tools for identifying and analysing ligands and protein–ligand complexes. Its application for structure-based drug design is illustrated.

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49

Kühl, Olaf. "The natural bite angle — Seen from a ligand's point of view." Canadian Journal of Chemistry 85, no. 3 (March 1, 2007): 230–38. http://dx.doi.org/10.1139/v07-023.

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The natural bite angle concept is examined using N,N′-bisphosphino urea ligands as rigid scaffolds. The ligand has an upper limit of about 95° for the observed bite angle in chelate complexes, but prefers a much lower one. The ligand can be described as possessing downward flexibility. The dependence of the bite angle on the P—P distance within the ligand and the M—P bond length is illustrated. The metal tries to force the ligand into its own preferred structure, whereas the ligand wants to achieve a short P—P distance. A truly rigid ligand such as the N,N′-bisphosphino urea family is thus seen to clearly discriminate between metal atoms according to their individual assertiveness, using the P—P distance in the complex as a measure. Although the natural bite angle concept is valid and helpful in determining the possible bite-angle range for ligands before it is actually synthesised, its practical applicability seems to be limited to those cases where the flexibility range of the ligand allows for only one metal-preferred bite angle to be realized.Key words: natural bite angle, ligand effects, ligand design.

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Burrows, Andrew D. "The Design and Applications of Multifunctional Ligands." Science Progress 85, no. 3 (August 2002): 199–217. http://dx.doi.org/10.3184/003685002783238799.

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The properties of a metal coordination complex are determined as much by the ligand set – the molecules and ions coordinated to the metal centre – as by the nature of the metal itself. The design and use of new ligands is consequently a major part of chemical research. This review considers the role of multifunctional ligands in three separate and distinct areas of chemistry. In homogeneous catalysis, the role of hybrid and hemilabile ligands is considered, and the introduction of functionalities designed to overcome problems of separation, either by tethering or solubilising, is discussed. In supramolecular chemistry, functionalities enabling the recognition and sensing of cations and anions are examined. In addition, ligands containing two or more faces are discussed for their role in metallodendrimer formation and self-assembly reactions, and the use of bifunctional ligands in crystal engineering is addressed. The application of metal complexes in medicine is examined by consideration of cis-platin and its derivatives as antitumour agents. Imaging agents are also discussed with the uses of gadolinium MRI contrast agents and γ-emitting technetium complexes highlighted.

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