Relevant bibliographies by topics / Molecular modeling study

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  1. Journal articles
  2. Dissertations / Theses
  3. Books
  4. Book chapters
  5. Conference papers
  6. Reports

Academic literature on the topic 'Molecular modeling study'

Author: Grafiati
Published: 6 June 2025
Last updated: 10 June 2025

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Journal articles on the topic "Molecular modeling study"

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Chandrasekaran, Rengaswami, Srinivas Janaswamy, and Victor J. Morris. "Acetan:glucomannan interactions—a molecular modeling study." Carbohydrate Research 338, no. 24 (2003): 2889–98. http://dx.doi.org/10.1016/j.carres.2003.08.018.

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Bharat Kumar S. Ankalagi, Nagaraj Gangadhar Hanshul, Ramprasad H., et al. "Molecular Modeling." international journal of engineering technology and management sciences 7, no. 3 (2023): 454–58. http://dx.doi.org/10.46647/ijetms.2023.v07i03.60.

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In this paper, the modelling of molecule is presented. Chemistry, as the central science, utilizes models in virtually every aspect of the discipline. Integral to the progress of chemistry has been its ability to draw from physics, mathematics, statistics, and computer science to develop new sub disciplines, such as computational chemistry. As computing hardware has become faster and more accessible, so to have techniques to perform modelling and simulations of molecular systems. Software systems today assist researchers in the study of molecular systems and provide mechanisms for deriving a rigorous and consistent explanation for the chemical or biological behaviour observed or help the researcher to develop a model for predictions. Molecular modelling is a field that encompasses a wide range of theoretical and computational methods used to represent the structure and behavior of molecules, ions, and particles. These models can be classified based on their length and time scales, ranging from electronic-level models to continuous-level models. One of the main applications of molecular modelling is in drug discovery, where it can be used to predict the activity and behavior of molecules in the body, aiding in the design of new drugs. Additionally, molecular modelling plays a crucial role in materials science, where it can be used to design new materials with specific properties, such as strength, flexibility, and conductivity. With advances in computing hardware and software, molecular modelling has become an increasingly powerful tool in the fields of chemistry, physics, biology, and materials science, allowing researchers to gain a deeper understanding of the behavior of molecules and particles at the molecular level. The work done & presented in this paper is the result of the mini-project work that has been done by the first sem engineering students of the college and as such there is little novelty in it and the references are being taken from various sources from the internet, the paper is being written by the students to test their writing skills in the starting of their engineering career and also to test the presentation skills during their mini-project presentation. The work done & presented in this paper is the report of the assignment / alternate assessment tool as a part and parcel of the academic assignment of the first year subject on nanotechnology & IoT.
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Ayadi, Leila, Damien Forget, Alain Martelli, Jean-François Constant, Martine Demeunynck, and Christian Coulombeau. "Molecular modeling study of DNA abasic sites." Theoretical Chemistry Accounts: Theory, Computation, and Modeling (Theoretica Chimica Acta) 104, no. 3-4 (2000): 284–89. http://dx.doi.org/10.1007/s002140000140.

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Gandhi, Neha, Brijesh K. Srivastava, Vidya B. Lohray, and Braj B. Lohray. "Oxazolidine-2-thiones: a molecular modeling study." Tetrahedron Letters 45, no. 33 (2004): 6269–72. http://dx.doi.org/10.1016/j.tetlet.2004.06.090.

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COX, M. B., P. ARJUNAN, and S. K. ARORA. "Naphthyridinomycin-DNA adducts: A molecular modeling study." Journal of Antibiotics 44, no. 8 (1991): 885–94. http://dx.doi.org/10.7164/antibiotics.44.885.

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P, Srivastava. "Comparative Modeling and Molecular Interaction Study for the Management of AMD and CRVO Ocular Disorder." Open Access Journal of Ophthalmology 8, no. 1 (2023): 1–13. http://dx.doi.org/10.23880/oajo-16000263.

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Age Related Macular Degeneration (AMD) and Central Retinal Vein Occlusion (CRVO) are the rare and leading cause of blindness among patients with ocular problem. Many proteins are reported in the progression of these ocular disorders. Proteins which are directly involved in the development of this disorder reported in the literature, their sequence related information retrieved from biological databases. In silico technique was implemented in order to characterize the properties and structures of the proteins using ProtParam. For studying about the potential phosphorylation sites in protein generally NetPhos server was used whereas for denoting the location of signal peptide cleavage sites and their presence the server which is used is SingalP server. For prediction of secondary structure prediction of proteins is done by using SOPMA. The SOSUI server performs the identification of trans-membrane regions. The 3D dimensional structure was modeled using Swiss Model Workspace and Modeller. Ramachandran plot was used to validate the stereochemical properties of the predicted structures because it is a very important step after 3D structure prediction. Docking of screened phytochemicals with selected proteins was performed by AutoDock. Docking study revealed that Curcumin (binding energy: -8.35) and Berberine (binding energy: -7.14) can be used as better therapeutic lead molecule for the cure of CRVO and AMD respectively.
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Soufi, W., M. Merad, F. BOUKLI Hacene, and S. Ghalem. "Study of Monoamine Oxidase-B and Indole Derivatives Using Two Molecular Docking Programs: Molegro and MOE." International Journal of Scientific Research and Management 8, no. 09 (2020): 25–31. http://dx.doi.org/10.18535/ijsrm/v8i09.c01.

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Inhibition of the enzyme Monoamine oxidase (MAO) is an important approach in the treatment of Parkinson’s disease. A series of indole derivatives were synthesised and evaluated as inhibitors of MAO-B may give insight to develop new ways of antiparkinson drug, In general, the derivatives were found to be selective MAO-B inhibitors with IC50 values . MAO-B inhibitors, are considered useful in the therapy of Parkinson’s disease since oxidation by MAO-B represents a major catabolic pathway of dopamine in the central nervous system . 
 Our goal of research is to study the inhibition of MAO-B by molecular modeling methods. Different molecular modeling tools are used to perform this work (molecular mechanics, molecular dynamics and molecular docking by two programms MDV ( molegro virtual docker) and MOE (modelling Opering Environment. The results obtained from this work, into which the inhibition of MAO-B by molecular modeling methods was elucidated, allow us to conclude that indole derivatives are promising reversible MAO-B inhibitors with a possible role in the treatment of neurodegenerative diseases such as Parkinson’s disease (PD).
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Martinho, Nuno, Helena Florindo, Liana Silva, Steve Brocchini, Mire Zloh, and Teresa Barata. "Molecular Modeling to Study Dendrimers for Biomedical Applications." Molecules 19, no. 12 (2014): 20424–67. http://dx.doi.org/10.3390/molecules191220424.

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Liang, Li, Naijue Zhu, Julian White, Courtney Brown, and Cheryl L. Klein‐Stevensx. "A crystallographic and molecular modeling study of butyrophenones." Journal of Pharmaceutical Sciences 87, no. 12 (1998): 1496–501. http://dx.doi.org/10.1021/js980253e.

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Skovstrup, Søren, Signe Grann Hansen, Troels Skrydstrup, and Birgit Schiøtt. "Conformational Flexibility of Chitosan: A Molecular Modeling Study." Biomacromolecules 11, no. 11 (2010): 3196–207. http://dx.doi.org/10.1021/bm100736w.

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Dissertations / Theses on the topic "Molecular modeling study"

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Nakkiew, Pichaya. "Synthesis and molecular modeling study of dolastatin 11 analogues." Diss., The University of Arizona, 2000. http://hdl.handle.net/10150/284265.

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Nine analogues of dolastatin 11, a potent antineoplastic agent from an Indian Ocean sea hare which interferes with microfilaments, were synthesized, including two natural ones. Although none of these analogues showed stronger activity than dolastatin 11, their syntheses gave better understanding of the structure-activity relationships for dolastatin 11 as described below. The complete lack of activity of the hydroxy acid obtained by hydrolysis of dolastatin 11 showed that the 30-membered ring may be necessary for activity. The high activity of the 3- and 7-nor derivatives showed that the 3- and 7-methyl groups are not needed for strong activity; the former is a drug candidate since it can be prepared pure more economically than dolastatin 11. The synthesis of Ala-epi-dolastatin 11 showed that this stereoisomer has greatly decreased activity, and that it is the persistent by-product in the dolastatin 11 synthesis. Molecular modeling studies showed most of these analogues to have conformations very sin-filar to those of dolastatin 11. However, the very weak activities of the two conformationally-restricted analogues synthesized suggests that none of the three lowest-energy conformations of dolastatin 11 is the binding conformation to F-actin. Two natural analogues isolated from Pacific Ocean blue-green algae were synthesized. The synthesis of the very active majusculamide C confirmed its structure, but the synthesis of the much less active lyngbyastatin 1 showed its configuration in the Ibu unit to have been assigned incorrectly, and that Ibu-epi-dolastatin 12 is a natural product which accompanies it. The broadness of the peaks in the NMR spectra of these two natural products was shown to be due to rotation about their Ibu-Ala amide bonds.
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Zhang, Mo. "Geopolymer, Next Generation Sustainable Cementitious Material − Synthesis, Characterization and Modeling." Digital WPI, 2015. https://digitalcommons.wpi.edu/etd-dissertations/455.

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Geopolymers have received increasing attention as a promising sustainable alternative to ordinary Portland cement (OPC). However, the relationship among the synthesis, geopolymerization process, microstructures, molecular strucutres and mechanical properties of geopolymers remains poorly understood. To fill this knowledge gap, this dissertation focuses on the correlation of chemical composition-reaction kinetics-microstructure-mechanical properties of geopolymers. This study also sheds light on the durability, environmental impact and engineering applications of geopolymers from practical perspectives. The first part of this dissertation presents a comprehensive study on red mud-class F fly ash based geopolymers (RFFG). Firstly, RFFG with a high 28-day mechanical strength were successfully synthesized under the ambient condition of 23°C and 40 to 50% relative humidity. A nominal Na/Al molar ratio of 0.6 ~ 0.8 with a Si/Al ratio of 2 was found to be a good starting chemical composition for RFFG synthesis. Secondly, the reaction kinetics and its relation to the mechanical properties of RFFG were investigated by monitoring the development of geopolymer gels, reaction rate, porosity and mechanical properties of RFFG samples cured at room temperature, 50°C and 80°C for up to 120 days. The asymmetric stretching FTIR band of Si-O-T (T is Si or Al) centered around 960-1000 cm-1, which is the characteristic band of geopolymer gels, was observed to shift to a lower wavenumber at the early stage of the synthesis and shift to a higher wavenumber later on during the synthesis. The shift of Si-O-T band indicates that the geopolymerization took place in three stages: dissolution to Al-rich gels at Stage I, Al-rich gels to Si-rich gels at Stage II and Si-rich gels to tectosilicate networks at Stage III. The mechanical strength of RFFG barely increased, increased slowly by a limited amount and developed significantly at these three stages, respectively. An elevated curing temperature enhanced the early strength of RFFG, whereas an excessively high curing temperature resulted in a higher pore volume that offset the early-developed strength. Lastly, the remaining mechanical properties of the RFFG samples after soaking in a pH = 3.0 sulfuric acid solution for up to 120 days and the concentration of heavy metals leached from RFFG samples after the soaking were measured. The RFFG samples’ resistance against sulfuric acid was found to be comparable to that of OPC, and leaching concentrations of heavy metals were much lower than the respective EPA limits for soil contaminations. The degradation in mechanical properties of the RFFG samples during soaking in the acid was attributed primarily to the depolymerization and dealumination of geopolymer gels. The second part of this dissertation is devoted to the investigation of nano-scale mechanical properties and molecular structures of geopolymer gels with grid-nanoindentation and molecular modeling. Four phases (e.g., porous phase, partially developed geopolymer gels, geopolymer gels and unreacted metakaolin or crystals) and their nano-mechanical properties were identified in metakaolin based geopolymers (MKG) with grid-nanoindentation technique. It was found that the proportion of geopolymer gels largely determines the mechanical strength of the resulting geopolymers while other factors (e.g., pores and cracks) also play some roles in macro-scale mechanical strength of geopolymers. The final setting time of the geopolymers increased with the increase in Si/Al ratio and the decrease in Na/Al ratio, while the proportion of geopolymer gels and macro-mechanical strength of geopolymers increased with the increase in both Si/Al and Na/Al molar ratios, within the range of 1.2~1.7 and 0.6~1.0, respectively. In the molecular modeling, a combined density function theory (DFT)-molecular dynamic (MD) modeling simulation was developed to “synthesize� geopolymers. DFT simulation was used to optimize reactive aluminate and silicate monomers, which were subsequently used in reactive MD simulations to model the polymerization process and computationally synthesize geopolymer gels. The influence of Si/Al ratio and simulation temperatures on geopolymerization and resulting molecules of geopolymer gels was also examined. The computationally polymerized molecular structures of geopolymer gels were obtained. The distribution of Si4(mAl) and radial distribution fuctions of Si-O, Al-O, O-O and Na-Al for the models were compared and qualitatively agreed well with the experimental results from nuclear magnetic resonance (NMR) and neutron/X-ray pair distribution function in previous literature. Three polymerization stages: oligomerization, ring formation and condensation, were identified based on the nature of polymerization process, which were found to be affected by the temperature and Si/Al ratio. A higher temperature enhanced the reaction rate while a lower Si/Al ratio resulted in more compact geopolymer networks. The final part of this dissertation presents an experimental feasibility study of using geopolymer in shallow soil stabilization, in which a lean clay was stabilized with MKG at different concentrations. The study confirmed that MKG can be used as a soil stabilizer for clayey soils and the unconfined compressive strength, Young’s modulus and failure strain are comparable to or even better than OPC when the MKG’s concentration is higher than 11%. The binding effect of geopolymer gels on the soil particles was confirmed as the main mechanism for the improvement in mechanical properties of the stabilized soils with the scanning electron microscopy imaging, energy dispersive X-ray spectroscopy analyses and X-ray diffractometry characterization.
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Vilona, Debora. "Organo-Polyoxometalates for acid catalysis : a combined experimental/modeling study." Thesis, Lyon, 2017. http://www.theses.fr/2017LYSE1190/document.

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Les Polyoxométallates (POMs) sont des nano-molécules anioniques faites par des métaux fortement oxydés et d'oxygène, dont la structure est facilement contrôlée en changeant les conditions synthétiques. Les POMs simples sont utilisés dans des processus industriels comme catalyseurs acides de Brønsted ou comme oxydants. Pour concevoir des nouvelles structures hybrides catalytiques pour la catalyse acide asymétrique (enzymes artificielles), façon Brønsted, nous avons fonctionnalisé le POM (P2W15V3O62)9- avec des ligands organiques (amides et urées). Des études pour comprendre comment le POM influence l'activité acide du ligand organique ont été faites : le POM permet d'améliorer l'acidité des protons du ligand grâce à son caractère electro-attracteur et à sa propriété d'agir comme un réservoir d'électrons. En plus, les POMs lacunaires (?1/?2-P2W17O61)10- étaient fonctionnalisés par des chaînes polyglyciniques de différentes longueurs, dans le but d'étudier par RMN à très haut-champ et par Dynamique Moléculaire quìels sont les facteurs critiques dirigeant les interactions intra-moléculaires en solution, entre les polypeptides et le POM. Le polyoxométallate permet de rigidifier les chaînes peptidiques, agissant comme accepteur des liaisons hydrogène contre les protons amidiques de la chaîne latérale. Nous avons démontré que l'interaction est une fonction de la longueur de chaîne peptidique, de la position de la lacune sur le POM et de la position spécifique du proton sur la chaine latérale<br>Polyoxometalates (POMs) are anionic nano-molecules made by highly oxidized metals and oxygen, whose structure can be easily controlled changing synthetic conditions. Thanks to their robustness, simple POMs are regularly used in industrial processes as Brønsted acids or oxidants. With the aim to rationally design new hybrid POM-based Brønsted acid catalysts for asymmetric catalysis (artificial enzymes), we functionalized the inorganic framework (P2W15V3O62)9- with organic moieties (amides and ureas) to understand how the POM can influence the acid activity of the organo ligands. We established that the POM allows to improve the acidity of the protons in the organo-ligands thanks to its electrowithdrawing character and its property to act as electron reservoir.In parallel, the lacunary (?1/?2-P2W17O61)10- POMs were functionalized with polyglycines chains of different lengths to understand through high-field NMR studies and Molecular Dynamics simulations which are the critical factors governing the intramolecular interactions in solution between polypeptides and the POM surface. The polyoxometalate rigidifies the peptide chains, acting as H-bonding acceptor versus the amidic protons of the lateral chain. We also demonstrated that the interaction is a function of the peptide chain length, the lacuna position on the POM and the amidic proton position on the lateral chain
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Govaerts, Cédric. "Study of the activation mechanisms of G protein-coupled receptors using molecular modeling." Doctoral thesis, Universite Libre de Bruxelles, 2001. http://hdl.handle.net/2013/ULB-DIPOT:oai:dipot.ulb.ac.be:2013/211640.

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Guo, Guanlun. "Stereo-selective binding of enantiomeric ligands in PPAR[gamma] : a molecular modeling study." HKBU Institutional Repository, 2013. http://repository.hkbu.edu.hk/etd_ra/1516.

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Paul, Kristian W. "Molecular modeling study of sulfate and phosphate adsorption at the mineral-water interface." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file, 223 p, 2009. http://proquest.umi.com/pqdweb?did=1654487581&sid=3&Fmt=2&clientId=8331&RQT=309&VName=PQD.

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Okyay, Çağla. "Experimental study and molecular dynamics (MD) modeling of a nucleic acid in nano-confinement." Electronic Thesis or Diss., université Paris-Saclay, 2024. https://www.biblio.univ-evry.fr/theses/2024/2024UPASF063.pdf.

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La technologie des nanopores s'est imposée comme un outil puissant pour étudier le transport biomoléculaire, en particulier pour la translocation et le dézippage des molécules d'ADN. Les études expérimentales ont montré la capacité des nanopores de l'α-hémolysine (αHL) à distinguer différentes séquences et orientations d'ADN. Cependant, les résultats expérimentaux fournissent principalement des informations sur le courant bloqué et le temps de translocation, laissant les détails au niveau moléculaire du processus de dézippage inexplorés. Bien que les simulations de dynamique moléculaire tout-atome soient informatives, elles sont limitées par des échelles de temps réduites. En revanche, les simulations de dynamique moléculaire à gros-grains utilisant le champ de force MARTINI permettent l'étude du transport de l'ADN sur des échelles de temps plus longues, se rapprochant ainsi de celles observées expérimentalement.Cette thèse explore les dynamiques de translocation de l'ADN simple-brin et de dézippage de l'ADN double-brin à travers le nanopore αHL à l'aide d'approches expérimentales et de simulations de dynamique moléculaire dirigées (SMD) à gros-grains. Les différences de temps de translocation entre les extrémités 3' et 5' de l'ADN simple-brin et les temps de dézippage de l'ADN double-brin dans différentes conditions, telles que la structure du duplex d'ADN et la tension appliquée, ont été observées dans les études expérimentales. En particulier, nous avons mesuré des temps de dézippage distincts pour les molécules d'ADN double-brin utilisées, et il a été observé que la dépendance du temps de dézippage à la tension appliquée suivait une loi exponentielle. À mesure que la longueur du duplex augmente, les mécanismes semblent changer en fonction de la structure du duplex. Cependant, les raisons derrière les comportements de translocation et de dézippage restent inaccessibles expérimentalement.En utilisant des simulations de dynamique moléculaire gros-grains, l'influence de l'orientation de l'ADN simple-brin, de la composition en séquences et de la force appliquée sur les dynamiques de translocation a été examinée de manière computationnelle. Nos résultats de simulation ont reproduit les principales observations expérimentales, telles que la large distribution des temps de translocation, les comportements de translocation dépendants de l'orientation, le rôle crucial des interactions électrostatiques entre l'ADN et le nanopore, soulignant l'impact des charges des phosphates de l'ADN sur les taux de translocation, et les dynamiques de translocation dépendantes des séquences sous des forces appliquées variables. En particulier, le rapport entre les temps de translocation des bases puriques et pyrimidiques a également été en bon accord avec les résultats expérimentaux. À la suite des simulations gros-grains, une relation non linéaire entre la vitesse de translocation et la force appliquée a été observée. De plus, les différences de conformations de l'ADN à l'intérieur du nanopore ont apporté des explications supplémentaires aux comportements de translocation dépendants de la séquence et de l'orientation.Cette étude valide le modèle MARTINI à gros-grains comme un outil efficace pour l'étude du transport de l'ADN, montrant sa capacité à compléter les travaux expérimentaux. Nos résultats suggèrent que les simulations de MD gros-grains sont bien adaptées pour dévoiler les mécanismes moléculaires du dézippage de l'ADN, offrant des perspectives inaccessibles par les techniques expérimentales actuelles<br>Nanopore technology has emerged as a powerful tool for studying biomolecular transport, particularly for the translocation and unzipping of DNA molecules. Experimental studies have shown the ability of α-hemolysin (αHL) nanopores to distinguish between different DNA sequences and ori-entations. However, experimental results primarily provide blocked current and translocation time information, leaving molecular-level details of the unzipping process unexplored. All-atom molecular dynamics (MD) simulations, though informative, are limited by short time scales. Coarse-grained (CG) MD simulations using the MARTINI force field, on the other hand, enable the study of DNA transport over extended time scales, approaching those observed experimentally.This thesis investigates the dynamics of both ssDNA translocation and dsDNA unzipping through the αHL nanopore using a combination of experimental techniques and CG-steered MD (SMD) simulations. Experimental studies explored the translocation times of ssDNA at the 3' and 5' ends, as well as the unzipping times of dsDNA under various conditions, including different duplex structures and applied voltages. Our findings on ssDNA translocation aligned with previous experimental and theoretical results, confirming faster translocation of 3' oriented ssDNA. Additionally, distinct unzipping times were observed for the different duplex structures under identical experimental conditions, with an exponential relationship noted between unzipping time and applied voltage. As the duplex length increased, the unzipping mechanisms appeared to vary depending on the duplex structure. However, the underlying molecular mechanisms behind these translocation and unzipping behaviors remain experimentally inaccessible, highlighting the need for further theoretical studies.By employing CG MD simulations, the influence of ssDNA orientation, sequence composition, and pulling force on translocation dynamics were computationally examined. Our simulation results reproduced the key experimental findings, such as the wide distribution of the translocation times, the orientation-dependent translocation behaviors, the crucial role of electrostatic interactions be-tween DNA and the nanopore, highlighting the impact of DNA phosphate charges on translocation rates, and the sequence-dependent translocation dynamics under varying applied forces. Specifically, the ratio of translocation times of purine and pyrimidine bases was also found to be in good agreement with the experimental findings. As a result of the CG simulations, a non-linear relation-ship between translocation velocity and the applied force was observed. Additionally, differences in DNA conformations inside the nanopore provided additional explanation for the sequence- and orientation-dependent translocation behaviors.This study validates the MARTINI CG model as an effective tool for investigating DNA transport, demonstrating its ability to complement experimental data. Our findings suggest that CG MD simulations are well suited for uncovering the molecular mechanisms underlying DNA unzipping, offering insights that are otherwise inaccessible through current experimental techniques
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Yin, Hong. "Kriging model approach to modeling study on relationship between molecular quantitative structures and chemical properties." HKBU Institutional Repository, 2005. http://repository.hkbu.edu.hk/etd_ra/598.

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Franco, Luís Fernando Mercier. "Study on the thermodynamics of bovine serum albumin aqueous solutions: experiments, modeling and molecular simulations." Universidade de São Paulo, 2015. http://www.teses.usp.br/teses/disponiveis/3/3137/tde-14072016-140814/.

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The interaction between two proteins into salt aqueous solutions is investigated throughout this thesis. Experiments, modeling and molecular simulations were carried out to get a better understanding of the phenomenon. Bovine serum albumin was used as a model protein. An analytical expression for the structure factor for globular proteins in aqueous solution is presented in this work. This expression was obtained considering an intermolecular potential given by the sum of a hard core, a van der Waals attractive and a screened Coulomb contribution. Experimental data of Small Angle X-Ray Scattering for bovine serum albumin in aqueous solutions containing sodium salts at different protein concentrations and pH values are also presented. The expression developed for the structure factor describes accurately these experimental data provided a dependence of the attractive parameter on protein concentration is established. An expression for the osmotic pressure was derived from the structure factor. With attractive parameters adjusted from X-ray scattering data, the osmotic pressure of bovine serum albumin aqueous solutions could be predicted with very good agreement with experimental data. A derivation of the thermodynamic potentials, such as the chemical potential, using the new osmotic equation of state is presented. Applying the phase equilibrium criterion, the fluid-fluid phase equilibrium for bovine serum albumin in salt aqueous solution was calculated. Although such separation was not experimentally observed at the isoelectric point, it was indeed experimentally observed for a pH value below the isoelectric point. The predictions seem to be valuable to discuss how ion specificity affects the phase diagram of proteins. To apply molecular dynamic techniques to simulate how proteins interact to each other in salt aqueous solutions, two new coarse-grained force fields are proposed. The first one, meant for sodium sulfate aqueous solution, avoids the unphysical association observed for non-polarizable atomistic force fields; and allows the prediction of thermodynamic and dynamic properties. The second one, meant for bovine serum albumin in aqueous solution, is used as a new strategy to evaluate the scattering form factor of proteins as a low resolution technique for protein structure prediction.<br>Nesta tese apresenta-se uma investigação sobre a interação entre duas proteínas em soluções aquosas salinas. Experimentos, modelagem e simulações moleculares foram realizadas para conseguir um melhor entendimento do fenômeno. Albumina de soro bovina foi usada como proteína modelo. Uma expressão para o fator de estrutura de proteínas globulares em solução aquosa é apresentada neste trabalho. Esta expressão foi obtida considerando-se um potencial intermolecular dado pela soma de um núcleo duro, uma contribuição atrativa tipo vander Waals e uma contribuição de potencial coulômbico blindado. Dados experimentais de espalhamento de raios-X a baixos ângulos para a albumina de soro bovino em soluções aquosas contendo sais de sódio com diferentes concentrações de proteína e valores de pH também são apresentados. A expressão desenvolvida para o fator de estrutura descreve com precisão estes dados experimentais, desde que uma dependência entre o parâmetro atrativo com a concentração de proteína seja estabelecida. Uma expressão para a pressão osmótica foi derivada do fator de estrutura. Com parâmetros atrativos ajustados aos dados de espalhamento de raios-X, a pressão osmótica da albumina de soro bovino em solução aquosa pôde ser predita com grande correlação com os dados experimentais. Uma derivação dos potenciais termodinâmicos usando a nova equação osmótica de estado é apresentada. Aplicando o critério de equilíbrio de fases, foi possível calcular o equilíbrio fluido-fluido para a albumina de soro bovino em solução aquosa. Embora tal separação não tenha sido observada experimentalmente em um pH igual ao ponto isoelétrico, ela foi de fato observada experimentalmente para um valor de pH menor do que o ponto isoelétrico. As predições parecem ser valiosas para discutir como a especificidade iônica afeta o diagrama de fases de proteínas. De modo a avaliar como proteínas interagem umas com as outras usando técnicas de dinâmica molecular, dois novos campos de força coarse-grained são propostos. O primeiro, para o sulfato de sódio em solução aquosa, evita a associação não-física que é observada para campos de força atomísticos não-polarizáveis. Este modelo é capaz de prever propriedades dinâmicas e termodinâmicas. O segundo, para a albumina de soro bovino em solução aquosa, é usado como uma nova estratégia para avaliar o fator de forma de espalhamento de proteínas como uma ferramenta de baixa resolução na predição de estruturas proteicas.
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Wang, Yanbin. "Molecular Modeling Study of Oxidative Degradation of Polyperfluoroethers Catalyzed by Iron Fluoride Surfaces : An Extended Hückel Theory Approach." Thesis, University of North Texas, 1995. https://digital.library.unt.edu/ark:/67531/metadc278315/.

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Extended Hückel methods are known to be a useful tool in understanding surface phenomena. Important quantities about atoms and chemical bonds can be obtained from this computationally simple method, although caution must be exercised in interpreting the results. Application of Extended Hückel calculations to large metal clusters reveals the role of d orbitals in solids. Basic ideas of constructing model compounds have been developed. Several model systems for surface chemisorption processes are constructed in order to understand the surface catalyzed oxidative degradation of polyperfluoroethers. The activation of oxygen molecules can be explained. The Lewis acid character of the iron fluoride surface can be predicted. Based on these results, mechanisms of the degradation processes are discussed.
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Books on the topic "Molecular modeling study"

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Wei, Wei, and C. Neal Stewart Jr., eds. Gene flow: monitoring, modeling and mitigation. CABI, 2021. http://dx.doi.org/10.1079/9781789247480.0000.

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Abstract Over two decades later, gene flow research as it pertains to genetically engineered crops is still going strong, even in the face of the absence of ecological disasters in the nearly 30 years of widescale biotech crop commercialization. Nonetheless, ecological timeframes are within the study scope of the sort of research performed to date covered in this book. These studies have greatly informed regulations that govern biotech crops. The chapters in this book capture various aspects of scientific disciplines that span from organismal studies, to population and community ecology, to molecular biology.
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Flint, Daniel Geoffrey. A molecular modelling study of covalently cross-linked peptides. University of Birmingham, 2003.

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Andriyanova, Mariya, Aslanli Aslanli, Nataliya Basova, et al. ORGANOPHOSPHORUS NEUROTOXINS. Publishing Center RIOR, 2020. http://dx.doi.org/10.29039/02026-5.

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The collective monograph is devoted to discussing the history of creation, studying the properties, neutralizing and using organophosphorus neurotoxins, which include chemical warfare agents, agricultural crop protection chemical agents (herbicides and insecticides) and medicines. The monograph summarizes the results of current scientific research and new prospects for the development of this field of knowledge in the 21st century, including the use of modern physicochemical methods for experimental study and theoretical analysis of biocatalysis and its mechanisms based on molecular modeling with supercomputer power. &#x0D; The book is intended for specialists who are interested in the current state of research in the field of organophosphorus neurotoxins. The monograph will be useful for students, graduate students, researchers specializing in the field of physical chemistry, physicochemical biology, chemical enzymology, toxicology, biochemistry, molecular biology and genetics, biotechnology, nanotechnology and biomedicine.
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Klein, David R. Organic Chemistry, 3e Loose-Leaf Print Companion WileyPLUS with WileyPLUS Blackboard Card, Study Guide, and Molecular Modeling Kit Set. Wiley & Sons, Incorporated, John, 2018.

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Klein, David R. Organic Chemistry, 3e Loose-Leaf Print Companion WileyPLUS with WileyPLUS LMS Card, Study Guide EPUB Card, and Molecular Modeling Kit Set. Wiley & Sons, Incorporated, John, 2018.

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Klein, David R. Organic Chemistry, 3e Loose-Leaf Print Companion WileyPLUS with WileyPLUS LMS Card, Study Guide EPUB Card, and Molecular Modeling Kit Set. Wiley & Sons, Incorporated, John, 2018.

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Appasani, Krishnarao, and Raghu Kiran Appasani, eds. Single-Molecule Science. Cambridge University Press, 2022. http://dx.doi.org/10.1017/9781108525909.

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Single Molecule Science (SMS) has emerged from developing, using and combining technologies such as super-resolution microscopy, atomic force microscopy, and optical and magnetic tweezers, alongside sophisticated computational and modelling techniques. This comprehensive, edited volume brings together authoritative overviews of these methods from a biological perspective, and highlights how they can be used to observe and track individual molecules and monitor molecular interactions in living cells. Pioneers in this fast-moving field cover topics such as single molecule optical maps, nanomachines, and protein folding and dynamics. A particular emphasis is also given to mapping DNA molecules for diagnostic purposes, and the study of gene expression. With numerous illustrations, this book reveals how SMS has presented us with a new way of understanding life processes. A must-have for researchers and graduate students, as well as those working in industry, primarily in the areas of biophysics, biological imaging, genomics and structural biology.
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Allen, Michael P., and Dominic J. Tildesley. Nonequilibrium molecular dynamics. Oxford University Press, 2017. http://dx.doi.org/10.1093/oso/9780198803195.003.0011.

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This chapter explains some of the fundamental issues associated with applying perturbations to a molecular dynamics simulation, along with practical details of methods for studying systems out of equilibrium. The main emphasis is on fluid flow and viscosity measurements. Spatially homogeneous perturbations are described to study shear and extensional flow. Non-equilibrium methods are applied to the study of heat flow and the calculation of the thermal conductivity. Issues of thermostatting, and the modelling of surface-fluid interactions for inhomogeneous systems, are discussed. The measurement of free energy changes through non-equilibrium work expressions such as those of Jarzynski and Crooks is also explained.
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Coveney, Peter V., and Shunzhou Wan. Molecular Dynamics: Probability and Uncertainty. Oxford University PressOxford, 2025. https://doi.org/10.1093/9780198893479.001.0001.

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Abstract This book explores the intersection of molecular dynamics (MD) simulation with advanced probabilistic methodologies to address the inherent uncertainties in the approach. Beginning with a clear and comprehensible introduction to classical mechanics, the book transitions into the probabilistic formulation of MD, highlighting the importance of ergodic theory, kinetic theory, and unstable periodic orbits, concepts which are largely unknown to current practitioners within the domain. It discussed ensemble-based simulations, free energy calculations and the study of polymer nanocomposites using multi-scale modelling, providing detailed guidance on performing reliable and reproducible computations. A thorough discussion on Verification, Validation, and Uncertainty Quantification (VVUQ) lays out a definitive approach to formulating the uncertainty of MD modelling and simulation. Its interaction with artificial intelligence is examined in the light of these issues. While machine learning (ML) methods offer some advantages and less often-noted drawbacks, the integration of ML with physics-based MD simulations may in future enhance our ability to predict new drugs and advanced materials. The final chapter, ‘The End of Certainty’, synthesizes these themes, advocating a systematic and careful approach to computational research and the embrace of uncertainty as an integral part of innovation. This book serves as a highly original, conceptual and comprehensible guide for researchers and practitioners, emphasizing the need for rapid, accurate, precise and actionable techniques in the rapidly-evolving field of molecular dynamics.
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Klein, David R. Set: CEGEPS Organic Chemistry 2e with Study Guide/Student Solutions Manual and Molecular Modelling Kit. Wiley & Sons, Incorporated, John, 2016.

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Book chapters on the topic "Molecular modeling study"

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Parry, Zahoor Ahmad, and Rajesh Pandey. "Molecular Modeling Techniques to Study Dendrimers." In Dendrimers in Medical Science. Apple Academic Press, 2017. http://dx.doi.org/10.1201/9781315366005-4.

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Gibbs, G. V., Monte B. Boisen, Lesa L. Beverly, and Kevin M. Rosso. "10. A Computational Quantum Chemical Study of the Bonded Interactions in Earth Materials and Structurally and Chemically Related Molecules." In Molecular Modeling Theory, edited by Randall T. Cygan and James D. Kubicki. De Gruyter, 2001. http://dx.doi.org/10.1515/9781501508721-013.

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Straub, Bernd F., Michael Bessel, and Regina Berg. "Dicopper Catalysts for the Azide Alkyne Cycloaddition: A Mechanistic DFT Study." In Modeling of Molecular Properties. Wiley-VCH Verlag GmbH & Co. KGaA, 2011. http://dx.doi.org/10.1002/9783527636402.ch13.

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Raskatov, Jevgenij A., and Guenter Helmchen. "Effects of Substituents on the Regioselectivity of Palladium-Catalyzed Allylic Substitutions: A DFT Study." In Modeling of Molecular Properties. Wiley-VCH Verlag GmbH & Co. KGaA, 2011. http://dx.doi.org/10.1002/9783527636402.ch12.

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Montanari, Carlos Alberto. "A CoMFA study on antileishmaniasis bisamidines." In Molecular Modeling and Prediction of Bioactivity. Springer US, 2000. http://dx.doi.org/10.1007/978-1-4615-4141-7_56.

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Li, Mingguang, and Joshua Reineke. "Physiologically Based Pharmacokinetic Modeling for Nanoparticle Toxicity Study." In Methods in Molecular Biology. Humana Press, 2012. http://dx.doi.org/10.1007/978-1-62703-002-1_24.

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Källblad, Per, and Philip M. Dean. "Property Patches in GPCRs: A Multivariate Study." In Molecular Modeling and Prediction of Bioactivity. Springer US, 2000. http://dx.doi.org/10.1007/978-1-4615-4141-7_116.

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Al Sharif, Merilin, Ivanka Tsakovska, Petko Alov, Vessela Vitcheva, Antonia Diukendjieva, and Ilza Pajeva. "Molecular Modeling Approach to Study the PPARγ–Ligand Interactions." In Methods in Molecular Biology. Springer New York, 2019. http://dx.doi.org/10.1007/978-1-4939-9195-2_22.

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Specks, Julia, Maria Nieto-Soler, Andres J. Lopez-Contreras, and Oscar Fernandez-Capetillo. "Modeling the Study of DNA Damage Responses in Mice." In Methods in Molecular Biology. Springer New York, 2015. http://dx.doi.org/10.1007/978-1-4939-2297-0_21.

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Schleicher, Jana. "Introduction to In Silico Modeling to Study ROS Dynamics." In Methods in Molecular Biology. Springer US, 2020. http://dx.doi.org/10.1007/978-1-0716-0896-8_1.

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Conference papers on the topic "Molecular modeling study"

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Ramachandran, S., and V. Jovancicevic. "Molecular Modeling of the Inhibition of Mild Steel CO2 Corrosion by Imidazolines." In CORROSION 1998. NACE International, 1998. https://doi.org/10.5006/c1998-98017.

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Abstract Imidazolines have been used to inhibit corrosion in carbon dioxide solutions. Molecular modeling techniques have been used to study the adsorption and film formation of imidazolines onto iron oxide. The studies have determined 1) the binding of imidazoline and amide functional groups to an iron oxide surface, 2) the orientation of imidazoline molecules on the surface, and 3) the cohesive energy of formation of a bilayer of imidazoline molecules as a function of alkyl chain length. Molecular modeling techniques aid the development of improved corrosion inhibitors by quantifying the role of different functional groups in an inhibitor.
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Ramachandran, S., M. B. Ward, and K. A. Bartrip. "Molecular Modeling of Corrosion of Iron in H2S Environments." In CORROSION 2002. NACE International, 2002. https://doi.org/10.5006/c2002-02240.

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Abstract Preventing corrosion in sour gas environments presents a serious challenge to oil producers. Corrosion inhibitors are often used in sour gas environments to prevent corrosion. In sour gas, depending upon the fugacities of carbon dioxide and hydrogen sulfide in the gas, temperature and pressure of the system, and brine chemistry, different types of iron sulfide and iron carbonate product layers are formed. Molecular modeling has previously been used in understanding the mechanism of corrosion inhibition in carbon dioxide systems. In this work, a new force field is developed to understand mackinawite, an important iron sufide scale formed during H2S corrosion. As many authors have found the dissolution of this scale to be a rate determining step during the corrosion of iron in H2S environments. This work forms an important step in using molecular modeling techniques to study the corrosion of iron in H2S environments and its inhibition.
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Ramachandran, S., V. Jovancicevic, and M. B. Ward. "Understanding Interactions between Corrosion Inhibitors & Iron Carbonate Films Using Molecular Modeling." In CORROSION 1999. NACE International, 1999. https://doi.org/10.5006/c1999-99007.

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Abstract Molecular modeling techniques have been used to study the adsorption and film formation of N-containing corrosion inhibitors on hematite (Fe2O3) and magnetite (Fe3O4) surfaces. In oilfield applications as temperature and carbon dioxide partial pressure vary, different corrosion products are formed on mild steel. FeCO3 is the predominant corrosion product at conditions of high partial pressures of carbon dioxide. In this work, molecular modeling techniques will be used to study the adsorption and film formation of N-containing corrosion inhibitors onto iron carbonate.
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Tang, Shidi, Xingxing Zhou, and Ming Ling. "Modeling Equivariant Neural Networks for Hardware Acceleration, a Case Study on the Molecular Docking Tool DiffDock." In 2024 IEEE Pacific Rim Conference on Communications, Computers and Signal Processing (PACRIM). IEEE, 2024. http://dx.doi.org/10.1109/pacrim61180.2024.10690224.

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Bendiksen, B., and J. S. Gill. "Molecular Modeling in Scale Control - An Experimental Verification and ITS Limitations." In CORROSION 1996. NACE International, 1996. https://doi.org/10.5006/c1996-96164.

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Abstract This work centers on the use of molecular modeling to study scale inhibition of alkaline earth scales such as calcium carbonate and calcium sulfate. The molecular modeling studies have shown the interaction of phosphonates with varied crystal faces of the scales. The software makes it possible to visualize the important crystal faces and match the geometry of the inhibitor to the crystal planes that determine the morphology of the resulting solid. Molecular Dynamics (MD) calculations can reveal specific interactions of inhibitors with scale surfaces. Quantitative Structure Activity Relationships (QSAR) between scale inhibition and calculated quantities have been used to build models that help to predict the structure of new scale inhibitors. Interaction energies of phosphonates over the surfaces of crystals can show differences in binding of phosphonate to specific crystal faces. The relative binding energies can be correlated to effectiveness in scale inhibition, and verified by experiment. However, simple energy calculations do not always explain the complicated process of scale inhibition. Comparison is made of the effectiveness of two phosphonates, hydroxy ethylidene diphosphonic acid (HEDP) and amino methylene phosphonate (AMP), in scale inhibition of CaCO3 and CaSO4. Relative energy (Erel) calculations are used to demonstrate molecular modeling for scale inhibition studies.
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Helenius, Vesa M., P. H. Hynninen, and Jouko E. Korppi-Tommola. "Molecular structures of chlorophyll a aggregates: spectroscopic and molecular modeling study." In Laser Spectroscopy of Biomolecules: 4th International Conference on Laser Applications in Life Sciences, edited by Jouko E. Korppi-Tommola. SPIE, 1993. http://dx.doi.org/10.1117/12.146105.

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Baumketner, A. "Molecular Dynamics Study of Protein Folding: Potentials and Mechanisms." In MODELING OF COMPLEX SYSTEMS: Seventh Granada Lectures. AIP, 2003. http://dx.doi.org/10.1063/1.1571312.

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Gubarev, Fedor A., Iuliia Liushnevskaya, Lin Li, Andrei V. Mostovshchikov, and Alexander P. Ilyin. "Laser monitor application for study of aluminum nanopowder ignition and combustion." In Laser Physics, Photonic Technologies, and Molecular Modeling, edited by Vladimir L. Derbov. SPIE, 2021. http://dx.doi.org/10.1117/12.2588461.

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Sumyanova, Tsagana B., Nataliya E. Borisova, Darya Y. Volkova, and Roman Pankov. "Study of the complexation reactions between dichloro-substituted 1,10-phenanthroline-2,9-dicarboxamide and lanthanide nitrates." In Laser Physics, Photonic Technologies, and Molecular Modeling, edited by Vladimir L. Derbov. SPIE, 2021. http://dx.doi.org/10.1117/12.2590745.

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Sumyanova, Tsagana B., Nataliya E. Borisova, Аrina А. Petukhova, and Anna A. Kirsanova. "Study of the complexation reaction between subtituted 6,6′-bis(diphenylphosphinoyl)-2,2′-bipyridyls and lanthanum ions." In Laser Physics, Photonic Technologies, and Molecular Modeling, edited by Vladimir L. Derbov. SPIE, 2022. http://dx.doi.org/10.1117/12.2623658.

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Reports on the topic "Molecular modeling study"

1

Prazniak, J. K., and C. H. Byers. A modeling study of vacuum sorption characteristics of carbon dioxide on 4A zeolite molecular sieves. Office of Scientific and Technical Information (OSTI), 1987. http://dx.doi.org/10.2172/6038249.

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Gurevitz, Michael, William A. Catterall, and Dalia Gordon. face of interaction of anti-insect selective toxins with receptor site-3 on voltage-gated sodium channels as a platform for design of novel selective insecticides. United States Department of Agriculture, 2013. http://dx.doi.org/10.32747/2013.7699857.bard.

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Voltage-gated sodium channels (Navs) play a pivotal role in excitability and are a prime target of insecticides like pyrethroids. Yet, these insecticides are non-specific due to conservation of Navs in animals, raising risks to the environment and humans. Moreover, insecticide overuse leads to resistance buildup among insect pests, which increases misuse and risks. This sad reality demands novel, more selective, insect killers whose alternative use would avoid or reduce this pressure. As highly selective insect toxins exist in venomous animals, why not exploit this gift of nature and harness them in insect pest control? Many of these peptide toxins target Navs, and since their direct use via transformed crop plants or mediator microorganisms is problematic in public opinion, we focus on the elucidation of their receptor binding sites with the incentive of raising knowledge for design of toxin peptide mimetics. This approach is preferred nowadays by agro-industries in terms of future production expenses and public concern. However, characterization of a non-continuous epitope, that is the channel receptor binding site for such toxins, requires a suitable experimental system. We have established such a system within more than a decade and reached the stage where we employ a number of different insect-selective toxins for the identification of their receptor sites on Navs. Among these toxins we wish to focus on those that bind at receptor site-3 and inhibit Nav inactivation because: (1) We established efficient experimental systems for production and manipulation of site-3 toxins from scorpions and sea anemones. These peptides vary in size and structure but compete for site-3 on insect Navs. Moreover, these toxins exhibit synergism with pyrethroids and with other channel ligands; (2) We determined their bioactive surfaces towards insect and mammalian receptors (see list of publications); (3) We found that despite the similar mode of action on channel inactivation, the preference of the toxins for insect and mammalian channel subtypes varies greatly, which can direct us to structural features in the basis of selectivity; (4) We have identified by channel loop swapping and point mutagenesis extracellular segments of the Navinvolved with receptor site-3. On this basis and using channel scanning mutagenesis, neurotoxin binding, electrophysiological analyses, and structural data we offer: (i) To identify the residues that form receptor site-3 at insect and mammalian Navs; (ii) To identify by comparative analysis differences at site-3 that dictate selectivity toward various Navs; (iii) To exploit the known toxin structures and bioactive surfaces for modeling their docking at the insect and mammalian channel receptors. The results of this study will enable rational design of novel anti-insect peptide mimetics with minimized risks to human health and to the environment. We anticipate that the release of receptor site-3 molecular details would initiate a worldwide effort to design peptide mimetics for that site. This will establish new strategies in insect pest control using alternative insecticides and the combined use of compounds that interact allosterically leading to increased efficiency and reduced risks to humans or resistance buildup among insect pests.
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