Academic literature on the topic 'Molecular docking. eng'
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Journal articles on the topic "Molecular docking. eng"
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Kanwar, Gurtej, Anish Kumar, and Anshika Mahajan. "Open source software tools for computer aided drug design." International Journal of Research in Pharmaceutical Sciences 9, no. 1 (March 12, 2018): 86. http://dx.doi.org/10.26452/ijrps.v9i1.1191.
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Computer-aided drug design (CADD) has revolutionized the drug discovery arena and it has reduced the costs associated with finding novel compounds which are having pharmaceutical importance. In CADD, the scientists use the computer software to discover biological active compounds. Molecular docking and energy minimization tools are essential components of structure based drug design. It is a significant tool in structural molecular biology and computer-assisted drug design. It reduces the laboratory workload of the end user and allows researchers to restrict their docking studies to the smallest and the most representative set of macromolecules and small molecules possible. This greatly enhances the productivity of researchers. Energy minimization is an important criterion for selecting a potential 3D molecule. In modeled structures, the 3D structure is affected is due to steric clashes. These clashes happen in a protein structure due to the overlap of non bonding atoms and with the assistance of energy minimization, steric clashes can be eradicated. The open software’s and databases provides a platform for scientists and scholars to carry out their research work in a better way. The docking tools are discussed in this review cover protein-ligand, protein-peptide as well as protein-nucleic acid docking. The tools described include AutoDock 4 and Vina, UCSF DOCK, FLIPDock, EADock, HADDOCK 2.2, SwissDock, PatchDock and ClusPro. In addition to the docking tools, energy minimization tools such as YASARA minimization server, KoBaMIN server and 3D refine server have also been discussed. This mini-review concentrates on open software tools which are free of cost and can be easily downloaded in the computers that are useful for CADD.
Keywords: Molecular docking; Energy minimization; Structure refinement; Drug design; CADD
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Xiao, Wei, Disha Wang, Zihao Shen, Shiliang Li, and Honglin Li. "Multi-Body Interactions in Molecular Docking Program Devised with Key Water Molecules in Protein Binding Sites." Molecules 23, no. 9 (September 11, 2018): 2321. http://dx.doi.org/10.3390/molecules23092321.
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Water molecules play an important role in modeling protein-ligand interactions. However, traditional molecular docking methods often ignore the impact of the water molecules by removing them without any analysis or keeping them as a static part of the proteins or the ligands. Hence, the accuracy of the docking simulations will inevitably be damaged. Here, we introduce a multi-body docking program which incorporates the fixed or the variable number of the key water molecules in protein-ligand docking simulations. The program employed NSGA II, a multi-objective optimization algorithm, to identify the binding poses of the ligand and the key water molecules for a protein. To this end, a force-field-based hydration-specific scoring function was designed to favor estimate the binding affinity considering the key water molecules. The program was evaluated in aspects of the docking accuracy, cross-docking accuracy, and screening efficiency. When the numbers of the key water molecules were treated as fixed-length optimization variables, the docking accuracy of the multi-body docking program achieved a success rate of 80.58% for the best RMSD values for the recruit of the ligands smaller than 2.0 Å. The cross-docking accuracy was investigated on the presence and absence of the key water molecules by four protein targets. The screening efficiency was assessed against those protein targets. Results indicated that the proposed multi-body docking program was with good performance compared with the other programs. On the other side, when the numbers of the key water molecules were treated as variable-length optimization variables, the program obtained comparative performance under the same three evaluation criterions. These results indicated that the multi-body docking with the variable numbers of the water molecules was also efficient. Above all, the multi-body docking program developed in this study was capable of dealing with the problem of the water molecules that explicitly participating in protein-ligand binding.
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Bai, Donglin, and Ao Hong Wang. "Extracellular domains play different roles in gap junction formation and docking compatibility." Biochemical Journal 458, no. 1 (January 20, 2014): 1–10. http://dx.doi.org/10.1042/bj20131162.
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GJ (gap junction) channels mediate direct intercellular communication and play an important role in many physiological processes. Six connexins oligomerize to form a hemichannel and two hemichannels dock together end-to-end to form a GJ channel. Connexin extracellular domains (E1 and E2) have been shown to be important for the docking, but the molecular mechanisms behind the docking and formation of GJ channels are not clear. Recent developments in atomic GJ structure and functional studies on a series of connexin mutants revealed that E1 and E2 are likely to play different roles in the docking. Non-covalent interactions at the docking interface, including hydrogen bonds, are predicted to form between interdocked extracellular domains. Protein sequence alignment analysis on the docking compatible/incompatible connexins indicate that the E1 domain is important for the formation of the GJ channel and the E2 domain is important in the docking compatibility in heterotypic channels. Interestingly, the hydrogen-bond forming or equivalent residues in both E1 and E2 domains are mutational hot spots for connexin-linked human diseases. Understanding the molecular mechanisms of GJ docking can assist us to develop novel strategies in rescuing the disease-linked connexin mutants.
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Worachartcheewan, Apilak, Napat Songtawee, Suphakit Siriwong, Supaluk Prachayasittikul, Chanin Nantasenamat, and Virapong Prachayasittikul. "Rational Design of Colchicine Derivatives as anti-HIV Agents via QSAR and Molecular Docking." Medicinal Chemistry 15, no. 4 (May 20, 2019): 328–40. http://dx.doi.org/10.2174/1573406414666180924163756.
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Background: Human immunodeficiency virus (HIV) is an infective agent that causes an acquired immunodeficiency syndrome (AIDS). Therefore, the rational design of inhibitors for preventing the progression of the disease is required. Objective: This study aims to construct quantitative structure-activity relationship (QSAR) models, molecular docking and newly rational design of colchicine and derivatives with anti-HIV activity. Methods: A data set of 24 colchicine and derivatives with anti-HIV activity were employed to develop the QSAR models using machine learning methods (e.g. multiple linear regression (MLR), artificial neural network (ANN) and support vector machine (SVM)), and to study a molecular docking. Results: The significant descriptors relating to the anti-HIV activity included JGI2, Mor24u, Gm and R8p+ descriptors. The predictive performance of the models gave acceptable statistical qualities as observed by correlation coefficient (Q2) and root mean square error (RMSE) of leave-one out cross-validation (LOO-CV) and external sets. Particularly, the ANN method outperformed MLR and SVM methods that displayed LOO−CV 2 Q and RMSELOO-CV of 0.7548 and 0.5735 for LOOCV set, and Ext 2 Q of 0.8553 and RMSEExt of 0.6999 for external validation. In addition, the molecular docking of virus-entry molecule (gp120 envelope glycoprotein) revealed the key interacting residues of the protein (cellular receptor, CD4) and the site-moiety preferences of colchicine derivatives as HIV entry inhibitors for binding to HIV structure. Furthermore, newly rational design of colchicine derivatives using informative QSAR and molecular docking was proposed. Conclusion: These findings serve as a guideline for the rational drug design as well as potential development of novel anti-HIV agents.
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Hamzeh-Mivehroud, Maryam, Zoha Khoshravan-Azar, and Siavoush Dastmalchi. "QSAR and Molecular Docking Studies on Non-Imidazole-Based Histamine H3 Receptor Antagonists." Pharmaceutical Sciences 26, no. 2 (June 27, 2020): 165–74. http://dx.doi.org/10.34172/ps.2019.64.
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Background: In the recent years, histamine H3 receptor (H3R) has been receiving increasing attention in pharmacotherapy of neurological disorders. The aim of the current study was to investigate structural requirements for the prediction of H3 antagonistic activity using quantitative structure-activity relationship (QSAR) and molecular docking techniques. Methods: To this end, genetic algorithm coupled partial least square and stepwise multiple linear regression methods were employed for developing a QSAR model. The obtained QSAR model was stringently assessed using different validation criteria. Results: The generated model indicated that connectivity information and mean absolute charge are two important descriptors for the prediction of H3 antagonistic activity of the studied compounds. To gain insight into the mechanism of interaction between studied molecules and H3R, molecular docking was performed. The most important residues involved in the ligand-receptor interactions were identified. Conclusion: The result of current study can be used for designing of new H3 antagonist and proposing structural modifications to improve H3 inhibitory potency.
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Malinak, David, Eugenie Nepovimova, Daniel Jun, Kamil Musilek, and Kamil Kuca. "Novel Group of AChE Reactivators—Synthesis, In Vitro Reactivation and Molecular Docking Study." Molecules 23, no. 9 (September 7, 2018): 2291. http://dx.doi.org/10.3390/molecules23092291.
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The acetylcholinesterase (AChE) reactivators (e.g., obidoxime, asoxime) became an essential part of organophosphorus (OP) poisoning treatment, together with atropine and diazepam. They are referred to as a causal treatment of OP poisoning, because they are able to split the OP moiety from AChE active site and thus renew its function. In this approach, fifteen novel AChE reactivators were determined. Their molecular design originated from former K-oxime compounds K048 and K074 with remaining oxime part of the molecule and modified part with heteroarenium moiety. The novel compounds were prepared, evaluated in vitro on human AChE (HssAChE) inhibited by tabun, paraoxon, methylparaoxon or DFP and compared to commercial HssAChE reactivators (pralidoxime, methoxime, trimedoxime, obidoxime, asoxime) or previously prepared compounds (K048, K074, K075, K203). Some of presented oxime reactivators showed promising ability to reactivate HssAChE comparable or higher than the used standards. The molecular modelling study was performed with one compound that presented the ability to reactivate GA-inhibited HssAChE. The SAR features concerning the heteroarenium part of the reactivator’s molecule are described.
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Temelkovski, Damjan, Tamas Kiss, Gabor Terstyanszky, and Pamela Greenwell. "Building Science Gateways for Analysing Molecular Docking Results Using a Generic Framework and Methodology." Journal of Grid Computing 18, no. 3 (July 5, 2020): 529–46. http://dx.doi.org/10.1007/s10723-020-09529-9.
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Abstract Molecular docking and virtual screening experiments require large computational and data resources and high-level user interfaces in the form of science gateways. While science gateways supporting such experiments are relatively common, there is a clearly identified need to design and implement more complex environments for further analysis of docking results. This paper describes a generic framework and a related methodology that supports the efficient development of such environments. The framework is modular enabling the reuse of already existing components. The methodology, which proposes three techniques that the development team can use, is agile and encourages active participation of end-users. Based on the framework and methodology, two prototype implementations of science-gateway-based docking environments are presented and evaluated. The first system recommends a receptor-ligand pair for the next docking experiment, and the second filters docking results based on ligand properties.
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Vazquez-Morado, Luis E., Ramon E. Robles-Zepeda, Adrian Ochoa-Leyva, Aldo A. Arvizu-Flores, Adriana Garibay-Escobar, Francisco Castillo-Yañez, and Alonso A. Lopez-zavala. "Biochemical characterization and inhibition of thermolabile hemolysin from Vibrio parahaemolyticus by phenolic compounds." PeerJ 9 (January 6, 2021): e10506. http://dx.doi.org/10.7717/peerj.10506.
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Vibrio parahaemolyticus (Vp), a typical microorganism inhabiting marine ecosystems, uses pathogenic virulence molecules such as hemolysins to cause bacterial infections of both human and marine animals. The thermolabile hemolysin VpTLH lyses human erythrocytes by a phospholipase B/A2 enzymatic activity in egg-yolk lecithin. However, few studies have been characterized the biochemical properties and the use of VpTLH as a molecular target for natural compounds as an alternative to control Vp infection. Here, we evaluated the biochemical and inhibition parameters of the recombinant VpTLH using enzymatic and hemolytic assays and determined the molecular interactions by in silico docking analysis. The highest enzymatic activity was at pH 8 and 50 °C, and it was inactivated by 20 min at 60 °C with Tm = 50.9 °C. Additionally, the flavonoids quercetin, epigallocatechin gallate, and morin inhibited the VpTLH activity with IC50 values of 4.5 µM, 6.3 µM, and 9.9 µM, respectively; while phenolics acids were not effective inhibitors for this enzyme. Boltzmann and Arrhenius equation analysis indicate that VpTLH is a thermolabile enzyme. The inhibition of both enzymatic and hemolytic activities by flavonoids agrees with molecular docking, suggesting that flavonoids could interact with the active site’s amino acids. Future research is necessary to evaluate the antibacterial activity of flavonoids against Vp in vivo.
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López-López, Edgar, Fernando Prieto-Martínez, and José Medina-Franco. "Activity Landscape and Molecular Modeling to Explore the SAR of Dual Epigenetic Inhibitors: A Focus on G9a and DNMT1." Molecules 23, no. 12 (December 11, 2018): 3282. http://dx.doi.org/10.3390/molecules23123282.
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In this work we discuss the insights from activity landscape, docking and molecular dynamics towards the understanding of the structure-activity relationships of dual inhibitors of major epigenetic targets: lysine methyltransferase (G9a) and DNA methyltranferase 1 (DNMT1). The study was based on a novel data set of 50 published compounds with reported experimental activity for both targets. The activity landscape analysis revealed the presence of activity cliffs, e.g., pairs of compounds with high structure similarity but large activity differences. Activity cliffs were further rationalized at the molecular level by means of molecular docking and dynamics simulations that led to the identification of interactions with key residues involved in the dual activity or selectivity with the epigenetic targets.
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Gaffin, Robert D., Kuppan Gokulan, James C. Sacchettini, Timothy E. Hewett, Raisa Klevitsky, Jeffrey Robbins, Vandana Sarin, David C. Zawieja, Gerald A. Meininger, and Mariappan Muthuchamy. "Changes in end-to-end interactions of tropomyosin affect mouse cardiac muscle dynamics." American Journal of Physiology-Heart and Circulatory Physiology 291, no. 2 (August 2006): H552—H563. http://dx.doi.org/10.1152/ajpheart.00688.2005.
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The ends of striated muscle tropomyosin (TM) are integral for thin filament cooperativity, determining the cooperative unit size and regulating the affinity of TM for actin. We hypothesized that altering the α-TM carboxy terminal overlap end to the β-TM counterpart would affect the amino-terminal association, which would alter the end-to-end interactions of TM molecules in the thin filament regulatory strand and affect the mechanisms of cardiac muscle contraction. To test this hypothesis, we generated transgenic (TG) mouse lines that express a mutant form of α-TM in which the first 275 residues are from α-TM and the last nine amino acids are from β-TM (α-TM9aaΔβ). Molecular analyses show that endogenous α-TM mRNA and protein are nearly completely replaced with α-TM9aaΔβ. Working heart preparations data show that the rates of contraction and relaxation are reduced in α-TM9aaΔβ hearts. Left ventricular pressure and time to peak pressure are also reduced (−12% and −13%, respectively). The ratio of maximum to minimum first derivatives of change in left ventricular systolic pressure with respect to time (ratio of +dP/d t to −dP/d t, respectively) is increased, but τ is not changed significantly. Force-intracellular calcium concentration ([Ca2+]i) measurements from intact papillary fibers demonstrate that α-TM9aaΔβ TG fibers produce less force per given [Ca2+]icompared with nontransgenic fibers. Taken together, the data demonstrate that the rate of contraction is primarily affected in TM TG hearts. Protein docking studies show that in the mutant molecule, the overall carbon backbone is perturbed about 1.5 Å, indicating that end-to-end interactions are altered. These results demonstrate that the localized flexibility present in the coiled-coil structures of TM isoforms is different, and that plays an important role in interacting with neighboring thin filament regulatory proteins and with differentially modulating the myofilament activation processes.
Dissertations / Theses on the topic "Molecular docking. eng"
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Sabbag, Mariana Pela. "Caracterização estrutural e das interações entre a Proteína G do hRSV e potenciais inibidores /." São José do Rio Preto : [s.n.], 2012. http://hdl.handle.net/11449/94808.
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Orientador: Fátima Pereira de SouzaBanca: Karina Alves de Toledo
Banca: Tereza Cristina Cardoso
Resumo: As infecções respiratórias agudas (IRAs) constituem a principal causa de mortalidade infantil no mundo, e o Vírus Respiratório Sincicial Humano (hRSV - Human Respiratory Syncytial Virus) é um dos principais agentes etiológicos das IRAs. Este vírus pertencente à família Paramyxoviridae, é envelopado, de simetria helicoidal, cujo genoma é RNA de fita simples não segmentada. A infectividade do vírus está relacionada com suas proteínas de membrana e dentre elas a glicoproteína G, que é responsável pela ligação do vírus à célula hospedeira e conseqüente instalação da infecção. Esta glicoproteína exerce um importante papel como antígeno de reconhecimento, sendo alvo para identificação do RSV através de anticorpos. Existem evidências de que esta proteína se liga a receptores glicosilados na célula hospedeira, porém ainda não foi descrito um receptor para a proteína G na célula. Para elucidar estes mecanismos de interação, foram realizados estudos experimentais e teóricos desta proteína. Os domínios solúveis da região N-terminal (1 a 38 aa) e C-terminal (67 a 298 aa), com 231 aminoácidos da glicoproteína G do hRSV foram clonados e a região N-terminal foi expressa em bactéria BL21 pLysS. Em paralelo, foi realizada a caracterização teórica desta proteína, e foram avaliados os possíveis sítios de interação da mesma com glicosaminoglicanos (heparina). Foram obtidos dois modelos teóricos para a proteína G do hRSV, bem como dois modelos de interação com heparina, determinando portanto, um possível sítio de ocorrência de interação. O conhecimento da estrutura da proteína G é de grande importância para elucidar a composição da estrutura e os mecanismos de interação com potenciais ligantes e deste modo, em um passo posterior, propor mecanismos de reconhecimento celular pelo hRSV, através de glicosaminoglicanos
Abstract: Acute Respiratory Infections (ARI) are the leading cause of infant mortality in the world, and the Human Respiratory Syncytial Virus (hRSV) is one of the main agents of ARI. This virus belongs to Paramyxoviridae family, has a lipidic envelope, helical symmetry and its genome is a single-stranded RNA. The viral infectivity is related to its membrane proteins and among them the G glycoprotein, which is responsible for binding the virus to the host cell and consequent infection. This glycoprotein plays an important role as antigen recognition, being the target for hRSV identification through antibodies. There are evidences that this protein binds to host cell glycosylated receptors, but it has not been described a receptor for G protein in the cell yet. To elucidate these interaction mechanisms and understand the process of viral infectivity, we performed experimental and theoretical studies of this protein. The soluble domains of the N-terminal (1-38 aa) and C-terminal regions (67-298 aa), with 231 amino acids of the hRSV G glycoprotein have been cloned and the N-terminal region was expressed in BL21 pLysS bacteria. In a later trial these peptides will be purified and biophysical tests will be done. It was also performed a theoretical characterization of this protein, to assess the possible interaction sites with glycosaminoglycan (heparin). It were obtained two theoretical models for the hRSV G protein as well as two interaction models with heparin, in order to determine a possible site of occurrence of interaction. Knowledge of G protein structure is of great importance to elucidate the mechanism of viral infectivity and interaction mechanisms with potential ligants, and the results obtained in this work will allow us, in a later step, to propose mechanisms of cellular recognition by hRSV through glycosaminoglycans
Mestre
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Daldrop, Peter. "Structure and molecular recognition in riboswitches." Thesis, University of Dundee, 2011. https://discovery.dundee.ac.uk/en/studentTheses/db338d42-75c1-43a6-be6a-11399f04989e.
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Riboswitches are cis-acting gene regulatory RNAs, which function without involvement of proteins. They have been implicated as drug targets and are attractive systems for the study of RNA-ligand binding and RNA folding. The purine riboswitch was used as a model system for RNA-ligand docking. Published binding data was successfully reproduced in silico and compounds predicted to bind the riboswitch in a virtual screening were tested experimentally. Structural data confirming the predicted binding mode for several cases was obtained. The problems encountered were not specific to RNA-ligand docking but known from the far more explored field of protein-ligand docking.The SAM-I riboswitch was also subjected to virtual ligand screening. This receptor is a system of greater complexity than the purine riboswitch and consequently posed a harder challenge to the docking protocol. After initial validation of the docking setup based on previously published data, a set of compounds selected from the in-house database of commercially available compounds was screened. One compound identfied in silico was cofirmed to bind experimentally.The k-turn motif found in the SAM-I riboswitch was investigated with respect to its folding. The k-turn motif was found to be foldable in context of the SAMI riboswitch as well as in isolation as was expected. Furthermore, mutations disrupting key interactions within the k-turn motif were found to be prohibitive of k-turn folding in isolation as well as in context of the riboswitch, leading to a loss of ligand binding. Interestingly, two sequences were identfied which fold in context of the riboswitch but do not fold in isolation. This confirms the contribution of tertiary interactions to k-turn folding. This conclusion was backed up with structural data is a system of greater complexity than the purine riboswitch and consequently posed a harder challenge to the docking protocol. After initial validation of the to its folding. The k-turn motif was found to be foldable in context of the SAMI riboswitch as well as in isolation as was expected. Furthermore, mutations disrupting key interactions within the k-turn motif were found to be prohibitive of k-turn folding in isolation as well as in context of the riboswitch, leading to a loss of ligand binding. Interestingly, two sequences were identi ed which fold in context of the riboswitch but do not fold in isolation. This con rms the contribution of tertiary interactions to k-turn folding. This conclusion was backed
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Dembla, Ekta Mayur [Verfasser], and Ute [Akademischer Betreuer] Becherer. "Biogenesis of large dense core vesicles and molecular mechanisms of dead-end docking in mouse chromaffin cells / Ekta Mayur Dembla ; Betreuer: Ute Becherer." Saarbrücken : Saarländische Universitäts- und Landesbibliothek, 2017. http://d-nb.info/1182312969/34.
Full textBook chapters on the topic "Molecular docking. eng"
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Basu, Anamika, Piyali Basak, and Anasua Sarkar. "Molecular-Docking-Based Anti-Allergic Drug Design." In Pharmaceutical Sciences, 711–26. IGI Global, 2017. http://dx.doi.org/10.4018/978-1-5225-1762-7.ch027.
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Allergens are foreign proteins that when come in contact of part(s) of human body stimulate the production of immunoglobulin types of proteins (antibodies). These allergens react with antibodies (immunoglobulin type E or IgE) produces allergic reactions, also known as immediate-type hypersensitivity reactions. As much as 20% of the general population may be affected by grass pollen as a major cause of allergic disease. EXPB class of proteins are known in the immunological literature as group-1 grass pollen allergens Molecular docking method can be used to identify the predicated the interaction of pollen allergen EXPB1 (Zea m 1), a beta-expansin and group-1 pollen allergen from maize with IgE molecules of human. The World Health Organization recognised allergen immunotherapy, as therapeutics for allergic diseases. RNA Interference (RNAi) is a biological process in which RNA molecules e.g. Small Interfering RNAs (siRNAs) inhibit gene expression, by cleavage and destruction of specific mRNA molecules. Use of Small Interfering RNA (siRNA) is a novel method in the induction of RNA Interference (RNAi), which is a potent method for therapeutics of allergic reactions. Due to various effects of STAT 6 proteins during hypersensitivity reactions caused by pollen allergens, mRNA of STAT6 gene is selected as target gene for allergy therapeutics via Post-Transcriptional Gene Silencing (PTGS). Using molecular docking study a specific sense siRNA is identified as anti allergic drug to treat allergic asthma during immediate type of hypersensitivity reaction, caused by Zea m 1 pollen allergen.
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Basu, Anamika, Piyali Basak, and Anasua Sarkar. "Molecular-Docking-Based Anti-Allergic Drug Design." In Advances in Medical Technologies and Clinical Practice, 232–48. IGI Global, 2016. http://dx.doi.org/10.4018/978-1-5225-0362-0.ch009.
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Allergens are foreign proteins that when come in contact of part(s) of human body stimulate the production of immunoglobulin types of proteins (antibodies). These allergens react with antibodies (immunoglobulin type E or IgE) produces allergic reactions, also known as immediate-type hypersensitivity reactions. As much as 20% of the general population may be affected by grass pollen as a major cause of allergic disease. EXPB class of proteins are known in the immunological literature as group-1 grass pollen allergens Molecular docking method can be used to identify the predicated the interaction of pollen allergen EXPB1 (Zea m 1), a beta-expansin and group-1 pollen allergen from maize with IgE molecules of human. The World Health Organization recognised allergen immunotherapy, as therapeutics for allergic diseases. RNA Interference (RNAi) is a biological process in which RNA molecules e.g. Small Interfering RNAs (siRNAs) inhibit gene expression, by cleavage and destruction of specific mRNA molecules. Use of Small Interfering RNA (siRNA) is a novel method in the induction of RNA Interference (RNAi), which is a potent method for therapeutics of allergic reactions. Due to various effects of STAT 6 proteins during hypersensitivity reactions caused by pollen allergens, mRNA of STAT6 gene is selected as target gene for allergy therapeutics via Post-Transcriptional Gene Silencing (PTGS). Using molecular docking study a specific sense siRNA is identified as anti allergic drug to treat allergic asthma during immediate type of hypersensitivity reaction, caused by Zea m 1 pollen allergen.
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Kumar, Ashwani, Ruchika Goyal, and Sandeep Jain. "Docking Methodologies and Recent Advances." In Methods and Algorithms for Molecular Docking-Based Drug Design and Discovery, 295–319. IGI Global, 2016. http://dx.doi.org/10.4018/978-1-5225-0115-2.ch012.
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Docking, a molecular modelling method, has wide applications in identification and optimization in modern drug discovery. This chapter addresses the recent advances in the docking methodologies like fragment docking, covalent docking, inverse docking, post processing, hybrid techniques, homology modeling etc. and its protocol like searching and scoring functions. Advances in scoring functions for e.g. consensus scoring, quantum mechanics methods, clustering and entropy based methods, fingerprinting, etc. are used to overcome the limitations of the commonly used force-field, empirical and knowledge based scoring functions. It will cover crucial necessities and different algorithms of docking and scoring. Further different aspects like protein flexibility, ligand sampling and flexibility, and the performance of scoring function will be discussed.
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Kumar, Ashwani, Ruchika Goyal, and Sandeep Jain. "Docking Methodologies and Recent Advances." In Oncology, 804–28. IGI Global, 2017. http://dx.doi.org/10.4018/978-1-5225-0549-5.ch031.
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Docking, a molecular modelling method, has wide applications in identification and optimization in modern drug discovery. This chapter addresses the recent advances in the docking methodologies like fragment docking, covalent docking, inverse docking, post processing, hybrid techniques, homology modeling etc. and its protocol like searching and scoring functions. Advances in scoring functions for e.g. consensus scoring, quantum mechanics methods, clustering and entropy based methods, fingerprinting, etc. are used to overcome the limitations of the commonly used force-field, empirical and knowledge based scoring functions. It will cover crucial necessities and different algorithms of docking and scoring. Further different aspects like protein flexibility, ligand sampling and flexibility, and the performance of scoring function will be discussed.
Conference papers on the topic "Molecular docking. eng"
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Jensen-McMullin, Cynthia, Mark Bachman, and Guann-Pyng Li. "Universal Microcarriers for Microfluidic Assays." In ASME 2007 5th International Conference on Nanochannels, Microchannels, and Minichannels. ASMEDC, 2007. http://dx.doi.org/10.1115/icnmm2007-30226.
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Bead and cell suspension based flow-through assays are popular for high throughput biological analysis. Several technologies incorporate a tagging scheme with beads to enable multiplexing. Modern flow-through systems such as flow cytometers and cell sorters are large, bulky and expensive; consequently, much research has been performed using microfluidics to miniaturize these systems. However, several problems remain with these systems, notably it remains difficult to perform manipulations on the beads (or cells), and in the case of multiplexed systems, it remains difficult to read the tags quickly. In this paper, we present a micromachined micro-carrier, referred to as a ‘micropallet’, designed to move through a microfluidic device, which helps to solve several of these problems. Micropallets are small carrier structures, micromachined out of plastic or other materials, that are used to carry attached biological or chemical samples through a microfluidic system (e.g., DNA, RNA, proteins, antibodies, adherent cells, organisms). Similar to conventional factory pallets that carry a product through an automated manufacturing line, micropallets are engineered to carry their cargo through a micro-scale system. Thus micropallets may contain shapes, structures and materials designed to interact with and work in a microfluidic system, such as for docking, sorting, manipulation and readout. Additionally, micropallets may include bar codes or other markings, and be engineered to optimally suit the cargo they carry (for example, a micropallet might contain 3-D structures and treated sections for cells, molecules or organisms to attach). Results are presented for the use of micropallets in cell assays, DNA assays and antibody assays. Micropallets may be designed to carry a sample through a microfluidic system or for use in a static assay system, enabling versatile customisation of the micropallets and flow system for design of a programmable system that interacts with the micropallets for detection, control and manipulation.