Academic literature on the topic 'DOCKING SCORE'
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Journal articles on the topic "DOCKING SCORE"
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Kumar, Harsh, Aastha Sharma, Davinder Kumar, Minakshi Gupta Marwaha, and Rakesh Kumar Marwaha. "3-(Substituted Aryl/alkyl)-5-((E)-4-((E)-(Substituted Aryl/alkyl)methyl)benzylidene) thiazolidin-2,4-dione Molecules: Design, ADME Studies and Molecular Docking Analysis as Potential Antimicrobial and Antiproliferative Agents." Asian Journal of Chemistry 34, no. 9 (2022): 2393–405. http://dx.doi.org/10.14233/ajchem.2022.23927.
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A library comprising of 60 synthesizable compounds from three different series having 20 compounds in each series of 3-(furan-2-carbonyl)-5-((E)-4-((E)-(substituted aryl/ alkyl)methyl)benzylidene)thiazolidine-2,4-dione (FC-1 to FC-20), 3-(butyl)-5-((E)-4-((E)-(substituted aryl/alkyl)methyl)benzylidene)thiazolidine-2,4-dione (NB-1 to NB-20) and 3-(allyl)-5-((E)-4-((E)- (substituted aryl/alkyl)methyl)benzylidene)thiazolidine-2,4-dione (NA-1 to NA-20) was designed and screened for antimicrobial and anticancer potential by molecular docking studies using S. aureus GyrB ATPase (PDB code: 3U2D) and CDK-8 (PDB code: 5FGK) proteins as possible drug targets, respectively by Schrödinger-Maestro v13.2. Molecular docking studies revealed, analogues NB-3 (docking score = -6.626), NA-3 (docking score = -6.315) and FC-20 (docking score = -5.552) displayed best docking score in each series, respectively against 3U2D and molecules NB-2 (docking score = -6.517), NA-20 (docking score = -7.668) and FC-12 (docking score = -4.931) exhibited best docking score in each series, respectively against 5FGK having better interaction with crucial amino acid. ADME results revealed all the analogues have significant scores within Qikprop range and also in close agreement with the Pfizer’s rule of five. These analogues can be used as lead structures for the development/ discovery of new anticancer and antimicrobial agents.
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Choi, Jieun, and Juyong Lee. "V-Dock: Fast Generation of Novel Drug-like Molecules Using Machine-Learning-Based Docking Score and Molecular Optimization." International Journal of Molecular Sciences 22, no. 21 (October 27, 2021): 11635. http://dx.doi.org/10.3390/ijms222111635.
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We propose a computational workflow to design novel drug-like molecules by combining the global optimization of molecular properties and protein-ligand docking with machine learning. However, most existing methods depend heavily on experimental data, and many targets do not have sufficient data to train reliable activity prediction models. To overcome this limitation, protein-ligand docking calculations must be performed using the limited data available. Such docking calculations during molecular generation require considerable computational time, preventing extensive exploration of the chemical space. To address this problem, we trained a machine-learning-based model that predicted the docking energy using SMILES to accelerate the molecular generation process. Docking scores could be accurately predicted using only a SMILES string. We combined this docking score prediction model with the global molecular property optimization approach, MolFinder, to find novel molecules exhibiting the desired properties with high values of predicted docking scores. We named this design approach V-dock. Using V-dock, we efficiently generated many novel molecules with high docking scores for a target protein, a similarity to the reference molecule, and desirable drug-like and bespoke properties, such as QED. The predicted docking scores of the generated molecules were verified by correlating them with the actual docking scores.
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Pamungkas, Tri Setyo, and Rosario Trijuliamos Manalu. "STUDI IN SILICO SENYAWA AKTIF ASAM JAWA (Tamarindus indica L.) SEBAGAI ANTIDIABETES MELALUI INHIBISI PROTEIN TYROSINE PHOSPHATASE." Jurnal Ilmiah Ibnu Sina (JIIS): Ilmu Farmasi dan Kesehatan 8, no. 1 (March 31, 2023): 134–44. http://dx.doi.org/10.36387/jiis.v8i1.1282.
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Tamarind leaves (Tamarindus indica L.) are widely cultivated in tropical countries, including Indonesia. Empirically, tamarind leaves are known to have anti-diabetic properties. In this study, an in-silico method was used to test the active compounds found in tamarind leaves (Tamarindus indica L.) as anti-diabetic agents through docking score analysis. The target protein used was Protein Tyrosine Phosphatase (5JNT) which is related to insulin resistance. Glimepiride and native ligand 5JNT were used as reference ligands, while the active compounds of tamarind leaves (Tamarindus indica L.) were used as the test ligands. There were 12 active compounds tested for drug-like properties based on the Lipinski Rule of Five, and 12 compounds met the criteria which were then tested through molecular docking using the PLANTS software. Based on the docking results, there were four compounds that had potential as anti-diabetic agents, namely linalool anthranilate, hexadecanol, pentadecanol, and benzyl benzoate, with docking scores of -85.889, -84.23032, -83.12325, and -81.54821 respectively. Although the docking scores of these compounds exceeded the score of the native ligand 5JNT, they did not exceed the score of the reference ligand glimepiride.
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Pratama, Mohammad Rizki Fadhil, Hadi Poerwono, and Siswandono Siswodihardjo. "Introducing a two‐dimensional graph of docking score difference vs. similarity of ligand‐receptor interactions." Indonesian Journal of Biotechnology 26, no. 1 (March 30, 2021): 54. http://dx.doi.org/10.22146/ijbiotech.62194.
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Observation of molecular docking results was generally performed by analyzing the docking score and the interacting amino acid residues separately either in tables or graphs. Sometimes it was not easy to rank the tested ligands’ docking results, especially if there were many ligands. This study aims to introduce a new way to analyze docking results with a two‐dimensional graph between the difference in docking score and the similarity of ligand‐receptor interactions. Molecular docking was performed with one reference ligand and several test ligands. The docking score difference was obtained between the test and the reference ligands as the graph’s x‐axis. Meanwhile, the y‐axis contains the similarity of ligand‐receptor interactions, obtained from the ratio of amino acid residues and the types of interactions between the test and reference ligands. Docking result analysis was more straightforward because two critical parameters were presented in one graph. This graph could be used to support the analysis of the docking results.
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Rizma, Baiq Ressa Puspita, Yek Zen Mubarok, Dian Fathita Dwi Lestari, and Agus Dwi Ananto. "Molecular Study of Antiviral Compound of Indonesian Herbal Medicine as 3CLpro and PLpro Inhibitor in SARS-COV-2." Acta Chimica Asiana 4, no. 2 (October 29, 2021): 127–34. http://dx.doi.org/10.29303/aca.v4i2.74.
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Rapid transmission of COVID-19 disease and the fatal effects of the disease lead researchers to use various way to find potential anti-COVID-19 compounds, including using modern approaches. Molecular docking is one of the methods that can be used to analyse antiviral compounds and its molecular target from Indonesian herbs that are believed to have properties as anti-COVID-19. This study aims to analyse antiviral compounds from 5 herbs that have the potential as inhibitors of PLpro and 3CLpro, which both are a non-structural protein in SARS-CoV-2 by molecular docking approach using PLANTS. Remdesivir triphosphate, the active metabolite of remdesivir, was used as the comparison compound in studies. The results showed docking scores obtained from interactions between natural ligands, remdesivir trifospat, curcumin, demetoksikurkumin, bisdemetoksikurkumin, luteolin, apigenin, kuersetin, kaempferol, formononrtin-7-O-glucoronide, androgafolide, and neoandrogafolide with PLpro are as follows -111,441, -103,827, -103,609, -102,363, -100,27,-79,6655, -78.6901, -80.9337, -79.4686, -82.1124, -79.1789, and -97.2452.Combination between quercetin, neoandrographolide, bisdemethoxycurcumin, demetoxycurcumin, and curcumin showed a synergy effect by reduce its docking score. Meanwhile its interaction with the protein 3CLpro showed docking score for those compounds as follows 64.0074, -86.1811, -81.428, -87.1625, -78.2899, -73.4345,-70,3368, -71.5539, -68.4321, -72.0154, -75.9777 and -93.7746.Combination between andrographolide, neoandrographolide, bisdemethoxycurcumin, demetoxycurcumin and curcumin, also shows synegy effect in 3CLpro allow them to reduce the docking score.This study concludes that curcumin was known as the most potent compound that act as a PLpro inhibitor based on a docking score of -103,609, while in 3CLpro all the compound have a potential to inhibit 3CLpro with demethosxycurcumin and neoandrogafolide as the most potent compound with a docking score -87,126 and -93.7746.
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Mateev, Emilio Viktorov, Iva Valkova, Maya Georgieva, and Alexander Zlatkov. "Suitable Docking Protocol for the Design of Novel Coumarin Derivatives with Selective MAO-B Effects." Journal of Molecular Docking 1, no. 1 (June 30, 2021): 40–47. http://dx.doi.org/10.33084/jmd.v1i1.2357.
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Recently, the application of molecular docking is drastically increasing due to the rapid growth of resolved crystallographic receptors with co-crystallized ligands. However, the inability of docking softwares to correctly score the occurred interactions between ligands and receptors is still a relevant issue. This study examined the Pearson’s correlation coefficient between the experimental monoamine oxidase-B (MAO-B) inhibitory activity of 44 novel coumarins and the obtained GOLD 5.3 docking scores. Subsequently, optimization of the docking protocol was carried out to achieve the best possible pairwise correlation. Numerous modifications in the docking settings such as alteration in the scoring functions, size of the grid space, presence of active waters, and side-chain flexibility were conducted. Furthermore, ensemble docking simulations into two superimposed complexes were performed. The model was validated with a test set. A significant Pearson’s correlation coefficient of 0.8217 was obtained for the latter. In the final stage of our work, we observed the major interactions between the top-scored ligands and the active site of 1S3B.
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Bajusz, Dávid, Anita Rácz, and Károly Héberger. "Comparison of Data Fusion Methods as Consensus Scores for Ensemble Docking." Molecules 24, no. 15 (July 24, 2019): 2690. http://dx.doi.org/10.3390/molecules24152690.
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Ensemble docking is a widely applied concept in structure-based virtual screening—to at least partly account for protein flexibility—usually granting a significant performance gain at a modest cost of speed. From the individual, single-structure docking scores, a consensus score needs to be produced by data fusion: this is usually done by taking the best docking score from the available pool (in most cases— and in this study as well—this is the minimum score). Nonetheless, there are a number of other fusion rules that can be applied. We report here the results of a detailed statistical comparison of seven fusion rules for ensemble docking, on five case studies of current drug targets, based on four performance metrics. Sevenfold cross-validation and variance analysis (ANOVA) allowed us to highlight the best fusion rules. The results are presented in bubble plots, to unite the four performance metrics into a single, comprehensive image. Notably, we suggest the use of the geometric and harmonic means as better alternatives to the generally applied minimum fusion rule.
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Scobie, D. R., D. O'Connell, C. A. Morris, and S. M. Hickey. "A preliminary genetic analysis of breech and tail traits with the aim of improving the welfare of sheep." Australian Journal of Agricultural Research 58, no. 2 (2007): 161. http://dx.doi.org/10.1071/ar05444.
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The area of naturally bare skin around the perineum was scored at weaning in lambs (n = 2152) from a composite flock of New Zealand crossbred sheep. Breech bareness was scored on a range from 1, where wool was growing right to the edges of the anus, to 5, where a large bare area surrounded the perineum. Bareness on the under surface of the tail was measured on a linear scale at tail docking. Dag score (degree of breech soiling) was recorded at weaning, on a scale of 0–5, where an increasing score indicated more dags. Dag score was taken as a measure of the risk of flystrike in the breech. Female lambs tended to have slightly greater (P < 0.001) breech bareness score (mean score 2.7) than males (mean score 2.6), whereas mean dag score of females was lower than that of males (0.45 v. 0.53; P < 0.05). Breech bareness score had a heritability of 0.33 ± 0.06, and the length of bare skin under the tail had a heritability of 0.59 ± 0.06. The genetic correlation between breech bareness score at weaning and length of bare skin under the tail at docking was positive (0.35 ± 0.10). These 2 traits had phenotypic correlations with dag score of –0.17 ± 0.02 and –0.03 ± 0.03, respectively, and genetic correlations with dag score of –0.30 ± 0.13 and 0.03 ± 0.12, respectively; negative values indicated a favourable relationship. Tails were removed at docking, so the phenotypic correlation of about zero between tail data and dag score at weaning was of little utility. Our results suggest that selecting for these 2 bareness traits could reduce dag formation and the associated risk of breech strike.
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Feher, Miklos, and Christopher I. Williams. "Reducing Docking Score Variations Arising from Input Differences." Journal of Chemical Information and Modeling 50, no. 9 (August 10, 2010): 1549–60. http://dx.doi.org/10.1021/ci100204x.
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Batool, Majda, Affifa Tajammal, Firdous Farhat, Francis Verpoort, Zafar Khattak, Mehr-un-Nisa, Muhammad Shahid, et al. "Molecular Docking, Computational, and Antithrombotic Studies of Novel 1,3,4-Oxadiazole Derivatives." International Journal of Molecular Sciences 19, no. 11 (November 15, 2018): 3606. http://dx.doi.org/10.3390/ijms19113606.
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A new series of 1,3,4-oxadiazoles derivatives was synthesized, characterized, and evaluated for their in vitro and in vivo anti-thrombotic activity. Compounds (3a–3i) exhibited significant clot lysis with respect to reference drug streptokinase (30,000 IU), and enhanced clotting time (CT) values (130–342 s) than heparin (110 s). High affinity towards 1NFY with greater docking score was observed for the compounds (3a, 3i, 3e, 3d, and 3h) than the control ligand RPR200095. In addition, impressive inhibitory potential against factor Xa (F-Xa) was observed with higher docking scores (5612–6270) with Atomic Contact Energy (ACE) values (−189.68 to −352.28 kcal/mol) than the control ligand RPR200095 (Docking score 5192; ACE −197.81 kcal/mol). In vitro, in vivo, and in silico results proposed that these newly synthesized compounds might be used as anticoagulant agents.
Dissertations / Theses on the topic "DOCKING SCORE"
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Guilhot-Gaudeffroy, Adrien. "Modélisation et score de complexes protéine-ARN." Thesis, Paris 11, 2014. http://www.theses.fr/2014PA112228/document.
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Cette thèse présente des résultats dans le domaine de la prédiction d’interactions protéine-ARN. C’est un domaine de recherche très actif, pour lequel la communauté internationale organise régulièrement des compétitions pour évaluer différentes techniques de prédictions in silico d’interactions protéine-protéine et protéine-ARN sur des données benchmarks (CAPRI, Critical Assessment of PRedictedInteractions), par prédiction en aveugle et en temps limité. Dans ce cadre, de nombreuses approches reposant sur des techniques d’apprentissage supervisé ont récemment obtenus de très bons résultats.Nos travaux s’inscrivent dans cette démarche.Nous avons travaillé sur des jeux de données de 120 complexes protéine-ARN extraits de la PRIDB non redondante (Protein-RNA Interface DataBase, banque de données de référence pour les interactions protéine-ARN). La méthodologie de prédiction d'interactions protéine-ARN a aussi été testée sur 40 complexes issus de benchmarks de l'état de l'art et indépendants des complexes de la PRIDB non redondante. Le faible nombre de structures natives et la difficulté de générer in silico des structures identiques à la solution in vivo nous a conduit à mettre en place une stratégie de génération de candidats par perturbation de l’ARN partenaire d’un complexe protéine-ARN natif. Les candidats ainsi obtenus sont considérés comme des conformations presque-natives si elles sont suffisamment proches du natif. Les autres candidats sont des leurres. L’objectif est de pouvoir identifier les presque natifs parmi l’ensemble des candidats potentiels, par apprentissage supervisé d'une fonction de score.Nous avons conçu pour l'évaluation des fonctions de score une méthodologie de validation croisée originale appelée le leave-"one-pdb"-out, où il existe autant de strates que de complexes protéine-ARN et où chaque strate est constituée des candidats générés à partir d'un complexe. L’une des approches présentant les meilleures performances à CAPRI est l’approche RosettaDock, optimisée pour la prédiction d’interactions protéine-protéine. Nous avons étendu la fonction de score native de RosettaDock pour résoudre la problématique protéine-ARN. Pour l'apprentissage de cette fonction de score, nous avons adapté l'algorithme évolutionnaire ROGER (ROC-based Genetic LearnER) à l'apprentissage d'une fonction logistique. Le gain obtenu par rapport à la fonction native est significatif.Nous avons aussi mis au point d'autres modèles basés sur des approches de classifieurs et de métaclassifieurs, qui montrent que des améliorations sont encore possibles.Dans un second temps, nous avons introduit et mis en oeuvre une nouvelle stratégie pour l’évaluation des candidats qui repose sur la notion de prédiction multi-échelle. Un candidat est représenté à la fois au niveau atomique, c'est-à-dire le niveau de représentation le plus détaillé, et au niveau dit “gros-grain”où nous utilisons une représentation géométrique basée sur des diagrammes de Voronoï pour regrouper ensemble plusieurs composants de la protéine ou de l’ARN. L'état de l'art montre que les diagrammes de Voronoï ont déjà permis d'obtenir de bons résultats pour la prédiction d'interactions protéine-protéine. Nous en évaluons donc les performances après avoir adapté le modèle à la prédiction d'interactions protéine-ARN. L’objectif est de pouvoir rapidement identifier la zone d’interaction (épitope) entre la protéine et l’ARN avant d’utiliser l’approche atomique, plus précise,mais plus coûteuse en temps de calcul. L’une des difficultés est alors de pouvoir générer des candidats suffisamment diversifiés. Les résultats obtenus sont prometteurs et ouvrent desperspectives intéressantes. Une réduction du nombre de paramètres impliqués de même qu'une adaptation du modèle de solvant explicite pourraient en améliorer les résultatsMy thesis shows results for the prediction of protein-RNA interactions with machine learning. An international community named CAPRI (Critical Assessment of PRedicted Interactions) regularly assesses in silico methods for the prediction of the interactions between macromolecules. Using blindpredictions within time constraints, protein-protein interactions and more recently protein-RNA interaction prediction techniques are assessed.In a first stage, we worked on curated protein-RNA benchmarks, including 120 3D structures extracted from the non redundant PRIDB (Protein-RNA Interface DataBase). We also tested the protein-RNA prediction method we designed using 40 protein-RNA complexes that were extracted from state-ofthe-art benchmarks and independent from the non redundant PRIDB complexes. Generating candidates identical to the in vivo solution with only a few 3D structures is an issue we tackled by modelling a candidate generation strategy using RNA structure perturbation in the protein-RNAcomplex. Such candidates are either near-native candidates – if they are close enough to the solution– or decoys – if they are too far away. We want to discriminate the near-native candidates from thedecoys. For the evaluation, we performed an original cross-validation process we called leave-”onepdb”-out, where there is one fold per protein-RNA complex and each fold contains the candidates generated using one complex. One of the gold standard approaches participating in the CAPRI experiment as to date is RosettaDock. RosettaDock is originally optimized for protein-proteincomplexes. For the learning step of our scoring function, we adapted and used an evolutionary algorithm called ROGER (ROC-based Genetic LearnER) to learn a logistic function. The results show that our scoring function performs much better than the original RosettaDock scoring function. Thus,we extend RosettaDock to the prediction of protein-RNA interactions. We also evaluated classifier based and metaclassifier-based approaches, which can lead to new improvements with further investigation.In a second stage, we introduced a new way to evaluate candidates using a multi-scale protocol. A candidate is geometrically represented on an atomic level – the most detailed scale – as well as on a coarse-grained level. The coarse-grained level is based on the construction of a Voronoi diagram over the coarse-grained atoms of the 3D structure. Voronoi diagrams already successfully modelled coarsegrained interactions for protein-protein complexes in the past. The idea behind the multi-scale protocolis to first find the interaction patch (epitope) between the protein and the RNA before using the time consuming and yet more precise atomic level. We modelled new scoring terms, as well as new scoring functions to evaluate generated candidates. Results are promising. Reducing the number of parameters involved and optimizing the explicit solvent model may improve the coarse-grained level predictions
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Henry, Thomas. "Modélisation des interactions protéine-glycanne à l'aide des techniques d'arrimage ("docking") moléculaire." Lille 1, 2005. https://pepite-depot.univ-lille.fr/RESTREINT/Th_Num/2005/50376-2005-99.pdf.
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La modélisation des interactions biomoléculaires est une technique performante dans les simulations informatiques. De nombreux modèles et logiciels permettent la simulation des interactions protéine-ligand et protéine-protéine. Le plus souvent le ligand est de petite taille (chimie thérapeutique). La simulation des interactions protéine-glycanne pose des problèmes spécifiques essentiellement dus à la taille du glycanne et à sa flexibilité. Plusieurs logiciels de "Docking" ont été testés en utilisant en particulier le complexe IL1α-glycanne comme exemple. Dans ce cas la modélisation a permis une amélioration significative de l'interaction, concernant l'orientation finale des groupements atomiques en contact. L'énergie d'interaction électrostatique a été utilisée comme fonction de score. La visualisation des surfaces électrostatiques permet une meilleure définition de la zone de contact au niveau atomique. Des améliorations des logiciels de "Docking" sont proposées sur cette base. Elles sont particulièrement utiles dans l'exploration de l'espace conformationnel du glycanne.
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KUMARI, AAKRITI. "DEVELOPMENT OF NOVEL VACCINE DEVELOPMENT STRATEGY BASED ON MULTIPLE RECEPTORS INTERACTION WITH CoV2 SPIKE PROTEIN." Thesis, 2022. http://dspace.dtu.ac.in:8080/jspui/handle/repository/19161.
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A severe acute respiratory syndrome known as covid19 was a threat to mankind globally in
the year 2020 and 2021. To date, 48 crores confirmed cases have been reported according to
WHO. The spike protein of coronavirus is essential for host cell recognition and host infection.
It engages ACE2 for entry into the host cell. However, there is growing evidence that the spike
protein and other structural protein binds with multiple receptors for viral infection. The key
to tackling this pandemic is to understand the receptor recognition by virus and its variability
in host cell infection and associated side effects. Our studies predicted interaction between S
protein and multiple human receptors, Toll-like receptors (TLR), Mannose receptor, Heat
shock protein HSPA5 or glucose-regulated protein (GRP78), and Ezrin, using molecular
docking and structural bioinformatics. Carbohydrate moieties present outside the surface of
spike protein which is known to be the driving force for internalization, inflammation, and
infection of the virus. Our Docking result shows that HSPA5 has the most proficient binding
with spike protein after ACE2 where threonine residue of the spike protein of A chain docked
with Arginine of the receptor. Understanding the binding sites for receptors with spike
protein, nucleocapsid protein, membranous protein, and envelope protein may help to fight
the disease and find a better vaccine coverage area. Hence, our research article provides
better vaccine coverage by finding the amino acid binding site using in-Silico methods.
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Syu, Ren-Guei, and 許人貴. "使用Support Vector Machine發展 SVM-Pose/SVM-Score Ensemble Docking 應用於預測N-methyl-D-aspartate的生物 活性." Thesis, 2013. http://ndltd.ncl.edu.tw/handle/27709944827659463105.
Full textBook chapters on the topic "DOCKING SCORE"
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Ranimol, G., C. B. Devipriya, and Swetha Sunkar. "Docking and Molecular Dynamics Simulation Studies for the Evaluation of Laccase Mediated Biodegradation of Triclosan." In Proceedings of the Conference BioSangam 2022: Emerging Trends in Biotechnology (BIOSANGAM 2022), 205–13. Dordrecht: Atlantis Press International BV, 2022. http://dx.doi.org/10.2991/978-94-6463-020-6_20.
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AbstractTriclosan (TCA) is an antibacterial and antimicrobial compound that is incorporated into toothpaste, soap, and liquid dishwasher. Continuous TCA exposure may contribute to the emergence of antibiotic-resistant bacteria in the microbiome. Triclosan also reacts to form dioxins, which bioaccumulate and are toxic to aquatic organisms, impedes the thyroid hormone metabolism of the human body. Laccases are multi copper-containing enzymes that can degrade the aromatic compounds and thus reduce their toxicity. To effectively degrade the compound, it is essential to understand the molecular function of the enzyme. Hence, a molecular docking study of laccase enzymes with Triclosan was done. The Tramates versicolor laccase structure was retrieved from PDB and ligand structure was taken from Pubchem. The binding mode and interaction of TCA and laccase were studied using Auto dock Vina software and the stability of the docked complex had been explored via Molecular Dynamics (MD) simulation study using Schrodinger Desmonde. The binding affinity score was found to be −6.5kcal/mol. The majority of the residues in RMSF were within the 2.5Å limit. The radius of gyration remained within the range from 21.7 to 22.1Å for Laccase – TCA complex throughout the 50 ns simulation. MD simulation results show that the enzyme complex remains stable all through the catalytic action.
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Srivastav, Vijay Kumar, Vineet Singh, and Meena Tiwari. "Recent Advancements in Docking Methodologies." In Methods and Algorithms for Molecular Docking-Based Drug Design and Discovery, 267–94. IGI Global, 2016. http://dx.doi.org/10.4018/978-1-5225-0115-2.ch011.
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Nowadays molecular docking has become an important methodology in CADD (Computer-Aided Drug Design)-assisted drug discovery process. It is an important computational tool widely used to predict binding mode, binding affinity and binding free energy of a protein-ligand complex. The important factors responsible for accurate results in docking studies are correct binding site prediction, use of suitable small-molecule databases, consistent docking pose, high dock score with good MD (Molecular Dynamics), clarity whether the compound is an inhibitor or agonist, etc. However, still there are several limitations which make it difficult to obtain accurate results from docking studies. In this chapter, the main focus is on recent advancements in various aspects of molecular docking such as ligand sampling, protein flexibility, scoring functions, fragment docking, post-processing, docking into homology models and protein-protein docking.
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Srivastav, Vijay Kumar, Vineet Singh, and Meena Tiwari. "Recent Advancements in Docking Methodologies." In Oncology, 848–75. IGI Global, 2017. http://dx.doi.org/10.4018/978-1-5225-0549-5.ch033.
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Nowadays molecular docking has become an important methodology in CADD (Computer-Aided Drug Design)-assisted drug discovery process. It is an important computational tool widely used to predict binding mode, binding affinity and binding free energy of a protein-ligand complex. The important factors responsible for accurate results in docking studies are correct binding site prediction, use of suitable small-molecule databases, consistent docking pose, high dock score with good MD (Molecular Dynamics), clarity whether the compound is an inhibitor or agonist, etc. However, still there are several limitations which make it difficult to obtain accurate results from docking studies. In this chapter, the main focus is on recent advancements in various aspects of molecular docking such as ligand sampling, protein flexibility, scoring functions, fragment docking, post-processing, docking into homology models and protein-protein docking.
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Ambure, Pravin, and Kunal Roy. "Scoring Functions in Docking Experiments." In Methods and Algorithms for Molecular Docking-Based Drug Design and Discovery, 54–98. IGI Global, 2016. http://dx.doi.org/10.4018/978-1-5225-0115-2.ch003.
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Molecular docking is a computational technique used to predict the binding orientation of a molecule while interacting with other molecule and finally quantify the inter-molecular interactions in terms of a binding score or binding affinity. In general, every docking algorithm comprises one or more “scoring function(s)” which is/are responsible for finding a precise binding pose as well as for predicting the binding affinity. In the last two decades, a significant development has been found in the field of scoring functions. In this chapter, the authors will discuss in detail about various types of scoring functions used in the docking experiments. This chapter will get the readers acquainted with different types of scoring functions available, their theoretical background, essential components, desired properties, and the important task performed by the scoring functions. The authors will also discuss the challenges faced by the scoring functions and their recent progress.
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Faryna, Aliaksandr, and Elena Kalinichenko. "N1-(3-(Trifluoromethyl)Phenyl) Isophthalamide Derivatives as Promising Inhibitors of Vascular Endothelial Growth Factor Receptor: Pharmacophore-Based Design, Docking, and MM-PBSA/MM-GBSA Binding Energy Estimation." In Biomedical Engineering. IntechOpen, 2022. http://dx.doi.org/10.5772/intechopen.107236.
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Targeting protein kinases is a common approach for cancer treatment. In this study, a series of novel terephthalic and isophthalic derivatives were constructed as potential type 2 protein kinase inhibitors adapting pharmacophore features of approved anticancer drugs of this class. Inhibitory activity of designed structures was studied in silico against various cancer-related protein kinases and compared with that of known inhibitors. Obtained docking scores, MM-PBSA/MM-GBSA binding energy, and RF-Score-VS affinities suggest that N1-(3-(trifluoromethyl) phenyl) isophthalamide could be considered as promising scaffold for the development of novel protein kinase inhibitors which are able to target the inactive conformation of vascular endothelial growth factor receptor.
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Garg, Saksham, Nikita Sharma, and Asmita Das. "Plant-Derived Antimicrobial Peptides Are Effective in Combating the Pathogenicity of SARS-CoV-2, a Novel Therapeutic Approach." In Advances in Transdisciplinary Engineering. IOS Press, 2022. http://dx.doi.org/10.3233/atde220796.
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The pandemic that started in 2019 in Wuhan caused a vast number of deaths worldwide due to the absence of effective therapy against SARS-CoV-2. The present study investigates the interaction of AMP with viral protein and host receptors. We screened plant-derived antimicrobial peptides (AMP) from the docking web server with the help of PDB ID. We selected five anti-microbial peptides based on their antiviral and physiological activities. The interaction of anti-microbial peptide and Mpro was analyzed using the HADDOCK web server. The results revealed that the minimum Z-score was obtained by the 6LU7-1N4N complex followed by 6LU7-1GPS docked complex. The docking results showed the interaction potency of AMP with 6LU7. The dynamic simulation study of 100ns was performed to check the stability of the docked complexes of AMP and 6LU7. From the stable and positive results of dynamics studies, we can conclude that these selected AMPs have immense potential to be used as therapeutic agents for the treatment of disease.
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Unissa, Ameeruddin Nusrath, and Luke Elizabeth Hanna. "Dissection of HIV-1 Protease Subtype B Inhibitors Resistance Through Molecular Modeling Approaches." In Big Data Analytics in HIV/AIDS Research, 149–70. IGI Global, 2018. http://dx.doi.org/10.4018/978-1-5225-3203-3.ch007.
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Protease (PR) is an important enzyme required for the posttranslational processing of the viral gene products of type-1 human immunodeficiency virus (HIV-1). Protease inhibitors (PI) act as competitive inhibitors that bind to the active site of PR. The I84V mutation contributes resistance to multiple PIs, and structurally, this mutation affects both sides of the enzyme active site. In order to get insights about this major resistance site to PR inhibitors using in silico approaches, in this chapter, the wild-type (WT) and mutant (MT) I84V of PR were modeled and docked with all PR inhibitors: Atazanavir, Darunavir, Indinavir, Lopinavir, Nelfinavir, Saquinavir, and Tipranavir. Docking results revealed that in comparison to the WT, the binding score was higher for the MT-I84V. Thus, it can be suggested that the high affinity towards inhibitors in the MT could be due to the presence of energetically favorable interactions, which may lead to tight binding of inhibitors with the MT protein, leading to the development of PR resistance against PIs in HIV-1 eventually.
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Marudhadurai, Thenmozhi, and Navabshan Irfan. "Computational Investigation of Versatile Activity of Piperine." In Advances in Medical Technologies and Clinical Practice, 127–39. IGI Global, 2019. http://dx.doi.org/10.4018/978-1-5225-7326-5.ch006.
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Piperine is known for its versatile therapeutic activity. It has been used for various disease conditions (e.g., cold, cough, etc.). Piperine is an alkaloid found in black pepper. It possesses various pharmacological actions like anti-inflammatory, anti-oxidant, anti-cholinergic, and anti-cancerous. The above-mentioned properties will be studied by selecting target proteins COX-2 protein, angiotensin converting enzyme, acetylcholineesterases, and survivin using computational docking study. This chapter explains the inhibition property of piperine against selected target protein from the results of docking studies. Based on the docking scores and protein-ligand interactions, piperine was found to bind well in the active site of the selected target proteins. It ensures the binding efficacy of piperine against selected target proteins. Docking scores and protein-ligand interactions plays an important role in its therapeutic activity.
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Raoufi, Ehsan, Bahar Bahramimeimandi, Mahsa Darestanifarahani, Fatemeh Hosseini, Mohammad Salehi-Shadkami, Hossein Raoufi, and Reza Afzalipour. "Docking-Based Screening of Cell-Penetrating Peptides with Antiviral Features and Ebola Virus Proteins as a Drug Discovery Approach to Develop a Treatment for Ebola Virus Disease." In Viral Outbreaks [Working Title]. IntechOpen, 2021. http://dx.doi.org/10.5772/intechopen.97222.
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Ebola drug discovery continues to be challenging as yet. Proteins of the virus should be targeted at the relevant biologically active site for drug or inhibitor binding to be effective. In this regard, by considering the important role of Ebola virus proteins in the viral mechanisms of this viral disease, the Ebola proteins are selected as our drug targets in this study. The discovery of novel therapeutic molecules or peptides will be highly expensive; therefore, we attempted to identify possible antigens of EBOV proteins by conducting docking-based screening of cell penetrating peptides (CPPs) that have antiviral potential features utilizing Hex software version 8.0.0. The E-value scores obtained in this research were very much higher than the previously reported docking studies. CPPs that possess suitable interaction with the targets would be specified as promising candidates for further in vitro and in vivo examination aimed at developing new drugs for Ebola infection treatment.
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Kotadiya, Manisha. "Drug Repurposing: Scopes in Herbal/Natural Products-based Drug Discovery and Role of in silico Techniques." In Drug Repurposing - Advances, Scopes and Opportunities in Drug Discovery [Working Title]. IntechOpen, 2023. http://dx.doi.org/10.5772/intechopen.109821.
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Natural products and their derivatives are the most promising and prolific resources in identifying the therapeutic small compounds with potential therapeutic activity. Nowadays, working with herbal or natural products can be boosted by collecting the data available for their chemical, pharmacological, and biological characteristics properties. Using in silico tools and methods, we can enhance the chances of getting a better result in a precise way. It can support experiments to emphasis their sources in fruitful directions. Though due to their limitations with respect to current knowledge, quality, quantity, relevance of the present data as well as the scope and limitations of cheminformatics methods, herbal product-based drug discovery is limited. The pharmaceutical re-profiling is done with the main objective to establish strategies by using approved drugs and rejected drug candidates in the diagnosis of new diseases. Drug repurposing offers safety lower average processing cost for already approved, withdrawn drug candidates. In silico methods could be oppressed for discovering the actions of un-investigated phytochemicals by identification of their molecular targets using an incorporation of chemical informatics and bioinformatics along with systems biological approaches, hence advantageous for small-molecule drug identification. The methods like rule-based, similarity-based, shape-based, pharmacophore-based, and network-based approaches and docking and machine learning methods are discussed.
Conference papers on the topic "DOCKING SCORE"
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Oda, Akifumi, Shuichi Fukuyoshi, Ryoichi Nakagaki, and Ohgi Takahashi. "Multi-Objective Optimizations for Selections of Protein-Ligand Docking Poses Using Pareto Optima as a Consensus Score." In Proceedings of the 12th Asia Pacific Physics Conference (APPC12). Journal of the Physical Society of Japan, 2014. http://dx.doi.org/10.7566/jpscp.1.016005.
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Abioye, Raliat, Chibuike Udenigwe, and Ogadimma Okagu. "Disaggregation of islet amyloid polypeptide fibrils as a potential anti-fibrillation mechanism of tetrapeptide TNGQ." In 2022 AOCS Annual Meeting & Expo. American Oil Chemists' Society (AOCS), 2022. http://dx.doi.org/10.21748/szym9744.
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Islet amyloid polypeptide (IAPP) fibrillation has been commonly associated with the exacerbation of type 2 diabetes prognosis. Consequently, inhibition of IAPP fibrillation to minimize β-cell cytotoxicity is an important approach towards β-cell preservation and type 2 diabetes management. In this study, three tetrapeptides, TNGQ, MANT, and YMSV, were identified as potential IAPP fibrillation inhibitors. The potential anti-fibrillation mechanisms of these tetrapeptides were monitored using thioflavin T (ThT) fluorescence assay, circular dichroism (CD) spectroscopy, dynamic light scattering (DLS) and molecular docking. ThT fluorescence kinetics and microscopy, as well as transmission electron microscopy, showed that TNGQ was the most effective inhibitor based on the absence of normal IAPP fibrillar morphology and alluded to its IAPP fibrillar disaggregatory potential. CD spectroscopy showed that TNGQ maintained the α-helical conformation of monomeric IAPP, while DLS confirmed the presence of varying fibrillation species. Molecular docking showed that interactions between TNGQ and MANT and monomeric IAPP favoured hydrogen bonding and electrostatic interactions. Furthermore, TNGQ bound at the IAPP surface, unlike YMSV, which had the highest docking score but interact mainly through hydrophobic interactions in the IAPP core. These findings indicate the potential of TNGQ in the development of peptide-based anti-fibrillation and antidiabetic nutraceuticals.
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Baba, Waqas, and Sajid Maqsood. "Novel antihypertensive and anticholesterolemic peptides from peptic hydrolysates of camel whey proteins." In 2022 AOCS Annual Meeting & Expo. American Oil Chemists' Society (AOCS), 2022. http://dx.doi.org/10.21748/qecs2081.
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Hypercholesterolemia and hypertension are major growing concerns that are managed by drugs that inhibit various metabolic enzymes. Milk hydrolysates have been reported to contain various bioactive peptides (BAP) that can inhibit various metabolic enzymes for enhancing human health. As such camel whey proteins were subjected to peptic hydrolysis using a full factorial model (33) with hydrolysis time, temperature, and enzyme concentration as factors. The resulting hydrolysates were analyzed for anti-hypercholesterolemic and hypertensive properties by studying the in vitro inhibition of various enzymatic markers. The hydrolysates with lowest IC50 values were further subjected to LC-MS-QTOF that revealed presence of 185 peptides. Selected peptides that had Peptide Ranker Score greater than 0.8 were further studied for prediction of possible interactions with enzyme markers: pancreatic lipase (PL) cholesterol esterase (CE) and angiotensin converting enzyme (ACE) using in silico analysis. The data generated suggested that most of the peptides could bind active site of PL while as only three peptides could bind active site of CE. Based on higher number of reactive residues in the bioactive peptides (BAP) and greater number of substrate binding sites, FCCLGPVPP was identified as potential CE inhibitory peptide while PAGNFLPPVAAAPVM, MLPLMLPFTMGY, and LRFPL were identified as PL inhibitors. While peptides PAGNFLP, FCCLGPVPP, PAGNFLMNGLMHR, PAVACCLPPLPCHM were identified as potential ACE inhibitors. Molecular docking of selected peptides showed hydrophilic and hydrophobic interactions between peptides and target enzymes. Moreover, due to the importance of renin in managing hypertension, peptides from hydrolysates with high ACE inhibiting potential were predicted for potential to interact with renin using in silico analysis. Molecular docking was subsequently employed to identify how the identified peptides, PVAAAPVM and LRPFL, could interact with renin and potentially inhibit it. Thus, non-bovine (camel) whey hydrolysates might be used as functional ingredients for production of functional foods with antihypertensive and anticholesterolemic properties.
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MITOMO, DAISUKE, YOSHIFUMI FUKUNISHI, JUNICHI HIGO, and HARUKI NAKAMURA. "CALCULATION OF PROTEIN–LIGAND BINDING FREE ENERGY USING SMOOTH REACTION PATH GENERATION (SRPG) METHOD: A COMPARISON OF THE EXPLICIT WATER MODEL, GB/SA MODEL AND DOCKING SCORE FUNCTION." In Proceedings of the 20th International Conference. PUBLISHED BY IMPERIAL COLLEGE PRESS AND DISTRIBUTED BY WORLD SCIENTIFIC PUBLISHING CO., 2009. http://dx.doi.org/10.1142/9781848165632_0008.
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Ghowel, Ahmed Samir. "Customer’s Waste at Dry-docking." In SNAME 5th World Maritime Technology Conference. SNAME, 2015. http://dx.doi.org/10.5957/wmtc-2015-289.
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Dry docking is a short period of time where a ship is placed inside a dry dock to finish a list of integrated jobs. During this period, any non-value work, generated by the Shipyard, is consider a waste of time and cost from the customer’s perspective. Different studies were made early to differentiate between value and non-value work done by the shipyard from the customer point of view. However author founds that, there are other different types of waste that generated by the customer himself which affects the project course. Therefore the burden of maximizing value and minimizing waste should be carried by the customer before the shipyard. And the shipyard in return should ensure that, because the loss impact on the shipyard will be more than on the customer. Case studies are utilized to demonstrate the customer’s waste and its impact on the shipyard during dry-docking. Showing the wastes from the shipyard’s perspective, instead of the customer’s, will enhance the customer’s scope and profit at the end of dry-docking. This will be guided by analytical methods to show, in figures, the owner’s loss and profit. The author’s objective, as project manager in a well-known shipyard, is to illustrate what is done and what should be done from the customer’s side to initiate and enforce Lean Ship repair. This paper explores the waste from the shipyard’s perspective, which if adopted by the customer, lean repair will be working in parallel on both sides.
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Fogel, Gary B., Jonathan Tran, Stephen Johnson, and David Hecht. "Machine learning approaches for customized docking scores: Modeling of inhibition of Mycobacterium tuberculosis enoyl acyl carrier protein reductase." In 2010 IEEE Symposium on Computational Intelligence in Bioinformatics and Computational Biology (CIBCB). IEEE, 2010. http://dx.doi.org/10.1109/cibcb.2010.5510700.
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Samir Ghowel, Ahmed. "The Concept of Floating Shipyard." In Abu Dhabi International Petroleum Exhibition & Conference. SPE, 2021. http://dx.doi.org/10.2118/207538-ms.
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Abstract Shipyards are known as a land-based facility that ships steer to for docking and repair. This study represents an introductory conceptual study for a new principle of developing a Floating shipyard: changing the phenomena of a fixed site shipyard into a self-propelled floating shipyard. This Floating Shipyard can travel and conduct dry-docking activities at the client's location or even lift the client's vessel and travel to the F-Yard extension, taking advantage of having comprehensive repair or conversion. The arising challenges to this floating shipyard, such as lay-offs, restructuring, and environmental legislation, requires a balanced solution. The solution of all this relies on adapting talent management and competitive production tools during this massive undergoing change in its backbone structure. The Floating shipyard, here named "F-Yard", changes the mindset of dry-dock. This is because F-Yard travels to the client's location or is capable of pick the client's unit nearby the cargo destination, where it can complete the required dry-dock or repair. The cutthroat advantage of the F-Yard comes from self-propelled, where the other approaches depend on others for mobilizing and anchoring from one location to another. In addition, F-Yard could serve other industries, due to its fully equipped workshops, that able to serve different market needs such as oil and gas and renewable energy...etc. These open the door for a variety of business scope. F-Yard depends on front-end engineering and marketing teams to optimize its route and sort the supply chain requirements.
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Luo, Jing, You Wang, Zhao Xinyu, and Jiatai Zhang. "A new conceptual design for subsea charging station." In 13th International Conference on Applied Human Factors and Ergonomics (AHFE 2022). AHFE International, 2022. http://dx.doi.org/10.54941/ahfe1002516.
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With deepening ocean development , a larger scale Internet of Underwater Things (IoUT) is being realized[1].More and more underwater equipment is being deployed, various ocean monitoring equipment, underwater robots and underwater group sites amongst others, all of which will be working in the deep sea for long periods of time in the foreseeable future[2].Due to the increasing working time and power consumption, it has become difficult for the high energy batteries carried by these facilities to cover their energy needs [3]. Therefore, it is necessary to solve the problem of electrical energy replenishment for underwater equipment.Based on Equinor’s Underwater Intervention Drone (UID) standard interface definition, Blue Logic have produced the world's first three universal, open-standard subsea drone docking stations.But this is not perfect, in the face of deeper waters, more complex multi-shape deep sea equipment charging needs, the current program is not enough to solve[4].Therefore, based on the IoUT scenario positioning, this research designs a subsea charging station that can serve multiple devices.The concept is similar to a land-based collection station for power banks, providing multiple sub-charging equipment that can be carried on the move to charge multiple subsea equipments of different types simultaneously.It also uses ocean energy to provide in-situ produced electricity for the underwater charging base station .Compared to Blue Logic's Subsea Drone Docking Station (SDS), it enables the multi-device charging needs of the IoUT using ultrasonic technology[5,6].In the long term, the combination of existing equipment will greatly reduce the cost of regional subsea long-term exploration and expand the scope of exploration[7].The paper will solve the following problems:1) How to solve the charging problem of long-distance survey of underwater equipments（e.g. AUV）?2) How to make the design applicable to charging usage scenarios common to different types, forms and sizes of underwater equipments?3) How to design underwater charging energy transmission more efficiently and sustainably?The research approach composed following parts:- Through literature research, sort out the development status of technical equipment such as underwater charging, underwater docking, underwater information transmission and marine power generation.- A structure interview with the opinions of deep-sea equipment designers and researchers to clarify the design requirements. - Analyze product features and problems and summarize the design process and direction through brainstorming method and solution building method.The design of the underwater multi-port charging base station solves the energy problem of deep-sea long-term survey equipment, with poor energy sustainability and low charging efficiency.This approach will enable true continuous subsea operations in extremely dynamic ocean environments.Although the project is still a conceptual design and various sensors are still being experimented with, it is forward-looking and instructive for future applications.References1.Wang X., Lu J., Peng W., &Song L.,(2021) Accelerating the construction of marine "new infrastructure" and promoting high-quality development of marine industry,Science & Technology Review,39(16),pp.76-80.2.Qu, Feng-Chong, Lai. , Liu, J.-Z., Tu, X.-B., Jiang, Y.,(2021)'Research and Application of Key Technologies for Marine Internet of Things', Telecommunications Science, 37, (7), pp. 25-33.3.Tian Y., Yuan R.,&Li X.,(2018)'Design and experiment of deep-sea microcurrent power generation system', Acta Energiae Solaris Sinica,Journal of China Academy of Electronics and Information Technology, 39, (4), pp. 873-878.4.SubseaDockingStation(SDS).[Online].Available:https://www.bluelogic.no/news-and-media/subsea-docking-station-sds-.5.Abicht, D., Torvestad, J.C., Solheimsnes, P.A., and Stenevik, K.A., ‘Underwater Intervention Drone Subsea Control System’, in Proceedings of the OTC, 2020.6.Wang Y., &Tian F.,(2019)'Research on acoustic wave-based charging planning in underwater sensing networks',Journal of China Academy of Electronics and Information Technology,14(11),pp.1183-11877.Cruz, N.A., Matos, A.C., Almeida, R.M., and Ferreira, B.M.: ‘A lightweight docking station for a hovering AUV’, in Proceedings of the IEEE, 2017, pp. 1-7.
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Hecht, David, Mars Cheung, and Gary B. Fogel. "Docking scores and QSAR using evolved neural networks for the Pan-inhibition of wild-type and mutant PfDHFR by cycloguanil derivatives." In 2009 IEEE Congress on Evolutionary Computation (CEC). IEEE, 2009. http://dx.doi.org/10.1109/cec.2009.4982957.
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Lam, Chun Ping, Ming Ho Ho, Shi Pan Siu, Ka Chun Lau, Yeung Yam, and Philip Wai Yan Chiu. "Implementation of a Novel Handheld Endoscopic Operation Platform (EndoGRASP)." In THE HAMLYN SYMPOSIUM ON MEDICAL ROBOTICS. The Hamlyn Centre, Imperial College London London, UK, 2023. http://dx.doi.org/10.31256/hsmr2023.20.
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Flexible endoscopes are widely used due to their effective treatment of various conditions with minimal surgery. Existing ESD platform, such as Incisionless operation platform (IOP) [1] and ANUBIScope [2], while they may offer reliable support for endoscopic bending, they lack the ability to provide precise motorized motion or may potentially restrict the maneuverability of the platform in confined endoluminal environments. Another more advanced operation platform, namely EndoMaster [3], while providing excellent visualization of the surgical area due to its compact design, which allowed for easy docking and prevented interference from the working arms, however, its complex operational requirements, where the surgeon must control the console remotely and manipulate the robotic arms using hand controls, can be time-consuming and challenging for the surgeon to master. Over-the-Scope Clip (OTSC) [4] use a device that places clips over the endoscope to hold tissue before removal, but the effectiveness of these clips in securing the tissue is sometimes inadequate, resulting in incomplete tissue acquisition and suboptimal surgical outcomes. Existing operating systems face challenges such as limited mobility, insufficient tissue collection, complex setup, and high costs. EndoGRASP, a novel handheld endoscopic platform, addresses these issues with its flexible robotic overtube and actuation unit. Optimized for efficient endoscopic submucosal dissection, it enhances patient safety and ensures precise, motorized control of the endoscope and instruments.