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Journal articles on the topic 'Dockan'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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1

Wang, Kai, Nan Lyu, Hongjuan Diao, et al. "GM-DockZn: a geometry matching-based docking algorithm for zinc proteins." Bioinformatics 36, no. 13 (2020): 4004–11. http://dx.doi.org/10.1093/bioinformatics/btaa292.

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Abstract Motivation Molecular docking is a widely used technique for large-scale virtual screening of the interactions between small-molecule ligands and their target proteins. However, docking methods often perform poorly for metalloproteins due to additional complexity from the three-way interactions among amino-acid residues, metal ions and ligands. This is a significant problem because zinc proteins alone comprise about 10% of all available protein structures in the protein databank. Here, we developed GM-DockZn that is dedicated for ligand docking to zinc proteins. Unlike the existing doc

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Firdayani, Susi Kusumaningrum, and Yosephine Ria Miranti. "POTENSI SENYAWA BIOAKTIF TANAMAN GENUS Phyllanthus SEBAGAI INHIBITOR REPLIKASI VIRUS HEPATITIS B." Jurnal Bioteknologi & Biosains Indonesia (JBBI) 4, no. 2 (2017): 85. http://dx.doi.org/10.29122/jbbi.v4i2.2589.

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Potency of Plant Bioactive Compounds from the Genus Phyllanthus as Hepatitis B Virus Replication InhibitorIn this research, simulations of molecular docking of Phyllanthus bioactive compounds were performed into the core protein of HBV. This simulation aimed to predict the interaction between compounds with virus core protein causing disruption of capsid formation and inhibiting its replication. The docking simulation was completed by Molegro Virtual Docker 6.0. The 3D stable conformation of molecule structures were docked into HBV core protein downloaded from Protein Data Bank, then the resul

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Lateef, Tooba, Sadaf Naeem, and Shamim A. Qureshi. "In-silico studies of HMG-Co A reductase inhibitors present in fruits of Withania coagulans Dunal (Solanaceae)." Tropical Journal of Pharmaceutical Research 19, no. 2 (2020): 305–12. http://dx.doi.org/10.4314/tjpr.v19i2.13.

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Purpose: To evaluate the antihypercholesterolemic effect of chemical constituents of W. coagulans by determining inhibitory effect of the compounds against HMG-CoA reductase, using in-silico methods. Method: Docking simulations of twenty-one chemical constituents, found in the fruits of W. coagulans were performed against HMGCR(PDB ID: 2Q1L) using Molegro Virtual Docker software. The best docked poses were then selected, based on the docking score and amino acids involved in the interaction within the ligand and active site of protein. Results: Five compounds viz. Coagulin D (comp

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Namekata, Kazuhiko, Xiaoli Guo, Atsuko Kimura, et al. "Roles of the DOCK-D family proteins in a mouse model of neuroinflammation." Journal of Biological Chemistry 295, no. 19 (2020): 6710–20. http://dx.doi.org/10.1074/jbc.ra119.010438.

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The DOCK-D (dedicator of cytokinesis D) family proteins are atypical guanine nucleotide exchange factors that regulate Rho GTPase activity. The family consists of Zizimin1 (DOCK9), Zizimin2 (DOCK11), and Zizimin3 (DOCK10). Functions of the DOCK-D family proteins are presently not well-explored, and the role of the DOCK-D family in neuroinflammation is unknown. In this study, we generated three mouse lines in which DOCK9 (DOCK9−/−), DOCK10 (DOCK10−/−), or DOCK11 (DOCK11−/−) had been deleted and examined the phenotypic effects of these gene deletions in MOG35–55 peptide-induced experimental auto

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Larrondo, C., H. Bustamante, E. Paredes, and C. Gallo. "Long-term hyperalgesia and traumatic neuroma formation in tail-docked lambs." Animal Welfare 28, no. 4 (2019): 443–54. http://dx.doi.org/10.7120/09627286.28.4.443.

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This study aimed to determine if tail-docking induces long-term hyperalgesia, chronic pain and histopathological changes in tail stumps of tail-docked lambs. Fifty male lambs of 45 days of age were randomly allocated in two groups. One group of 25 lambs was tail-docked using a hot cautery iron and a second group of 25 lambs was subjected only to handling as a control group (undocked lambs). Prior to tail-docking and at intervals of 15, 30, 60 and 90 days after the procedure, infra-red thermography (IT) and mechanical nociceptive thresholds (MNTs) tests were carried out in both lambs' tails/stu

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Sandercock, D. A., A. Monteiro, E. M. Scott, and A. M. Nolan. "The effect of tail-docking neonate piglets on ATF-3 and NR2B immunoreactivity in coccygeal dorsal root ganglia and spinal cord dorsal horn neurons: Preliminary data." Scandinavian Journal of Pain 3, no. 3 (2012): 184–85. http://dx.doi.org/10.1016/j.sjpain.2012.05.031.

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AbstractBackground/aimsTail docking neonatal piglets remains a controversial animal welfare issue. Although banned in the UK, it is widely practiced in many countries as a safeguard against tail biting among pigs reared in intensive systems. Concerns exist whether tail docking can induce chronic pain in later life. This preliminary study examined the effects of partial tail amputation on activating transcription factor 3 (ATF3), a marker of peripheral nerve injury and regeneration and NMDA-glutamate receptor NR2B subunit which participates in the mediation of chronic pain.MethodsProcedures wer

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Widiyana, Anita Puspa, Galih Satrio Putra, Luthfi Ahmad Muchlashi, Mellany Ika Sulistyowaty, and Tutuk Budiati. "Design and Molecular Docking Studies of Quinazoline Derivatives as Antiproliferation." JURNAL FARMASI DAN ILMU KEFARMASIAN INDONESIA 3, no. 2 (2018): 44. http://dx.doi.org/10.20473/jfiki.v3i22016.44-48.

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Background: Nowadays, a lot of new active substances as anticancer agents have been developed. One of the protein targets of anticancer is selective cyclooxygenase-2 (COX-2). Selective COX-2 is the regulator of cell proliferation. Objective: In this research, quinazoline derivatives were used to design the anticancer agent through a selective COX-2 inhibition. The potential activity of quinazoline derivatives could be increased by substitution in position 2 and 3 of quinazolinone. Molecular docking of selective COX-2 inhibition was required to predict their antiproliferation activity. Methods:

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Akbal-Delibas, Bahar, Roshanak Farhoodi, Marc Pomplun, and Nurit Haspel. "Accurate refinement of docked protein complexes using evolutionary information and deep learning." Journal of Bioinformatics and Computational Biology 14, no. 03 (2016): 1642002. http://dx.doi.org/10.1142/s0219720016420026.

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One of the major challenges for protein docking methods is to accurately discriminate native-like structures from false positives. Docking methods are often inaccurate and the results have to be refined and re-ranked to obtain native-like complexes and remove outliers. In a previous work, we introduced AccuRefiner, a machine learning based tool for refining protein–protein complexes. Given a docked complex, the refinement tool produces a small set of refined versions of the input complex, with lower root-mean-square-deviation (RMSD) of atomic positions with respect to the native structure. The

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Yelo, Estefania, Lourdes Gimeno, Maria Victoria Bernardo, Maria Juliana Majado, Maria Rocio Alvarez, and Antonio Parrado. "Molecular Cloning of DOCK10/Zizimin3, a Novel Cdc42/Rac-Interacting Protein Specifically Induced by IL4 in B Lymphocytes." Blood 108, no. 11 (2006): 939. http://dx.doi.org/10.1182/blood.v108.11.939.939.

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Abstract Interleukin-4 (IL4) induces proliferation, differentiation and survival of B lymphocytes. IL4 protects CLL B cells from death by apoptosis. Gene expression analysis suggest that IL4 pathways are activated in CLL cells. We have identified DOCK10/Zizimin3 as an IL4-induced gene in CLL cells, and have obtained its full length sequence after cloning 1960 bp at its 5′ terminus by RACE-PCR. The human DOCK10/ZIZ3 sequence coded for a protein with 2180 amino acids and a predicted Mr of 250K. DOCK10/ZIZ3 shared homology with the other two members of the Zizimin family, and is the largest among

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Schäfer, Theo, Urs O. Karli, Felix E. Schweizer, and Max M. Burger. "Docking of chromaffin granules—A necessary step in exocytosis?" Bioscience Reports 7, no. 4 (1987): 269–79. http://dx.doi.org/10.1007/bf01121448.

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Putative docking of secretory vesicles comprising recognition of and attachment to future fusion sites in the plasma membrane has been investigated in chromaffin cells of the bovine adrenal medulla and in rat phaeochromocytoma (PC 12) cells. Upon permeabilization with digitonin, secretion can be stimulated in both cell types by indreasing the free Ca2+-concentration to μM levels. Secretory activity can be elicited up to 1 hr after starting permeabilization and despite the loss of soluble cytoplasmic components indicating a stable attachment of granules to the plasma membrane awaiting the trigg

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Ihrke, Amber, Pedro Riviera, Rosemary LoGuidice, Michelle Guiffrida, and Kathleen Neforos. "Prevalence of Spondylosis Deformans in Tailed Versus Tail-Docked Rottweilers." Journal of the American Animal Hospital Association 55, no. 6 (2019): 301–5. http://dx.doi.org/10.5326/jaaha-ms-6966.

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ABSTRACT Tail docking is a routine procedure for rottweilers in the United States and Canada. A cross-sectional comparative study was conducted in tailed (n = 25) and docked (n = 39) rottweilers ≥5 yr old to compare prevalence and severity of spondylosis deformans in the lumbar spine between groups. The prevalence of spondylosis was 68.0% in tailed dogs and 76.9% in docked dogs, which was not significantly different (P = .563). Distribution of spondylosis severity did not significantly differ between tailed and docked dogs (P = .102). Logistic regression found moderate to severe spondylosis wa

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Mali, Pooja, Shourya Pratap, Raghvendra S. Badhauria, and Himanshu Gurjar. "DOCKING STUDIES OF AMINOHYDANTOIN DERIVATIVES AS ANTIMALARIAL AGENTS." Journal of Drug Delivery and Therapeutics 8, no. 5-s (2018): 322–26. http://dx.doi.org/10.22270/jddt.v8i5-s.1983.

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Objective: Docking studies of aminohydantoin derivatives as antimalarial agents. A novel derivative of aminohydantoins was selected from the literature. Method: in-silco studies using docking methodology. The compounds were sketched and energy minimized using Chem draw ultra and Chem 3D ultra respectively. Further, the compounds were docked into Plasmodium falciparum transferase inhibitor (3L7) using Molegro Virtual Platform. Twenty eight compounds were docked into the active site of Pf-lactate dehydrogenase cavity and all of them found to have similar binding interactions of a co-crystalized

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Ruiz-Lafuente, Natalia, Alfredo Minguela, Jose M. Moraleda, Manuel Muro, and Antonio Parrado. "Variable Distribution of DOCK-D Proteins between Cytosol and Nucleoplasm in Cell Lines, Effect of Interleukin-4 on DOCK10 in B-Cell Lymphoid Neoplasms, and Validation of a New DOCK10 Antiserum for Immunofluorescence Studies." Antibodies 10, no. 3 (2021): 33. http://dx.doi.org/10.3390/antib10030033.

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Dedicator-of-cytokinesis (DOCK), a family of guanine-nucleotide exchange factors (GEFs), comprises four subfamilies, named from A to D. DOCK-D comprises DOCK9, DOCK10, and DOCK11. The GEF activity involves translocation from the cytoplasm to the plasma membrane (PM), as assessed by the transfection of tagged proteins. However, the cellular localization of endogenous DOCK proteins is poorly understood. In this paper, to gain a better understanding of the role of the DOCK-D proteins, we studied their distribution between cytosol and nucleoplasm in 11 cell lines. DOCK-D proteins were distributed

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Herskin, Mette S., Pierpaolo Di Giminiani, Birthe M. Damgaard, and Karen Thodberg. "Acute behavioural responses to tail docking in piglets – Effects of increasing docking length?" Scandinavian Journal of Pain 3, no. 3 (2012): 185–86. http://dx.doi.org/10.1016/j.sjpain.2012.05.034.

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AbstractBackground and aimTail docking has been suggested as an animal model of neuropathy and pain based on findings of relations between the degree of neuroma formation and the docking length. We examined effects of docking length on behaviour of piglets during and 6 h after tail docking.MethodsPiglets were tail docked 2–4 d post-partum. We used 53 piglets and four treatments: intact (I), removal of either 25 (Q), 50 (H) or 75% (T) of the tail. The piglets were kept with sow and littermates under production conditions, and docked using a gas-heated instrument. Behaviour was observed during d

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Tripathi, Parul, Saad Sabir Siddiqui, Anju Sharma, Parul Johri, and Aditi Singh. "MOLECULAR DOCKING STUDIES OF CURCUMA LONGA AND ALOE VERA FOR THEIR POTENTIAL ANTICANCER EFFECTS." Asian Journal of Pharmaceutical and Clinical Research 11, no. 4 (2018): 314. http://dx.doi.org/10.22159/ajpcr.2018.v11i4.23995.

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Objective: In this paper, docking study is presented to use these phytocompounds for their prospective role in various types of cancers.Methods: A group of the different set of phytocompounds (aloesin, barbaloin, curcumin, and emodin) were taken and docked into the active sites of Topoisomerase I, a 91-kDa monomer (having 765 amino acids), is encoded by a single copy gene (Top 1) located on chromosome 20q12–13.2 using Autodock4 Software. The docking studies of the selected proteins were also docked to study the anticancerous property of the selected phytocompounds.Result: These studies were ba

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Shen, Yu-Fang, Gan-Hong Chen, Shu-Hsien Lin, and Gialih Lin. "Molecular modeling and docking calculations of 4-acyloxy-biphenyl-4′-N-butylcarbamates as potential inhibitors of human butyrylcholinesterase." Canadian Journal of Chemistry 94, no. 1 (2016): 72–77. http://dx.doi.org/10.1139/cjc-2015-0414.

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The kinetic studies and drug designs of butyrylcholinesterase play an important role in the development of Alzheimer’s disease therapeutics. In this research, automated docking studies were performed to provide useful insights into butyrylcholinesterase inhibition binding modes with designed 4-acyloxy-biphenyl-4′-N-butylcarbamates (compounds 1–8). Moreover, several significant linear correlations between experimental and calculated docking results are observed. Among compounds 1–7, compound 3, which exhibits the strongest hydrophobicity and has four carbonyl hydrogen bindings, shows the highes

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Morrison, Rebecca, and Paul Hemsworth. "Tail Docking of Piglets 1: Stress Response of Piglets to Tail Docking." Animals 10, no. 9 (2020): 1701. http://dx.doi.org/10.3390/ani10091701.

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This experiment compared the stress responses of piglets to tail docking. Two hundred and eighty-eight piglets were allocated to the following treatments at 2 d post-farrowing: (1) sham handling treatment; (2) surgical castration; (3) tail docking using clippers; (4) tail docking using a cauterising iron. Blood samples were collected at 15 min, 30 min and 24 h post-treatment and analysed for total plasma cortisol. Behaviours indicative of pain, such as escape attempts, vocalisations and standing with head lowered were measured. Cortisol concentrations at 15 min post-treatment were higher (p &l

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Viscardi, AV, and PV Turner. "Use of meloxicam, buprenorphine, and Maxilene® to assess a multimodal approach for piglet pain management, part 2: tail-docking." Animal Welfare 28, no. 4 (2019): 499–510. http://dx.doi.org/10.7120/09627286.28.4.499.

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Piglets on commercial pig farms are often tail-docked to reduce the incidence of tail-biting. While this is a painful procedure, piglets are often not provided analgesia or anaesthesia for pain relief. The objectives of this study were to assess a multimodal approach to managing tail-docking pain in piglets, using 0.4 mg kg–1 meloxicam (MEL), 0.04 mg kg–1 buprenorphine (BUP), and Maxilene® (MAX), a topical anaesthetic. The effectiveness of each drug and drug combination was evaluated using behavioural indicators, vocalisation, and facial grimace analysis. This study also assessed whether male

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Chaudhary, Hammad Tufail, and Shahida Hasnain. "IN-SILICO ANALYSIS." Professional Medical Journal 23, no. 02 (2016): 217–22. http://dx.doi.org/10.29309/tpmj/2016.23.02.1074.

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ntroduction: Different pathogen reducing technologies are being implementedwhich includes S-303. CD-61 is important receptor for clotting. Pathogen reducing agents arebeing studied extensively to probe its effects. Objective: We conducted this study to reviewthe docking of S-303 at CD-61, to look into the effect of S-303 on function of platelets. StudyDesign: This was an observational study. Setting: In-silico study. Period: March 2015 toAugust 2015. Method: The study was carried out in-silico. PDB (Protein data bank) code ofTirofiban bound to CD-61 was 2vdm. CD-61 was docked with Tirofiban us

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Chakraborty, Sandeep. "DOCLASP - Docking ligands to target proteins using spatial and electrostatic congruence extracted from a known holoenzyme and applying simple geometrical transformations." F1000Research 3 (October 31, 2014): 262. http://dx.doi.org/10.12688/f1000research.5145.1.

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The ability to accurately and effectively predict the interaction between proteins and small drug-like compounds has long intrigued researchers for pedagogic, humanitarian and economic reasons. Protein docking methods (AutoDock, GOLD, DOCK, FlexX and Glide to name a few) rank a large number of possible conformations of protein-ligand complexes using fast algorithms. Previously, it has been shown that structural congruence leading to the same enzymatic function necessitates the congruence of electrostatic properties (CLASP). The current work presents a methodology for docking a ligand into a ta

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Chakraborty, Sandeep. "DOCLASP - Docking ligands to target proteins using spatial and electrostatic congruence extracted from a known holoenzyme and applying simple geometrical transformations." F1000Research 3 (November 13, 2014): 262. http://dx.doi.org/10.12688/f1000research.5145.2.

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The ability to accurately and effectively predict the interaction between proteins and small drug-like compounds has long intrigued researchers for pedagogic, humanitarian and economic reasons. Protein docking methods (AutoDock, GOLD, DOCK, FlexX and Glide to name a few) rank a large number of possible conformations of protein-ligand complexes using fast algorithms. Previously, it has been shown that structural congruence leading to the same enzymatic function necessitates the congruence of electrostatic properties (CLASP). The current work presents a methodology for docking a ligand into a ta

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Hashizume, Kristina, Yi-Shan Cheng, Jenna L. Hutton, Chi-hua Chiu, and Chavela M. Carr. "Yeast Sec1p Functions before and after Vesicle Docking." Molecular Biology of the Cell 20, no. 22 (2009): 4673–85. http://dx.doi.org/10.1091/mbc.e09-02-0172.

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Sec1/Munc18 (SM) proteins bind cognate soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complexes and stimulate vesicle membrane fusion. Before fusion, vesicles are docked to specific target membranes. Regulation of vesicle docking is attributed to some but not all SM proteins, suggesting specialization of this earlier function. Yeast Sec1p seems to function only after vesicles are docked and SNARE complexes are assembled. Here, we show that yeast Sec1p is required before and after SNARE complex assembly, in support of general requirements for SM proteins in both v

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Morrison, Rebecca, and Paul Hemsworth. "Tail Docking of Piglets 2: Effects of Meloxicam on the Stress Response to Tail Docking." Animals 10, no. 9 (2020): 1699. http://dx.doi.org/10.3390/ani10091699.

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This experiment assessed the efficacy of the cauterisation procedure with or without pain relief (injectable meloxicam) in mitigating the acute stress response to tail docking. Male piglets (n = 432) were allocated to the following treatments at 2-d post-farrowing: (1) no handling, (2) sham handling, (3) tail docked using clippers, (4) tail docked using a cauteriser, (5) meloxicam + clipper, and (6) meloxicam + cauteriser. Meloxicam treatments used Metacam® at 5 mg/mL injected i.m. 1 h prior to tail docking. Blood samples were collected at 15 and 30 min post-treatment and analysed for total pl

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Gulsevin, Alican, and Jens Meiler. "An Investigation of Three-Finger Toxin—nAChR Interactions through Rosetta Protein Docking." Toxins 12, no. 9 (2020): 598. http://dx.doi.org/10.3390/toxins12090598.

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Three-finger toxins (3FTX) are a group of peptides that affect multiple receptor types. One group of proteins affected by 3FTX are nicotinic acetylcholine receptors (nAChR). Structural information on how neurotoxins interact with nAChR is limited and is confined to a small group of neurotoxins. Therefore, in silico methods are valuable in understanding the interactions between 3FTX and different nAChR subtypes, but there are no established protocols to model 3FTX–nAChR interactions. We followed a homology modeling and protein docking protocol to address this issue and tested its success on thr

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Mahankali Sravani, Akash Kumaran, Aditi Tulshiram Dhamdhere, and Nachimuthu Senthil Kumar. "Computational Molecular Docking Analysis and Visualisation of Anthocyanins for Anticancer Activity." International Journal for Research in Applied Sciences and Biotechnology 8, no. 1 (2021): 154–61. http://dx.doi.org/10.31033/ijrasb.8.1.18.

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Various invitro and computational methods were implemented to evaluate the anticancer potential of anthocyanidins, namely cyanidin, malvidin, delphinidin, peonidin, pelargonidin, and petunidin. These anthocyanidins were docked with CDK-2, CDK-6 and IGF-1R kinase proteins. Additionally, known inhibitors (KIs) such as SU9516, Palbociclib, OSI-906 are compared with their respective macromolecules, including, CDK-2, CDK-6 and IGF-1R kinase, in to compare results of the study based on Lipinski rule of 5. The Auto Dock Tool (Autodock 4) was used for molecular docking, and the docked complex compound

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Chaves, Rui C., and Jean-Luc Pellequer. "DockAFM: benchmarking protein structures by docking under AFM topographs." Bioinformatics 29, no. 24 (2013): 3230–31. http://dx.doi.org/10.1093/bioinformatics/btt561.

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Ogungbe, Ifedayo V., and William N. Setzer. "Cruzain Inhibition by Terpenoids: A Molecular Docking Analysis." Natural Product Communications 3, no. 6 (2008): 1934578X0800300. http://dx.doi.org/10.1177/1934578x0800300607.

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A molecular docking analysis has been carried out using monoterpene and sesquiterpene hydrocarbons and triterpenoids that have shown enzyme inhibitory activity as ligands for the cysteine protease cruzain. The binding energies of the docked ligands roughly correlate with their inhibitory activities. The orientations of the docked ligands are consistent with a mechanism whereby these hydrophobic compounds dock into a hydrophobic pocket near the active site, thereby blocking binding of the protein target to the protease.

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Karademir, Levent B., Hiroshi Aoyama, Benny Yue, Honghong Chen, and Donglin Bai. "Engineered Cx26 variants established functional heterotypic Cx26/Cx43 and Cx26/Cx40 gap junction channels." Biochemical Journal 473, no. 10 (2016): 1391–403. http://dx.doi.org/10.1042/bcj20160200.

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Gap junction (GJ) channels mediate direct intercellular communication and are composed of two docked hemichannels (connexin oligomers). It is well documented that the docking and formation of GJs are possible only between compatible hemichannels (or connexins). The mechanisms of heterotypic docking compatibility are not fully clear. We aligned the protein sequences of docking-compatible and -incompatible connexins with that of connexin26 (Cx26). We found that two docking hydrogen bond (HB)-forming residues on the second extracellular domain (E2) of Cx26 and their equivalent residues are well c

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Malhotra, Sony, and R. Sowdhamini. "Interactions among Plant Transcription Factors Regulating Expression of Stress-responsive Genes." Bioinformatics and Biology Insights 8 (January 2014): BBI.S16313. http://dx.doi.org/10.4137/bbi.s16313.

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Plants are simultaneously subjected to a variety of stress conditions in the field and are known to combat the hostile conditions by up/downregulating number of genes. There exists a significant level of cross-talk between different stress responses in plants. In this study, we predict the interacting pairs of transcription factors that regulate the multiple abiotic stress-responsive genes in the plant Arabidopsis thaliana. We identified the interacting pair(s) of transcription factors (TFs) based on the spatial proximity of their binding sites. We also examined the interactions between the pr

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Oberst, P., D. A. Sandercock, P. Di Giminiani, S. A. Edwards, and P. J. Brunton. "The effect of tail docking in neonatal pigs on the central expression of genes involved in modulating anxiety-like behaviour." Scandinavian Journal of Pain 8, no. 1 (2015): 53. http://dx.doi.org/10.1016/j.sjpain.2015.04.020.

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Abstract Background Adverse experiences in early life, such as exposure to stress, can have long term detrimental effects on the future physiology and behaviour of the animal. Typically animals exposed to such experiences are more anxious and more reactive to stress in later life. Tail biting is a major problem in modern pig production, both in terms of animal welfare and productivity. Tail docking in early postnatal life is common practice to reduce risk of this problem, but causes pain and may alter pain sensitivity. Aims To investigate whether a significant painful experience in early life

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Viscardi, Abbie V., and Patricia Turner. "12 A multimodal approach for piglet pain management after tail docking." Journal of Animal Science 97, Supplement_2 (2019): 6–7. http://dx.doi.org/10.1093/jas/skz122.011.

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Abstract Millions of piglets on commercial production farms are tail docked each year to reduce the incidence of tail biting. While this procedure is known to be painful, piglets in the United States are often not provided analgesia or anesthesia for pain relief. The objectives of this study were to assess a multimodal approach to managing tail docking pain in piglets, using 0.4 mg/kg meloxicam (MEL), 0.04 mg/kg buprenorphine (BUP), and Maxilene® (MAX). The effectiveness of each drug and drug combination was evaluated using behavioral indicators, vocalization, and facial grimace analysis. This

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Sonawane, Ravindra S., Kiran D. Patil, and Avinash V. Patil. "Design, Synthesis and Pharmacological Evaluation of Novel Imidazopyridine Analogues as Proton Pump Antagonist." Asian Journal of Chemistry 32, no. 4 (2020): 776–82. http://dx.doi.org/10.14233/ajchem.2020.22433.

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A series of novel imidazopyridine derivatives as proton pump inhibitors was designed with compounds of CID data base and explored considering AZD0865 as standard. Many compounds were identified and docked in proton pump ATPase pocket (PDB ID: 4ux2). Molecular docking studies revealed that many compounds showed good proton pump ATPase inhibitory activity. The docking poses revealed the interaction of ligands with amino acid. The standard drug AZD0865 had docking score of -7.112302 and displayed interactions with Asn138 and Asp137. A series of novel imidazopyridine derivatives as proton pump inh

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Wu, Yao, Yiwen Gu, Mary K. Morphew, et al. "All three components of the neuronal SNARE complex contribute to secretory vesicle docking." Journal of Cell Biology 198, no. 3 (2012): 323–30. http://dx.doi.org/10.1083/jcb.201106158.

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Before exocytosis, vesicles must first become docked to the plasma membrane. The SNARE complex was originally hypothesized to mediate both the docking and fusion steps in the secretory pathway, but previous electron microscopy (EM) studies indicated that the vesicular SNARE protein synaptobrevin (syb) was dispensable for docking. In this paper, we studied the function of syb in the docking of large dense-core vesicles (LDCVs) in live PC12 cells using total internal reflection fluorescence microscopy. Cleavage of syb by a clostridial neurotoxin resulted in significant defects in vesicle docking

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Notman, A. B., H. L. Heath, and J. Hill. "Welfare of the neonate lamb immediately after tail-docking." Proceedings of the British Society of Animal Science 1999 (1999): 108. http://dx.doi.org/10.1017/s1752756200002635.

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Tail docking of new born lambs is a routine practice in the United Kingdom. It has been used as a strategy to reduce the impact of myriasis (blowfly strike). There is only a limited period of time after birth (up to seven days) during which lambs can be docked without the use of anaethesia. Tail docking may have a detrimental effect on the ewe-lamb bond if the process leads to significant and sustained pain. French, Wall and Morgan (1994) suggested lambs suffer acute pain immediately after the procedure of docking but this potential disturbance of normal behaviour during the first few days of

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Marai, I. F. M., M. N. El-Gaafary, and B. A. K. Ahmed. "A note on effect of docking on skin structure and characteristics of the fleece in Rahmani fat-tailed sheep." Animal Science 55, no. 2 (1992): 292–94. http://dx.doi.org/10.1017/s0003356100037594.

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The histological characteristics of the skin of docked and undocked fat-tailed sheep were studied at 15-day intervals between birth and 90 days of age, then every 30 days until 180 days and every 3 months until 1 year of age. Data presented in this paper were recorded at birth, 30, 60, 120,180 and 360 days of age. The fleece characteristics were studied at 1·0,1·5 and 2·0 years of age.The skin structure was similar in docked and undocked Rahmani sheep and did not differ from that of other breeds of sheep.The effect of docking was significant at most ages of the study on internal diameter of pr

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Geng, Cunliang, Yong Jung, Nicolas Renaud, Vasant Honavar, Alexandre M. J. J. Bonvin, and Li C. Xue. "iScore: a novel graph kernel-based function for scoring protein–protein docking models." Bioinformatics 36, no. 1 (2019): 112–21. http://dx.doi.org/10.1093/bioinformatics/btz496.

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Abstract Motivation Protein complexes play critical roles in many aspects of biological functions. Three-dimensional (3D) structures of protein complexes are critical for gaining insights into structural bases of interactions and their roles in the biomolecular pathways that orchestrate key cellular processes. Because of the expense and effort associated with experimental determinations of 3D protein complex structures, computational docking has evolved as a valuable tool to predict 3D structures of biomolecular complexes. Despite recent progress, reliably distinguishing near-native docking co

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Wit, Heidi de. "Molecular mechanism of secretory vesicle docking." Biochemical Society Transactions 38, no. 1 (2010): 192–98. http://dx.doi.org/10.1042/bst0380192.

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Docking, the stable association of secretory vesicles with the plasma membrane, is considered to be the necessary first step before vesicles gain fusion-competence, but it is unclear how vesicles dock. In adrenal medullary chromaffin cells, access of secretory vesicles to docking sites is controlled by dense F-actin (filamentous actin) beneath the plasma membrane. Recently, we found that, in the absence of Munc18-1, the number of docked vesicles and the thickness of cortical F-actin are affected. In the present paper, I discuss the possible mechanism by which Munc18-1 modulates cortical F-acti

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Camacho, Carlos J., David W. Gatchell, S. Roy Kimura, and Sandor Vajda. "Scoring docked conformations generated by rigid-body protein-protein docking." Proteins: Structure, Function, and Genetics 40, no. 3 (2000): 525–37. http://dx.doi.org/10.1002/1097-0134(20000815)40:3<525::aid-prot190>3.0.co;2-f.

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Wang, Hao, Ray Ishizaki, Jun Xu, et al. "The Rab27a effector exophilin7 promotes fusion of secretory granules that have not been docked to the plasma membrane." Molecular Biology of the Cell 24, no. 3 (2013): 319–30. http://dx.doi.org/10.1091/mbc.e12-04-0265.

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Granuphilin, an effector of the small GTPase Rab27a, mediates the stable attachment (docking) of insulin granules to the plasma membrane and inhibits subsequent fusion of docked granules, possibly through interaction with a fusion-inhibitory Munc18-1/syntaxin complex. However, phenotypes of insulin exocytosis differ considerably between Rab27a- and granuphilin-deficient pancreatic β cells, suggesting that other Rab27a effectors function in those cells. We found that one of the putative Rab27a effector family proteins, exophilin7/JFC1/Slp1, is expressed in β cells; however, unlike granuphilin,

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Packová, Anna, Adam Rogers, and Daniela Takáčová. "The legal implication of certain interventions prohibited by law in the United Kingdom and Slovakia – a review." Acta Veterinaria Brno 89, no. 4 (2020): 375–82. http://dx.doi.org/10.2754/avb202089040375.

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Mutilation of dogs is an emotive and controversial subject for veterinarians and animal keepers. The elective docking of a dog’s tail is illegal under both UK and Slovak law except for specific breeds that are intended to be used for specific purposes while the elective cropping of dogs’ ears is illegal under all circumstances. In the EU, there is much variation between countries with some having a total ban on these procedures and others allowing elective ear cropping specifically. Under the current UK as well as Slovak legislation there is no legal requirement for a central monitoring of the

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Beteringhe, Adrian, Ciprian Racuciu, Constantin Balan, Elena Stoican, and Luminita Patron. "Molecular Docking Studies Involving Transitional Metal Complexes (Zn(II), Co(II), Cu(II), Fe(II), Ni(II) with Cholic Acid (AC) as Ligand against Aurora A Kinase." Advanced Materials Research 787 (September 2013): 236–40. http://dx.doi.org/10.4028/www.scientific.net/amr.787.236.

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Colorectal cancer is a malignant tumor, one of the main types of cancer which produces a large number of deaths each year in many countries around the world. The main objective of this work is to employ various bioinformatics tools to perform docking of the transitional metal complexes (Zn (II), Co (II), Cu (II), Fe (II), Ni (II)) with cholic acid (AC) as ligand against Aurora A Kinase (RCSB Protein Data Bank code: 2X6E). Molegro Virtual Docker (MVD) was used for the docking process. The molecular docking score and the values of the statistic parameter Root Mean Square Deviation (RMSD) are pre

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Geumann, Ulf, Sina Victoria Barysch, Peer Hoopmann, Reinhard Jahn, and Silvio O. Rizzoli. "SNARE Function Is Not Involved in Early Endosome Docking." Molecular Biology of the Cell 19, no. 12 (2008): 5327–37. http://dx.doi.org/10.1091/mbc.e08-05-0457.

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Docking and fusion of transport vesicles constitute elementary steps in intracellular membrane traffic. While docking is thought to be initiated by Rab-effector complexes, fusion is mediated by SNARE (N-ethylmaleimide-sensitive factor [NSF] attachment receptor) proteins. However, it has been recently debated whether SNAREs also play a role in the establishment or maintenance of a stably docked state. To address this question, we have investigated the SNARE dependence of docking and fusion of early endosomes, one of the central sorting compartments in the endocytic pathway. A new, fluorescence-

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

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Objective: Cancer is the major worldwide problem. It arises due to uncontrolled growth of cells. In the present study a series of novel coumarin derivatives were designed and computationallyoptimized to investigate the interaction between designed ligands and 10 pdb files of five selected proteins. The objective here was to analyse in silico anticancerous activity of designed ligands to reduce cost and time for getting novel anticancerous drug with minimum side effects.Methods: Docking studies were performed to find outmaximum interaction between designed ligands and selected five proteins usi

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Daddam, Jayasimha R., Basha Sreenivasulu, Katike Umamahesh, Kotha Peddanna, and Dowlathabad M. Rao. "In Silico Studies on Anti-Stress Compounds of Ethanolic Root Extract of Hemidesmus indicus L." Current Pharmaceutical Biotechnology 21, no. 6 (2020): 502–15. http://dx.doi.org/10.2174/1389201021666191211152754.

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Background: Alternative medicine is available for those diseases which cannot be treated by conventional medicine. Ayurveda and herbal medicines are important alternative methods in which the treatment is done with extracts of different medicinal plants. This work is concerned with the evaluation of anti-stress bioactive compounds from the ethanolic root extract of Hemidesmus indicus. Methods: Gas chromatography and Mass Spectrum studies are used to identify the compounds present in the ethanolic extract based on the retention time, area. In order to perform docking studies, Vasopressin model

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Beny, Ruslin, Nindy Rachma Az Yana, and Mesi Leorita. "Desain Turunan Senyawa Leonurine Sebagai Kandidat Obat Anti Inflamasi." Jurnal Farmasi Galenika (Galenika Journal of Pharmacy) (e-Journal) 6, no. 1 (2020): 181–91. http://dx.doi.org/10.22487/j24428744.2020.v6.i1.15025.

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In this research, there was docking process of leonurine compounds and their derivatives to Cyclooxygenase-2 (COX-2) enzyme as an anti-inflammatory. The receptor code used is 6COX which is downloaded from the protein data bank site (PDB). The aims of this study was to investigate the interaction of leonurine compounds and their derivatives against COX-2 receptors. All compounds are docked using AutoDock 4.2 software. The docking validation is performed by tethering the ligand-receptor with the parameter of the Root Mean Square Deviation (RMSD) value <2 Å. From the docking validation results

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Mubashir, Nageen, Rida Fatima, and Sadaf Naeem. "Identification of Novel Phyto-chemicals from Ocimum basilicum for the Treatment of Parkinson’s Disease using In Silico Approach." Current Computer-Aided Drug Design 16, no. 4 (2020): 420–34. http://dx.doi.org/10.2174/1573409915666190503113617.

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Background: Parkinson’s disease is characterized by decreased level of dopaminergic neurotransmitters and this decrease is due to the degradation of dopamine by protein Monoamine Oxidase B (MAO-B). In order to treat Parkinson’s disease, MAO-B should be inhibited. Objective: To find out the novel phytochemicals from plant Ocimum basilicum that can inhibit MAO-B by using the in silico methods. Methods: The data of chemical constituents from plant Ocimum basilicum was collected and inhibitory activity of these phytochemicals was then predicted by using the Structure-Based (SB) and Ligand-Based Vi

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Saikia, Surovi, and Manobjyoti Bordoloi. "Molecular Docking: Challenges, Advances and its Use in Drug Discovery Perspective." Current Drug Targets 20, no. 5 (2019): 501–21. http://dx.doi.org/10.2174/1389450119666181022153016.

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Molecular docking is a process through which small molecules are docked into the macromolecular structures for scoring its complementary values at the binding sites. It is a vibrant research area with dynamic utility in structure-based drug-designing, lead optimization, biochemical pathway and for drug designing being the most attractive tools. Two pillars for a successful docking experiment are correct pose and affinity prediction. Each program has its own advantages and drawbacks with respect to their docking accuracy, ranking accuracy and time consumption so a general conclusion cannot be d

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Woodruff, Madeleine Eloise, Rebecca Doyle, Grahame Coleman, Lauren Hemsworth, and Carolina Munoz. "Knowledge and attitudes are important factors in farmers’ choice of lamb tail docking length." Veterinary Record 186, no. 10 (2020): 319. http://dx.doi.org/10.1136/vr.105631.

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BackgroundTail docking is common practice in the sheep industry to prevent soiling of the breech and flystrike. To ensure optimal healing after tail docking and reduce the risk of arthritis, perineal cancers and prolapses, it is recommended to dock tails equivalent to the length of the vulva. However, recent studies have found that some tails are docked too short (24–86 per cent).MethodsTo address this issue, this study aimed to identify key drivers behind tail docking length decisions. Two focus groups, phone (n=30) and online surveys (n=21) were conducted in regional Victoria, Australia to e

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Kaushik, Pawan, Sukhbir Lal Khokra, A. C. Rana, and Dhirender Kaushik. "Pharmacophore Modeling and Molecular Docking Studies on Pinus roxburghii as a Target for Diabetes Mellitus." Advances in Bioinformatics 2014 (July 10, 2014): 1–8. http://dx.doi.org/10.1155/2014/903246.

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The present study attempts to establish a relationship between ethnopharmacological claims and bioactive constituents present in Pinus roxburghii against all possible targets for diabetes through molecular docking and to develop a pharmacophore model for the active target. The process of molecular docking involves study of different bonding modes of one ligand with active cavities of target receptors protein tyrosine phosphatase 1-beta (PTP-1β), dipeptidyl peptidase-IV (DPP-IV), aldose reductase (AR), and insulin receptor (IR) with help of docking software Molegro virtual docker (MVD). From th

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Jofily, Paula, Pedro G. Pascutti, and Pedro H. M. Torres. "Improving Blind Docking in DOCK6 through an Automated Preliminary Fragment Probing Strategy." Molecules 26, no. 5 (2021): 1224. http://dx.doi.org/10.3390/molecules26051224.

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Probing protein surfaces to accurately predict the binding site and conformation of a small molecule is a challenge currently addressed through mainly two different approaches: blind docking and cavity detection-guided docking. Although cavity detection-guided blind docking has yielded high success rates, it is less practical when a large number of molecules must be screened against many detected binding sites. On the other hand, blind docking allows for simultaneous search of the whole protein surface, which however entails the loss of accuracy and speed. To bridge this gap, in this study, we

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