Docking simulations
Identification of novel PTPRQ phosphatase inhibitors based on the virtual screening with docking simulations
... The docking library for PTPRQ comprising about 260,000 synthetic and natural com- pounds was constructed from the latest version of the chemical database distributed by Interbioscreen ...with docking ...
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Survey of public domain software for docking simulations and virtual screening
... It should be noted, however, that even serial codes can be used efficiently for virtual screening by exploiting the ‘embarrassing parallelism’ of docking; this involves simply screening subsets of compounds from ...
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HUMAN GLUTATHIONE S-TRANSFERASE A1-1 BINDING WITH NATURALLY OCCURRING LIGANDS: ASSESSMENT BY DOCKING SIMULATIONS
... Human GST A1-1 is a homodimer that belongs to the Alpha class, and each monomer contains 222 amino acids. Several crystal structures of human GST A1-1 have been reported, both of the apo form and various ligand complexes ...
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Glutathione transferase P1 1 binding with naturally occurring ligands: assessment by docking simulations
... naturally. Simulations were per- formed with commercial docking software and with GST monomer or dimer as ...the docking simulations suggest that the enzyme subunit interface may be important ...
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The development of an affinity evaluation and prediction system by using protein–protein docking simulations and parameter tuning
... Abstract: A system was developed to evaluate and predict the interaction between protein pairs by using the widely used shape complementarity search method as the algorithm for docking simulations between ...
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Exploring MIA QSARs for farnesyltransferase inhibitory effect of antimalarial compounds refined by docking simulations
... Two series of farnesyltransferase (FTase) inhibi- tors were grouped and their antimalarial activi- ties modeled by means of multivariate image analysis applied to quantitative structure-activ- ity relationship ...
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COMPUTER AIDED DESIGN OF SELECTIVE CALCIUM CHANNEL BLOCKERS: USING PHARMACOPHORE – BASED AND DOCKING SIMULATIONS
... The docking analysis was firstly carried out on the cyclooxygenase binding site in the 3HS5 obtained from the RCSB Protein Data Bank, http://www.rcsb.org/pdb, where the residues were bonded more closely to the ...
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Host-Guest Interactions of α−Mangostin with (α,β,γ)−Cyclodextrins: Semi-Empirical Quantum Mechanical Methods of PM6 and PM7
... for docking simulation using AutoDock Tools ...molecular docking simulations. The docking parameter files were according to Lamarckian Genetic Algorithm (LGA) with: 100 number of runs, 150 ...
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KRDS: a web server for evaluating drug resistance mutations in kinases by molecular docking
... in docking scores and in docking conformations induced by a certain muta- ...the docking simulation in GOLD, the T315I mutation reduced the binding affinities of imatinib, ...
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New Binding Mode of SLURP Protein to a7 Nicotinic Acetylcholine Receptor Revealed by Computer Simulations
... dynamics simulations followed by clustering, to identify repre- sentative ...molecular docking of the ten most massive clusters to α7-nAChRs in order to test if structural variability can affect ...binding. ...
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Synthesis of novel 2-(piperazino-1-yl-alkyl)-1H-benzimidazole derivates and assessment of their interactions with the D2 dopamine receptor
... Most of the receptor–ligand interactions in OBS, observed in molecular docking simulations, persisted for a significant portion of MD run (>20 % total simulation time). Compounds with significant DRD2 ...
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Lactoperoxidase inhibition by tautomeric propylthiouracils
... molecular docking simulations have been performed to evaluate the inter-molecular properties for the PTU counterparts (Table 2 and Scheme ...important docking parameters is E B (Binding energy), ...
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Modeling, molecular dynamics, and docking assessment of transcription factor rho: a potential drug target in <em>Brucella melitensis</em> 16M
... flexible docking for the interaction phenomenon of the template consists of ligand-related inhibitor molecules from the ZINC (ZINC Is Not Commercial) database using a structure-based virtual screening strategy ...
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Docking simulation between HIV peptidase inhibitors and Trypanosoma cruzi aspartyl peptidase
... molecular docking simulations aiming to pre- dict inhibitory potential (docking scores) and the inter- molecular interactions of the HIV aspartic peptidase inhibitors towards the active sites of the ...
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Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets
... initial docking box is calculated from the coor- dinates of a bound ligand in the crystal structure, and the box dimensions in x, y and z are increased by 10 ...[9]. Docking simulations using ...
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Download Download PDF
... methodology,[33] docking simulations were carried out to compare the binding modes of the test and reference ...blind docking calculation was performed to identify the preferred binding site within ...
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Identification of Small Molecule Memapsin Inhibitors via Computation based Virtual Screening
... Docking simulations end with 6 compounds that were able to inhibit the activity of ...concomitant docking of IO2 and F2I (which are knowen memapsin inhibitors) in 2IRZ ...flexible docking for ...
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Self assembly in heterogeneous modular robots
... Self-reconfigurable modular robots has became a popular research topic since late 1980’s. From the CEBOT [1] to the SYMBRION project [2], more than 30 systems have been developed over 2 decades. Although earlier studies ...
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“Molecular Docking Studies of 1,3,4-thiadiazoles as Novel Peptide Deformylase Inhibitors as Potential Antibacterial Agents” by Annapoorna Vadivelu, V.Gopal, C. Uma Maheswara Reddy, India.
... To counter increasing levels of pathogen resistance new classes of antibiotics are needed without delay. The metalloenzyme peptide deformylase (PDF) correspond to one of the most promising bacterial targets in the search ...
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Synthesis, characterization, docking studies and bio efficacy evaluation of novel chalcones
... To conclude, We have established an easy, high yielding convenient and green methods for the synthesis of (2E)-3- [3-(4-Methylphenyl)-1-phenyl-1H-pyrazol-4-yl]-1-(naphthalen-2-yl)prop-2-en-1-one (1a), ...
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