Computational Drug Discovery and Design
Hence, this activity is growing but currently is not a major focus for the pharma industry in general. The authors recognize tha ...
MARTINI is a widely used CG model but cannot be used for modeling backbone conformational transitions owing to the use of an el ...
This screening strategy is likely to work best where the cap- tured conformation is less affected by the bound Fab/VHH domain [ ...
protein allostery: CAP as a model system. Biophys Rev 7:175–182 Dinner AR, Sˇali A, Smith LJ et al (2000) Understanding protein ...
sampling: simple improvements for enhanced mixing. J Chem Phys 135(19):194110 Yu T-Q, Lu J, Abrams CF et al (2016) Multi- scale ...
simulations. Proc Natl Acad Sci 112:7454–7459 Kozakov D, Grove LE, Hall DR et al (2015) The FTMap family of web servers for det ...
Westfield GH, Rasmussen SGF, Su M et al (2011) Structural flexibility of the Gαs α-helical domain in theβ2-adrenoceptor Gs comp ...
Lo ̈hr T, Jussupow A, Camilloni C (2017) Metadynamic metainference: convergence towards force field independent structural ense ...
milliseconds simulations concur with aniso- tropic network model predictions. J Chem Phys 139:121912 Lockless SW, Ranganathan R ...
equilibrium? Phys Chem Chem Phys 14:8662–8677 Ufimtsev IS, Luehr N, Martinez TJ (2011) Charge transfer and polarization in solv ...
Chapter 18 Applications of the NRGsuite and the Molecular Docking Software FlexAID in Computational Drug Discovery and Design Lo ...
wide range of applications in computer-assisted drug design. Molecular docking gained interest in the early stages of the drug d ...
the target flexibility [14, 15] to account for conformational changes that occur upon binding [16], mostly because proteins exis ...
compare results. The methodology explained here will allow the user to repeat the experiment with any complex and could easily b ...
After the installation of both PyMOL and the NRGsuite, the last step required is to open PyMOL and install the NRGsuite as a plu ...
H1N1 neuraminidase solved by X-ray crystallography at a resolu- tion 1.45 A ̊(PDB: 3B7E) (seeNote 10). All the subsequent steps ...
accessible surface of the target as a potential binding site for the ligand during a molecular docking simulation, it is highly ...
containing the _sph_tag are displayed in the list. The selected cleft will flash in the PyMOL viewer. Generally, the largest cle ...
3.3 Configure, Perform, and Analyze the Molecular Docking Experiment with the FlexAID Interface The FlexAID interface permits us ...
residues ARG152A, GLU276A, ARG118A, ARG292A, and ASP151A (seeNote 15) specifically contribute to bind zanamivir (seeNote 26). C ...
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